CA2281930A1 - Design, synthesis and use of specific polyamide dna-binding ligands - Google Patents
Design, synthesis and use of specific polyamide dna-binding ligands Download PDFInfo
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Abstract
The invention encompasses improved selective polyamides for binding to specific nucleotide sequences of double stranded DNA as well as methods for designing and synthesizing polyamide DNA binding ligands that are selective for an identified specific nucleotide sequence. The 3-hydroxy-N-methylpyrrole/N-methylpyrrole carboxamide pair specifically recognizes the T.A
base pair, while the N-methylpyrrole/3-hydroxy-N-methylpyrrole pair recognizes A.T nucleotide pairs. Similarly, an N-methylimidizole/N-methylpyrrole carboxamide pair specifically recognizes the G.C nucleotide pair, and the N-methylpyrrole/N-methylimidizole carboxamide pair recognizes the C.G nucleotide pair.
base pair, while the N-methylpyrrole/3-hydroxy-N-methylpyrrole pair recognizes A.T nucleotide pairs. Similarly, an N-methylimidizole/N-methylpyrrole carboxamide pair specifically recognizes the G.C nucleotide pair, and the N-methylpyrrole/N-methylimidizole carboxamide pair recognizes the C.G nucleotide pair.
Description
DESIGN, SYNTHESIS AND USE OF SPECIFIC
POLYAMIDE DNA-BINDING LIGANDS
The U.S. Government has certain rights in this invention pursuant to Grant Nos. GM
26453, 27681 and 47530 awarded by the National Institute of Health.
1o This application is a continuation-in-part of PCT/L7S97103332 filed February 20, 1997, Serial No. 08/853,522 filed May 8, 1997 and PCTIL1S 97/12722 filed July 21, 1997 which are continuation-in-part applications of Serial No. 08/837,524, filed April 21, 1997, Serial No.
08/607,078, filed February 26, 1996, provisional application Serial No.
60/042,022, f led April 16, 1997 and provisional application Serial No. 60/043,444, filed April 8, 1997.
BACKGROUND OF THE INVENTION
Field of the Invention 2o This invention relates to polyamides which bind to predetermined sequences in the minor groove of double stranded DNA.
Description of the Related Art The design of synthetic ligands that read the information stored in the DNA
double helix has been a long standing goal of chemistry. Cell-permeable small molecules which target predetermined DNA sequences are useful for the regulation of gene-expression.
Oligodeoxynucleotides that recognize the major groove of double-helical DNA
via triple-helix formation bind to a broad range of sequences with high affinity and specificity. Although oligonucleotides and their analogs have been shown to interfere with gene expression, the triple helix approach is limited to purine tracks and suffers from poor cellular uptake. The development of pairing rules for minor groove binding polyamides derived from N-methylpyrrole (Py) and N-methylimidazole (Im) amino acids provides another code to control sequence specificity. An ImlPy pair distinguishes G~C from C~G and both of these from A~T or ,35 T~A base pairs. Wade, W.S., Mrksich, M. & Dervan, P.B. describes the design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif. J. Am. Chem. Soc. 114, 8783-8794 (1992); Mrksich, M. et al.
describes antiparallel side-by-side motif for sequence specific-recognition in the minor groove of DNA by the designed peptide I -methyliinidazole-2-carboxamidenetropsin. Proc. Natl. Acad.
Sci. USA 89, 7586-7590 (1992); Trauger, J.W., Baird, E. E. Dervan, P.B. describes the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996). A
Py/Py pair specifies A~T from G~C but does not distinguish A~T from T~A. Pelton, J.G. &
Wemmer, D.E.
describes the structural characterization of a 2-1 distamycin A-d(CGCAAATTTGGC) complex by two-dimensional NMR. Proc. Natl. Acad. Sci. USA 86, 5723-5727 (1989);
White, S., Baird, E. E. & Dervan, P.B. Describes the effects of the A~T/T~A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA. Biochemistry 35, 12532-12537 (1996);
l0 White, S., Baird, E. E. & Dervan, P. B. describes the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides. Chem. c~ Biol. 4, 569-578 (1997); White, S., Baird, E. E. & Dervan, P.B. describes the S'-3' N-C orientation preference for polyamide binding in the minor groove. New methods of designing selective compounds and the resulting specific polyamide binding ligands that are designed to target an identified sequence of double stranded DNA are needed to overcome the A~T/T~A degeneracy of pyrrole-imidazole polyamide recognition.
SUMMARY OF THE INVENTION
It has been found that a new aromatic amino acid, 3-hydroxy-N-methylpyrrole (Hp) when incorporated into a polyamide and paired opposite Py, provides the means to discriminate A~T from T~A. Unexpectedly, the replacement of a single hydrogen atom on the pyrrole with a hydroxy group in a Hp/Py pair regulates the affinity and the specificity of a polyamide by an order of magnitude. Utilizing Hp together with Py and Im in polyamides to form four aromatic amino acid pairs (Im/Py, Py/Im, Hp/Py, and Py/Hp) provides a code to distinguish all four Watson-Crick base pairs in the minor groove of DNA.
3o The present invention provides a method for designing specific polyamides suitable for use as DNA-binding ligands, as well as compositions comprising such polyamides, that are selective for an identified target sequence of double stranded DNA.
Preferably, the designed specific polyamides are characterized by a dissociation constant of less than 1 nM, as measured by DNase I footprint titration, and greater than ten-fold selectivity for the identified target sequence over related mismatch sequences, based on the ratio of the corresponding dissociation constants measured by DNase I footprint titrations.
The invention encompasses improved polyamides for binding to the minor groove of double stranded ("duplex") DNA. The polyamides are in the form of a hairpin comprising two groups of at least three consecutive carboxamide residues, the two groups covalently linked by an aliphatic amino acid residue, preferably ~y-aminobutyric acid or 2,4 diaminobutyric acid, the consecutive carboxamide residues of the first group pairing in an antiparallel manner with the consecutive carboxamide residues of the second group in the minor groove of double stranded to DNA. The improvement relates to the inclusion of a binding pair of Hp/Py carboxamides in the polyamide to bind to a T~A base pair in the minor groove of double stranded DNA or Py/Hp carboxamide binding pair in the polyamide to bind to an A~T base pair in the minor groove of double stranded DNA. The improved polyamides have at least three consecutive carboxamide pairs for binding to at least three DNA base pairs in the minor groove of a duplex DNA sequence that has at least one A~T or T~A DNA base pair, the improvement comprising selecting a Hp/Py carboxamide pair to correspond to a T~A base pair in the minor groove or a Py/Hp carboxamide pair to bind to an A~T DNA base pair in the minor groove. Preferably the binding of the carboxamide pairs to the DNA base pairs modulates the expression of a gene.
In general, the method provides specific polyamides suitable for use as DNA-binding ligands that are selective for identified target sequences of double stranded DNA having a coding strand sequence of the form 5'-WN1N2 . . , NmW-3' where N is a nucleotide chosen from the group A, T, C and G, W is a nucleotide chosen from the group A and T, and with the coresponding paired antiparallel strand 3'-W'N' 1N'2 , , , N'mW'-5' where N' is a nucleotide chosen from the group T, A, G and C respectively to form Watson-Crick pase pairs, W is a nucleotide chosen from the group T and A respectively to form Watson-Crick pase pairs, and m is an integer having a value from 3 to 6 inclusive.
The preferred corresponding designed specific polyamides resulting from this invention are of the form X 1 X2 . . . Xm-y-X(m + 1 ) . . . X(2m-1 )X2m-~-Dp wherein X l , X2, Xm, X(m + 1 ), X(2m - 1 )~ ~d X2m are carboxamide residues forming carboxamide binding pairs Xl/X2m~ X2/X(2m-1)~ Xm/X(m + 1), and y is y-aminobuytic acid or 2,4 diaminobutyric acid and Dp is dimethylaminopropylamide, and where carboxamide binding pair X I /X2m corresponds to base pair N I ~N' l, carboxamide binding pair X2/X~2m-1) corresponds to base pair N2~N'2, carboxamide binding pair Xm/X~m+1 ) corresponds to base pair Nm~N'm.
In general, the specific polyamide DNA-binding ligands were designed by using a method that comprises the steps of identifying the target DNA sequence 5'-WNIN2 . , . NmW-3'; representing the identified sequence as 5'-Wab . . . xW-3', wherein a is a first nucleotide to be bound by the X I carboxamide residue, b is a second nucleotide to be bound by the X2 to carboxamide residue, and x is the corresponding nucleotide to be bound by the Xm carboxamide residue; defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence.
Carboxamide residues were selected sequentially as follows: Im was selected as the X 1 carboxamide residue and Py as the X2m carboxamide residue if a was G. Py was selected as the X I carboxamide residue and Im as the X2m carboxamide residue if a was C.
Hp was selected as the Xl carboxamide residue and Py as the X2m carboxamide residue if a was T. Py was selected as the Xl carboxamide residue and Hp as the X2m carboxamide residue if a .was A.
The remaining carboxamide residues were selected in the same fashion. Im was selected as the X2 carboxamide residue and Py as the X2m-1 carboxamide residue if b was G. Py was selected as the X2 carboxamide residue and Im as the X2m-1 carboxamide residue if b was C.
Hp was selected as the X2 carboxamide residue and Py as the X2m_ 1 carboxamide residue if b was T. Py was selected as the X2 carboxamide residue and Hp as the X2m-1 carboxamide residue if b was A.
The selection of carboxamide residues was continued through m iterations. In the last iteration, Im was selected as the Xm carboxamide residue and Py as the Xm+1 carboxamide 3o residue if x was G. Py was selected as the Xm carboxamide residue and Im as the Xm+1 carboxamide residue if x was C. Hp was selected as the Xm carboxamide residue and Py as the Xm+1 carboxamide residue if x was T. Py was selected as the Xm carboxamide residue and Hp as the Xm+1 carboxamide residue if x was A.
POLYAMIDE DNA-BINDING LIGANDS
The U.S. Government has certain rights in this invention pursuant to Grant Nos. GM
26453, 27681 and 47530 awarded by the National Institute of Health.
1o This application is a continuation-in-part of PCT/L7S97103332 filed February 20, 1997, Serial No. 08/853,522 filed May 8, 1997 and PCTIL1S 97/12722 filed July 21, 1997 which are continuation-in-part applications of Serial No. 08/837,524, filed April 21, 1997, Serial No.
08/607,078, filed February 26, 1996, provisional application Serial No.
60/042,022, f led April 16, 1997 and provisional application Serial No. 60/043,444, filed April 8, 1997.
BACKGROUND OF THE INVENTION
Field of the Invention 2o This invention relates to polyamides which bind to predetermined sequences in the minor groove of double stranded DNA.
Description of the Related Art The design of synthetic ligands that read the information stored in the DNA
double helix has been a long standing goal of chemistry. Cell-permeable small molecules which target predetermined DNA sequences are useful for the regulation of gene-expression.
Oligodeoxynucleotides that recognize the major groove of double-helical DNA
via triple-helix formation bind to a broad range of sequences with high affinity and specificity. Although oligonucleotides and their analogs have been shown to interfere with gene expression, the triple helix approach is limited to purine tracks and suffers from poor cellular uptake. The development of pairing rules for minor groove binding polyamides derived from N-methylpyrrole (Py) and N-methylimidazole (Im) amino acids provides another code to control sequence specificity. An ImlPy pair distinguishes G~C from C~G and both of these from A~T or ,35 T~A base pairs. Wade, W.S., Mrksich, M. & Dervan, P.B. describes the design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif. J. Am. Chem. Soc. 114, 8783-8794 (1992); Mrksich, M. et al.
describes antiparallel side-by-side motif for sequence specific-recognition in the minor groove of DNA by the designed peptide I -methyliinidazole-2-carboxamidenetropsin. Proc. Natl. Acad.
Sci. USA 89, 7586-7590 (1992); Trauger, J.W., Baird, E. E. Dervan, P.B. describes the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996). A
Py/Py pair specifies A~T from G~C but does not distinguish A~T from T~A. Pelton, J.G. &
Wemmer, D.E.
describes the structural characterization of a 2-1 distamycin A-d(CGCAAATTTGGC) complex by two-dimensional NMR. Proc. Natl. Acad. Sci. USA 86, 5723-5727 (1989);
White, S., Baird, E. E. & Dervan, P.B. Describes the effects of the A~T/T~A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA. Biochemistry 35, 12532-12537 (1996);
l0 White, S., Baird, E. E. & Dervan, P. B. describes the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides. Chem. c~ Biol. 4, 569-578 (1997); White, S., Baird, E. E. & Dervan, P.B. describes the S'-3' N-C orientation preference for polyamide binding in the minor groove. New methods of designing selective compounds and the resulting specific polyamide binding ligands that are designed to target an identified sequence of double stranded DNA are needed to overcome the A~T/T~A degeneracy of pyrrole-imidazole polyamide recognition.
SUMMARY OF THE INVENTION
It has been found that a new aromatic amino acid, 3-hydroxy-N-methylpyrrole (Hp) when incorporated into a polyamide and paired opposite Py, provides the means to discriminate A~T from T~A. Unexpectedly, the replacement of a single hydrogen atom on the pyrrole with a hydroxy group in a Hp/Py pair regulates the affinity and the specificity of a polyamide by an order of magnitude. Utilizing Hp together with Py and Im in polyamides to form four aromatic amino acid pairs (Im/Py, Py/Im, Hp/Py, and Py/Hp) provides a code to distinguish all four Watson-Crick base pairs in the minor groove of DNA.
3o The present invention provides a method for designing specific polyamides suitable for use as DNA-binding ligands, as well as compositions comprising such polyamides, that are selective for an identified target sequence of double stranded DNA.
Preferably, the designed specific polyamides are characterized by a dissociation constant of less than 1 nM, as measured by DNase I footprint titration, and greater than ten-fold selectivity for the identified target sequence over related mismatch sequences, based on the ratio of the corresponding dissociation constants measured by DNase I footprint titrations.
The invention encompasses improved polyamides for binding to the minor groove of double stranded ("duplex") DNA. The polyamides are in the form of a hairpin comprising two groups of at least three consecutive carboxamide residues, the two groups covalently linked by an aliphatic amino acid residue, preferably ~y-aminobutyric acid or 2,4 diaminobutyric acid, the consecutive carboxamide residues of the first group pairing in an antiparallel manner with the consecutive carboxamide residues of the second group in the minor groove of double stranded to DNA. The improvement relates to the inclusion of a binding pair of Hp/Py carboxamides in the polyamide to bind to a T~A base pair in the minor groove of double stranded DNA or Py/Hp carboxamide binding pair in the polyamide to bind to an A~T base pair in the minor groove of double stranded DNA. The improved polyamides have at least three consecutive carboxamide pairs for binding to at least three DNA base pairs in the minor groove of a duplex DNA sequence that has at least one A~T or T~A DNA base pair, the improvement comprising selecting a Hp/Py carboxamide pair to correspond to a T~A base pair in the minor groove or a Py/Hp carboxamide pair to bind to an A~T DNA base pair in the minor groove. Preferably the binding of the carboxamide pairs to the DNA base pairs modulates the expression of a gene.
In general, the method provides specific polyamides suitable for use as DNA-binding ligands that are selective for identified target sequences of double stranded DNA having a coding strand sequence of the form 5'-WN1N2 . . , NmW-3' where N is a nucleotide chosen from the group A, T, C and G, W is a nucleotide chosen from the group A and T, and with the coresponding paired antiparallel strand 3'-W'N' 1N'2 , , , N'mW'-5' where N' is a nucleotide chosen from the group T, A, G and C respectively to form Watson-Crick pase pairs, W is a nucleotide chosen from the group T and A respectively to form Watson-Crick pase pairs, and m is an integer having a value from 3 to 6 inclusive.
The preferred corresponding designed specific polyamides resulting from this invention are of the form X 1 X2 . . . Xm-y-X(m + 1 ) . . . X(2m-1 )X2m-~-Dp wherein X l , X2, Xm, X(m + 1 ), X(2m - 1 )~ ~d X2m are carboxamide residues forming carboxamide binding pairs Xl/X2m~ X2/X(2m-1)~ Xm/X(m + 1), and y is y-aminobuytic acid or 2,4 diaminobutyric acid and Dp is dimethylaminopropylamide, and where carboxamide binding pair X I /X2m corresponds to base pair N I ~N' l, carboxamide binding pair X2/X~2m-1) corresponds to base pair N2~N'2, carboxamide binding pair Xm/X~m+1 ) corresponds to base pair Nm~N'm.
In general, the specific polyamide DNA-binding ligands were designed by using a method that comprises the steps of identifying the target DNA sequence 5'-WNIN2 . , . NmW-3'; representing the identified sequence as 5'-Wab . . . xW-3', wherein a is a first nucleotide to be bound by the X I carboxamide residue, b is a second nucleotide to be bound by the X2 to carboxamide residue, and x is the corresponding nucleotide to be bound by the Xm carboxamide residue; defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence.
Carboxamide residues were selected sequentially as follows: Im was selected as the X 1 carboxamide residue and Py as the X2m carboxamide residue if a was G. Py was selected as the X I carboxamide residue and Im as the X2m carboxamide residue if a was C.
Hp was selected as the Xl carboxamide residue and Py as the X2m carboxamide residue if a was T. Py was selected as the Xl carboxamide residue and Hp as the X2m carboxamide residue if a .was A.
The remaining carboxamide residues were selected in the same fashion. Im was selected as the X2 carboxamide residue and Py as the X2m-1 carboxamide residue if b was G. Py was selected as the X2 carboxamide residue and Im as the X2m-1 carboxamide residue if b was C.
Hp was selected as the X2 carboxamide residue and Py as the X2m_ 1 carboxamide residue if b was T. Py was selected as the X2 carboxamide residue and Hp as the X2m-1 carboxamide residue if b was A.
The selection of carboxamide residues was continued through m iterations. In the last iteration, Im was selected as the Xm carboxamide residue and Py as the Xm+1 carboxamide 3o residue if x was G. Py was selected as the Xm carboxamide residue and Im as the Xm+1 carboxamide residue if x was C. Hp was selected as the Xm carboxamide residue and Py as the Xm+1 carboxamide residue if x was T. Py was selected as the Xm carboxamide residue and Hp as the Xm+1 carboxamide residue if x was A.
In one preferred embodiment, the polyamide includes at least four consecutive carboxamide pairs for binding to at least four base pairs in a duplex DNA
sequence. In another preferred embodiment, the polyamide includes at least five consecutive carboxamide pairs for binding to at least five base pairs in a duplex DNA sequence. In yet another preferred embodiment, the polyamide includes at least six consecutive carboxamide pairs for binding to at least six base pairs in a duplex DNA sequence. In one preferred embodiment, the improved polyamides have four carboxamide binding pairs that will distinguish A~T, T~A, C~G and G~C
to base pairs in the minor groove of a duplex DNA sequence. The duplex DNA
sequence can be a regulatory sequence, such as a promoter sequence or an enhancer sequence, or a gene sequence, such as a coding sequence or a non-coding sequence. Preferably, the duplex DNA
sequence is a promoter sequence.
More specifically, "polyamidc" refers to a polymer of polyamide subunits of the formula.
Y! X N R3 N
X
O ~n O y~ ~ R4 ~N
a b c where R1 is chosen from H, NH2, SH, Cl, Br, F, N-acetyl, or N-formyl where R2 is C 1 _ 100 alkyl (preferably C 1 _ 10 alkyl such as methyl, ethyl, isopropyl), C 1 _ 100 alkylamine (preferably C 1 _ l p alkylamine such as ethylamine), C 1-100 alkyldiamine (preferably C1-10 alkyldiamine such as N,N-dimethylpropylamine), a C1-100 alkylcarboxylate (preferably a C 1-10 alkylcarboxylate such as-CH2COOH), C 1 _ 100 alkenyl (preferably C 1 _ I O
alkenyl such as CH2CH=CH2), or a C 1 _ 100 alkynyl (preferably C 1-10 alkynyl such as -CH2C---CH3), or a C1_100L, where L groups can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-$-yloxy}-butyrate, tartaric acid, (+)-a.-tocopheral. Most preferably R2 is H, (CH2)mCH3, (CH2)mNH2, (CH2)mSH, (CH2)mOH, (CH2)m~52~ (CH2)mORS, (CH2)mSRS, where RS - (CH2)mCH3, (CH2)m~2~
(CH2)mSH, (CH2)mOH and m is an integer from 0 to 6.
where R3 is chosen from H, NH2, OH, SH, Br, Cl, F, OMe, CH20H, CH2SH, CH2NH2.
where R4 is -NH(CH2)0-100~6R~ or NI-I(CH2}pC0 NH(CH2}0-100~6R~ or NHR6 or NH(CH2)pCONHR6. Where R6 and R~ are independently chosen from H, Cl, NO, N-acetyl, benzyl, C 1 _ 100 alkyl, C 1-100 alkylamine, C 1-100 alkyldiamine, C 1-100 alkylcarboxylate, C 1 _ 1 o 100 alkenyl, a C 1 _ 100 alkynyl, or a C 1-1 OOL~ where L groups can be independently chosen from but is not limited to arylboranic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, an oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-a-tocopheral. Where p is an integer value ranging from 0 to 12. In the preferred form of the present invention Rf and R~ are H, and the resulting amine modified polyamide is coupled to an amine reactive molecule in order to generate a bifiznction polyamide conjugate.Where the amine reactive molecule is chosen from but not limited to the following:
2o aryiboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds , solid phase supports, an oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-a-tocopheral.
where X and Y are chosen from the following, N, CH, COH, CCH3, CNH2, CC1, CF.
a is an integer chosen from values of 0 or 1 b is an integer chosen integer values ranging from 1 to 5.
c is an integer value ranging from 2 to 10.
3o Hereinafter, N-methylpyrrolecarboxamide may be referred to as "Py", N-methylimidazolecarboxamide may be referred to as "Im", y-aminobutyric acid may referred to as "y", (3-alanine may be referred to as "(3", glycine may be referred to as "G", dimethylaminopropylamide may be referred to as "Dp", and ethylenediaminetetraacetic acid may be referred to as "EDTA":
The preparation and the use of polyamides for binding in the minor groove of double s stranded DNA are extensively described in the art. This invention is an improvement of the existing technology that uses 3-hydroxy-N-methyIpyrrole to provide carboxamide binding pairs for DNA binding polyamides.
The invention encompasses polyamides having y-aminobutyric acid or a substituted y-1o arninobutyric acid to form a hairpin with a member of each carboxamide pairing on each side of it. Preferably the substituted y-aminobutyric acid is a chiral substituted y-aminobutyric acid such as (R)-2,4-diaminohutyric acid. In addition, the polyamides may contain an aliphatic amino acid residue, preferably a (3-alanine residue, in place of a Hp or Py carboxamide.
The [3-alanine residue is represented in formulas as (3. The ~-alanine residue becomes a member of a t s carboxamide binding pair. The invention further includes the substitution as a X3/(3 binding pair for non-Im containing binding pair. Thus, binding pairs in addition to the Im/Py, Py/Im, Hp/Py and Py/Hp are Iml(3, ~3/Im, Py/~, ~3/PY, Hp/~, ~3/Hp, and (3/~i.
The polyamides of the invention can have additional moieties attached covalently to the 2o polyamide. Preferably the additional moieties are attached as substituents at the amino terminus of the polyamide, the carboxy terminus of the polyamide, or at a chiral (R)-2,4-diaminobutyric acid residue. Suitable additional moieties include a detectable labeling group such as a dye, biotin or a hapten. Other suitable additional moieties are DNA reactive moieties that provide for sequence specific cleavage of the duplex DNA.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 illustrates the structure of polyamide 1 2 and 3.
.3o Figure 2 illustrates the pairing of polyamides to DNA base pairs.
Figure 3 illustrates the DNase footprint titration of compounds 2 and 3.
sequence. In another preferred embodiment, the polyamide includes at least five consecutive carboxamide pairs for binding to at least five base pairs in a duplex DNA sequence. In yet another preferred embodiment, the polyamide includes at least six consecutive carboxamide pairs for binding to at least six base pairs in a duplex DNA sequence. In one preferred embodiment, the improved polyamides have four carboxamide binding pairs that will distinguish A~T, T~A, C~G and G~C
to base pairs in the minor groove of a duplex DNA sequence. The duplex DNA
sequence can be a regulatory sequence, such as a promoter sequence or an enhancer sequence, or a gene sequence, such as a coding sequence or a non-coding sequence. Preferably, the duplex DNA
sequence is a promoter sequence.
More specifically, "polyamidc" refers to a polymer of polyamide subunits of the formula.
Y! X N R3 N
X
O ~n O y~ ~ R4 ~N
a b c where R1 is chosen from H, NH2, SH, Cl, Br, F, N-acetyl, or N-formyl where R2 is C 1 _ 100 alkyl (preferably C 1 _ 10 alkyl such as methyl, ethyl, isopropyl), C 1 _ 100 alkylamine (preferably C 1 _ l p alkylamine such as ethylamine), C 1-100 alkyldiamine (preferably C1-10 alkyldiamine such as N,N-dimethylpropylamine), a C1-100 alkylcarboxylate (preferably a C 1-10 alkylcarboxylate such as-CH2COOH), C 1 _ 100 alkenyl (preferably C 1 _ I O
alkenyl such as CH2CH=CH2), or a C 1 _ 100 alkynyl (preferably C 1-10 alkynyl such as -CH2C---CH3), or a C1_100L, where L groups can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-$-yloxy}-butyrate, tartaric acid, (+)-a.-tocopheral. Most preferably R2 is H, (CH2)mCH3, (CH2)mNH2, (CH2)mSH, (CH2)mOH, (CH2)m~52~ (CH2)mORS, (CH2)mSRS, where RS - (CH2)mCH3, (CH2)m~2~
(CH2)mSH, (CH2)mOH and m is an integer from 0 to 6.
where R3 is chosen from H, NH2, OH, SH, Br, Cl, F, OMe, CH20H, CH2SH, CH2NH2.
where R4 is -NH(CH2)0-100~6R~ or NI-I(CH2}pC0 NH(CH2}0-100~6R~ or NHR6 or NH(CH2)pCONHR6. Where R6 and R~ are independently chosen from H, Cl, NO, N-acetyl, benzyl, C 1 _ 100 alkyl, C 1-100 alkylamine, C 1-100 alkyldiamine, C 1-100 alkylcarboxylate, C 1 _ 1 o 100 alkenyl, a C 1 _ 100 alkynyl, or a C 1-1 OOL~ where L groups can be independently chosen from but is not limited to arylboranic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, an oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-a-tocopheral. Where p is an integer value ranging from 0 to 12. In the preferred form of the present invention Rf and R~ are H, and the resulting amine modified polyamide is coupled to an amine reactive molecule in order to generate a bifiznction polyamide conjugate.Where the amine reactive molecule is chosen from but not limited to the following:
2o aryiboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds , solid phase supports, an oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-a-tocopheral.
where X and Y are chosen from the following, N, CH, COH, CCH3, CNH2, CC1, CF.
a is an integer chosen from values of 0 or 1 b is an integer chosen integer values ranging from 1 to 5.
c is an integer value ranging from 2 to 10.
3o Hereinafter, N-methylpyrrolecarboxamide may be referred to as "Py", N-methylimidazolecarboxamide may be referred to as "Im", y-aminobutyric acid may referred to as "y", (3-alanine may be referred to as "(3", glycine may be referred to as "G", dimethylaminopropylamide may be referred to as "Dp", and ethylenediaminetetraacetic acid may be referred to as "EDTA":
The preparation and the use of polyamides for binding in the minor groove of double s stranded DNA are extensively described in the art. This invention is an improvement of the existing technology that uses 3-hydroxy-N-methyIpyrrole to provide carboxamide binding pairs for DNA binding polyamides.
The invention encompasses polyamides having y-aminobutyric acid or a substituted y-1o arninobutyric acid to form a hairpin with a member of each carboxamide pairing on each side of it. Preferably the substituted y-aminobutyric acid is a chiral substituted y-aminobutyric acid such as (R)-2,4-diaminohutyric acid. In addition, the polyamides may contain an aliphatic amino acid residue, preferably a (3-alanine residue, in place of a Hp or Py carboxamide.
The [3-alanine residue is represented in formulas as (3. The ~-alanine residue becomes a member of a t s carboxamide binding pair. The invention further includes the substitution as a X3/(3 binding pair for non-Im containing binding pair. Thus, binding pairs in addition to the Im/Py, Py/Im, Hp/Py and Py/Hp are Iml(3, ~3/Im, Py/~, ~3/PY, Hp/~, ~3/Hp, and (3/~i.
The polyamides of the invention can have additional moieties attached covalently to the 2o polyamide. Preferably the additional moieties are attached as substituents at the amino terminus of the polyamide, the carboxy terminus of the polyamide, or at a chiral (R)-2,4-diaminobutyric acid residue. Suitable additional moieties include a detectable labeling group such as a dye, biotin or a hapten. Other suitable additional moieties are DNA reactive moieties that provide for sequence specific cleavage of the duplex DNA.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 illustrates the structure of polyamide 1 2 and 3.
.3o Figure 2 illustrates the pairing of polyamides to DNA base pairs.
Figure 3 illustrates the DNase footprint titration of compounds 2 and 3.
_g_ Figure 4 illustrates a list of the structures of representative Hp containing polyamides. ' Figure 5 schematically illustrates a method for the design of eight carboxamide residue hairpin polyamide compounds suitable for recognition of 6-by 5'-V~~fl'JNNW-3' sequences in the minor groove of double stranded DNA.
Figure 6 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a ~3-alanine residue in order to enhance the DNA
binding properties of certain eight carboxamide residue hairpin polyamide compounds.
Figure 7 schematically illustrates a method for the design of ten carboxamide residue hairpin polyamide compounds suitable for recognition of 7-by 5'-WNT12~1NNW-3' sequences in the t o minor groove of double stranded DNA.
Figure 8 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a (3-alanine residue in order to enhance the DNA
binding properties of certain tcn carboxamide residue hairpin polyamide compounds.
Figure 9 schematically illustrates a method for determining the position of an additional t 5 aromatic amino acid residue that should be replaced with a (3-alanine residue in order to enhance the DNA binding properties of certain ten carboxamide residue hairpin poiyamide compounds.
Figure 10 schematically illustrates a method for the design of twelve carboxamide residue hairpin polyamide compounds suitable for recognition of 8-by S'-VJhfIJNNW-3' sequences in the minor groove of double stranded DNA.
20 Figure 11 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a ~-alanine residue in order to enhance the DNA
binding properties of certain twelve carboxamide residue hairpin polyamide compounds.
DETAILED DESCRIPTION OF THE INVENTION
Within this application, unless otherwise stated, definitions of the terms and illustration of the techniques of this application may be found in any of several well-known references such as: Sambrook, J., e1 al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press (1989); Goeddel, D., ed., Gene Expression Technology, Methods in Enzymology, 185, Academic Press, San Diego, CA (1991); "Guide to Protein Purification" in Deutshcer, M.P., ed., Methods in Enzymology, Academic Press, San Diego, CA ( 1989); Innis, et al., PCR Protocols: A Guide to Methods and Applications, Academic Press, San Diego, CA
(1990); Freshney, R.L, Culture of Animal Cells: A Manual of Basic Technique, 2"d Ed., Alan Liss, Inc. New York, NY (1987); Murray, E.J., ed., Gene Transfer and Expression Protocols, pp.
109-128, The Humana Press Inc., Clifton, NJ and Lewin, B., Genes Vl, Oxford University Press, New York (1997).
For the purposes of this application, a promoter is a regulatory sequence of DNA- that is involved in the binding of RNA polymerase to initiate transcription of a gene.
A gene is a segment of DNA involved in producing a peptide, polypeptide or protein, including the coding region, non-coding regions preceding ("leader") and following ("trailer") the coding region, as well as intervening non-coding sequences ("introns") between individual coding segments ("exons"). Coding refers to the representation of amino acids, start and stop signals in a three base "triplet" code. Promoters are often upstream (" '5 to") the transcription initiation site of the corresponding gene. Other regulatory sequences of DNA in addition to promoters are known, including sequences involved with the binding of transcription factors, including response elements that are the DNA sequences bound by inducible factors. Enhancers comprise yet another group of regulatory sequences of DNA that can increase the utilization of promoters, and can function in either orientation (S'-3' or 3'-5') and in any location (upstream or downstream) relative to the promoter. Preferably, the regulatory sequence has a positive activity, i.e., binding of an endogeneous ligand (e.g. a transcription factor) to the regulatory sequence increases transcription, thereby resulting in increased expression of the corresponding target gene. In such a case, interference with transcription by binding a polyamide to a regulatory sequence would reduce or abolish expression of a gene.
The promoter may also include or be adjacent to a regulatory sequence known in the art as a silencer-. A silencer sequence generally has a negative regulatory effect on expression of the gene. In such a case, expression of a gene may be increased directly by using a poiyamide to prevent binding of a factor to a silencer regulatory sequence or indirectly, by using a polyamide to block transcription of a factor to a silencer regulatory sequence.
It is to be understood that the polyamides of this invention bind to double stranded DNA
in a sequence specific manner. The function of a segment of DNA of a given sequence, such as 5'-TATAAA-3', depends on its position relative to other functional regions in the DNA
sequence. In this case, if the sequence 5'-TATAAA-3' on the coding strand of DNA is 3o positioned about 30 base pairs upstream of the transcription start site, the sequence forms part of the promoter region (Lewin, Genes UI, pp. 831-835). On the other hand, if the sequence 5'-TATAAA-3' is downstream of the transcription start site in a coding region and in proper register with the reading frame, the sequence encodes the tyrosyl and lysyl amino acid residues (Lewin, Genes Vl, pp. 213-215).
While not being held to one hypothesis, it is believed that the binding of the polyamides of this invention modulate gene expression by altering the binding of DNA
binding proteins, such as RNA polymerase, transcription factors, TBF, TFIIIB and other proteins.
The effect on gene expression of polyamide binding to a segment of double stranded DNA is believed to be related to the function, e.g., promoter, of that segment of DNA.
to It is to be understood by one skilled in the art that the improved polyamides of the present invention may bind to any of the above-described DNA sequences or any other sequence having a desired effect upon expression of a gene. In addition, U.S. Patent No. 5,578,444 describes numerous promoter targeting sequences from which base pair sequences for targeting an improved polyamide of the present invention may be identified.
It is generally understood by those skilled in the art that the basic structure of DNA in a living cell includes both major and a minor groove. For the purposes of describing the present invention, the minor groove is the narrow groove of DNA as illustrated in common molecular 2o biology references such as Lewin, B., Genes vl, Oxford University Press, New York (1997).
To affect gene expression in a cell, which may include causing an increase or a decrease in gene expression, a effective quantity of one or more polyamide is contacted with the cell and internalized by the cell. The cell may be contacted in vivo or in vitro.
Effective extracellular concentrations of polyamides that can modulate gene expression range from about 10 nanomolar to about 1 micromolar. Gottesfeld, J.M., et al., Nature 387 202-205 (1997). To determine effective amounts and concentrations of polyamides in vitro, a suitable number of cells is plated on tissue culture plates and various quantities of one or more polyamide are added to separate wells. Gene expression following exposure to a polyamide can be monitored in the cells or 3o medium by detecting the amount of the protein gene product present as determined by various techniques utilizing specific antibodies, including ELISA and western blot.
Alternatively, gene expression following exposure to a polyamide can be monitored by detecting the amount of messenger RNA present as determined by various techniques, including northern blot and RT-PCR.
Similarly, to determine effective amounts and concentrations of polyamides for -in vivo administration, a sample of body tissue or fluid, such as plasma, blood, urine, cerebrospinal ~ fluid, saliva, or biopsy of skin, muscle, liver, brain or other appropriate tissue source is analyzed.
Gene expression following exposure to a polyamide can be monitored by detecting the amount ' of the protein gene product present as determined by various techniques utilizing specific antibodies, including ELISA and western blot. Alternatively, gene expression following exposure to a polyamide can be monitored by the detecting the amount of messenger RNA
present as determined by various techniques, including northern blot and RT-PCR.
The polyamides of this invention may be formulated into diagnostic and therapeutic compositions for in vivo or in vitro use. Representative methods of formulation may be found in Remington: The Science and Practice of Pharmacy, 19th ed., Mack Publishing Co., Easton, PA
(1995).
For in vivo use, the polyamides may be incorporated into a physiologically acceptable pharmaceutical composition that is administered to a patient in need of treatment or an animal for medical or research purposes. The polyamide composition comprises pharmaceutically acceptable earners, excipients, adjuvants, stabilizers, and vehicles. The composition may be in 2o solid, liquid, gel, or aerosol form. The polyamide composition of the present invention may be administered in various dosage forms orally, parentally, by inhalation spray, rectally, or topically. The term parenteral as used herein includes, subcutaneous, intravenous, intramuscular, intrasternal, infusion techniques or intraperitoneally.
The selection of the precise concentration, composition, and delivery regimen is influenced by, inter alia, the specific pharmacological properties of the particular selected compound, the intended use, the nature and severity of the condition being treated or diagnosed, the age, weight, gender, physical condition and mental acuity of the intended recipient as well as the route of administration. Such considerations are within the purview of the skilled artisan.
3o Thus, the dosage regimen may vary widely, but can be determined routinely using standard methods.
Polyamides of the present invention are also useful for detecting the presence of double stranded DNA of a specific -sequence for diagnostic or preparative purposes.
The sample containing the double stranded DNA can be contacted by polyamide linked to a solid substrate, thereby isolating DNA comprising a desired sequence. Alternatively, poIyamides linked to a suitable detectable marker, such as biotin, a hapten, a radioisotope or a dye molecule, can be contacted by a sample containing double stranded DNA.
The design of bifunctional sequence specific DNA binding molecules requires the integration of two separate entities: recognition and functional activity.
Polyamides that specifically bind with subnanomolar affinity to the minor groove of a predetermined sequence of double stranded DNA are linked to a functional molecule, providing the corresponding bifunctional conjugates useful in molecular biology, genomic sequencing, and human medicine.
Polyamides of this invention can be conjugated to a variety of functional molecules, which can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotides, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-~,-tocopheral, psoralen, EDTA, methidium, 2o acridine, Ni(II)~Gly-Gly-His, TO, Dansyl, pyrene, N-bromoacetamide, and gold particles. Such bifunctional polyamides are useful for DNA affinity capture, covalent DNA
modification, oxidative DNA cleavage, and DNA photocleavage. Such bifunctional polyamides are useful for DNA detection by providing a polyamide linked to a detectable label. Detailed instructions for synthesis of such bifunctional polyamides can be found in copending U.S.
provisional application 60/043,444, the teachings of which are incorporated by reference.
DNA complexed to a labeled polyamide can then be determined using the appropriate detection system as is well known to one skilled in the art. For example, DNA
associated with a polyamide linked to biotin can be detected by a streptavidin / alkaline phosphatase system.
The present invention also describes a diagnostic system, preferably in kit form, for assaying for the presence of the double stranded DNA sequence bound by the polyamide of this invention in a body sample, such brain tissue, cell suspensions or tissue sections, or body fluid samples such as CSF, blood, plasma or serum, where it is desirable to detect the presence, and preferably the amount, of the double stranded DNA sequence bound by the polyamide in the sample according to the diagnostic methods described herein.
The diagnostic system includes, in an amount sufficient to perform at least one assay, a specific polyamide as a separately packaged reagent. Instructions for use of the packaged reagents) are also typically included. As used herein, the term "package"
refers to a solid matrix or material such as glass, plastic (e.g., polyethylene, polypropylene or polycarbonate), paper, foil and the like capable of holding within fixed limits a polyamide of the present 1 o invention. Thus, for example, a package can be a glass vial used to contain milligram quantities of a contemplated polyamide or it can be a microliter plate well to which microgram quantities of a contemplated polyamide have been operatively affixed, i.e., linked so as to be capable of being bound by the target DNA sequence. "Instructions for use" typically include a tangible expression describing the reagent concentration or at least one assay method parameter such as the relative amounts of reagent and sample to be admixed, maintenance time periods for reagent or sample admixtures, temperature, buffer conditions and the like. A
diagnostic system of the present invention preferably also includes a detectable label and a detecting or indicating means capable of signaling the binding of the contemplated polyamide of the present invention to the target DNA sequence. As noted above, numerous detectable labels, such as biotin, and detecting or indicating means, such as enzyme-linked (direct or indirect) streptavidin, are well known in the art.
As used herein, "subnanomolar affinity" means binding that is characterized by a dissociation constant, Kd , of less than 1 nM, as measured by DNase I
footprint titration.
Preferably, polyamides of the present invention are characterized by subnanomolar binding affinity for the identified target DNA sequence. As used herein, the "selectivity" of the binding of a polyamide to a DNA sequence is the ratio of the dissociation constant, Kd , as measured by DNase I footprint titration of binding the polyamide to a mismatch DNA
sequence divided by the corresponding dissociation constant of the binding of the polyamide to the identified target 3o DNA sequence. Preferably, polyamides of the present invention are characterized by a selectivity of 5 or greater, more preferably a selectivity of greater that 10.
r The exemplary polyamide that illustrates the compositions and methods of the present invention is polyamide 3 of Figure 1, ImImHpPy-y-ImPyPyPy-~3-Dp. This polyamide was designed according to the method of the present invention to target the identified sequence 5'-WGGTCW-3'. See Table 5, below, Sequence No. 36 and the corresponding sequence of carboxamide binding pairs. Polyamide 3 binds an identified target sequence 5'-TGGTCA-3' with a dissociation constant, as measured by DNase I footprint titration, of 0.48 nM, i.e., with subnanomolar affinity as defined herein (see Table 1, below). The polyamide binds to the mismatch sequence 5'-TGGACA-3' with a dissociation contant of 37 nM, yielding a selectivity, as defined herein, of 77 (Table 1 ).
to Figure 1 shows representative structures of polyamides. ImImPyPy-y-ImPyPyPy-~3-Dp (1), ImImPyPy-y-ImHpPyPy-/3-Dp (2), and ImlmHpPy-y-ImPyPyPy-(3-Dp (3). (Hp = 3-hydroxy-N-methylpyrrole, Im = N-methylimidazole, Py = N-methylpyrrole, (3 = ~i-alanine, y = y-aminobutyric acid, Dp = Dimethylaminopropylamide). Polyamides were synthesized by solid phase methods using Boc-protected 3-methoxypyrrole, imidazole, and pyrrole aromatic amino acids, cleaved from the support by aminolysis, deprotected with sodium thiophenoxide, and purified by reversed phase HPLC. Baird, E. E. & Dervan, P. B. describes the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chern. Soc. 118, 6141-6146 (1996); also see PCT US 971003332. The identity and purity of the polyamides were 2o verified by'H NMR, analytical HPLC, and matrix-assisted laser-desorption ionization time-of flight mass spectrometry (MALDI-TOF MS-monoisotopic): 1 1223.6 {1223.6 calculated), 2 1239.6 (1239.6 calculated); 3 1239.6 (1239.6 calculated).
Figure 2 illustrates binding models for polyamides 1-3 in complex with 5'-TGGTCA-3' and 5'-TGGACA-3' (A~T and T~A in fourth position highlighted). Filled and unfilled circles represent imidazole and pyrrole rings respectively; circles containing an H
represent 3-hydroxypyrrole, the curved line connecting the polyamide subunits represents y-aminobutyric acid, the diamond represents (3-alanine, and the + represents the positively charged dimethylaminopropylamide tail group.
Figure 3 shows quantitative DNase I footprint titration experiments with polyamides 2 and 3 on the 3' 3~P labeled 250-by pJK6 EcoRIIPvuII restriction fragment. Lane 1, intact DNA;
lanes 2-11 DNase I digestion products in the presence of 100, 50, 20, 10, 5, 2, l, 0.5, 0.2, 0.1 nM
-I s-polyamide, respectively; lane 12, DNase I digestion products in the absence of polyamide; lane 13, adenine-specific chemical sequencing. Iverson, B. L. & Dervan, P. B.
describes an adenine-specific DNA chemical sequencing reaction. Methods ~nzymol. 15, 7823-7830 (1987). All reactions were done in a total volume of 400 p,L. A polyamide stock solution or Hz0 was added to an assay buffer containing radiolabeled restriction fragment, with the final solution conditions of 10 mM Tris-HC1, 10 mM KC1, 10 mM MgCh, 5 mM CaCl2, pH 7Ø Solutions were allowed to equilibrate for 4-12 h at 22 °C before initiation of footprinting reactions.
Footprinting reactions, separation of cleavage products, and data analysis were carried out as described. White, S., Baird, E. E. & Dervan, P. B. Effects of the A~T/T~A
degeneracy of to pyrrole-imidazole polyamide recognition in the minor groove of DNA.
Biochemistry 35, 12532-12537 (1996).
Figure 4 shows the structure and equilibrium dissociation constant for numerous compounds of the present invention. Polyamides are shown in complex with their respective 1s match site. Filled and unfilled circles represent imidazole (Im) and pyrrole (Py) rings, respectively; circles containing an H represent 3-hydroxypyrrole (Hp), the curved line connecting the polyamide subunits represents y-aminobutyric acid (y), the diamond represents ~3-alanine (~3), and the + represents the positively charged dimethylaminopropylamide tail group (Dp). The equilibrium dissociation constants are the average values obtained from three DNase 2o I footprint titration experiments. The standard deviation for each set is less than 15% of the reported number. Assays were earned out in the presence of 10 mM Tris~HCI, 10 mM KCI, 10 mM MgCl2, and 5 mM CaClz at pH 7.0 and 22°C.
Four-ring polyamide subunits, covalently coupled to form eight-ring hairpin structures, 2s bind specifically to 6-by target sequences at subnanomolar concentrations.
Trauger, J.W., Baird, E. E. & Dervan, P.B. describe the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996); Swalley, S. E., Baird, E. E. &
Dervan, P. B.
describe the discrimination of 5'-GGGG-3', S'-GCGC-3', and 5'-GGCC'3' sequences in the minor groove of DNA by eight-ring hairpin polyamides. J. Am. Chem. Soc. 119, 30 ( 1997). The DNA-binding affinities of three eight-ring hairpin polyamides shown in Figure 1 as compound 1, 2, and 3 containing pairings of Im/Py, Py/Im opposite G~C, C~G and either Py/Py, Hp/Py, or Py/Hp at a common single point opposite T~A and A~T has been determined.
Equilibrium dissociation constants (K~) for ImImPyPy-y-ImPyPyPy-(3-Dp 1, ImImPyPy-y-ImHpPyPy-~i-Dp 2, ImImHpPy-y-ImPyPyPy-~3-Dp 3 of Figure 1 are shown in Table 1.
3s Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K. describe a quantitative DNase footprint titration method for studying protein-DNA interactions. Methods Enzymol. 130, 132-181 {1986); The Kd values were determined by quantitative DNase I footprint titration experiments: on a 3' 32P-labeled 250-by DNA fragment containing the target sites, 5'-TGGACA-3' and 5'-TGGTCA-3' which differ by a single A~T base pair in the fourth position.
The DNase footprint gels are shown in Figure 3.
S
TABLE 1 Equilibrium dissociation constants%
Polyamidet 5'-TGG_TCA-3' 5'-TGGACA-3' KrelT
5'-T G G T C A-3' 5'-T G G 'A C A-3' 1 PyIPy + + 2.0 3'-A C C A G T-5' 3'-A C C T G T-5' K~ = 0.077 nM Kd = 0.15 nM
5'-T G G T C A-3' S'-T G G A. C A-3' 2 PyIHp + H + H a.of~
3'-A C C Fa G T-5' 3'-A C C T G T-5' Kd = 15 nM Kd = 0.83 nM
5'-T G G T C A-3' S'-T G G A' C A-3' H H
3 Hp/Py + +
3'-A C C 11 G T-5' 3'-A C C T G T-5' Kd = 0.48 nM K~ =37 nM
*The reported dissociation constants are the average values obtained from three DNase I footprint titration experiments. The standard deviation for each data set is less than 15% of the reported number. Assays were carried out in the presence of 10 mM Tris~HCI, 10 mM KCI, 10 mM MgCl2, and 5 mM CaCl2 at pI-i 7.0 and 22 °C.
Ring pairing opposite T~A and A~T in the fourth position.
Calculated as Kd(5'-TGGACA-3')/Kd(5'-TGGTCA-3').
Based on the pairing rules for polyamide-DNA complexes both of these sequences are a match for control polyamide 1 which places a Py/Py pairing opposite to A~T and T~A at both sites. It was determined that polyamide 1 (Py/Py) binds to 5'-TGGTCA-3' and 5'-TGGACA-3' within a factor of 2 (K~ = 0.077 or 0.15 nM respectively). In contrast, poiyamide 2 {Py/Hp) binds to 5'-TGGTCA-3' and 5'-TGGACA-3' with dissociation constants which differ by a factor of 18 (K~ = 15 nM and 0.83 nM respectively). By reversing the pairing in polyamide 3 (Hp/Py) the dissociation constants differ again in the opposite direction by a 15 factor of 77 (KD = 0.48 nM and 37 nM respectively). Control experiments performed on separate DNA fragments; reveal that neither a S'-TGGGCA-3' or a 5'-TGG_CCA-3' site is bound by polyamide 2 or 3 at concentrations < 100 nM, indicating that the Hp/Py and Py/Hp ring pairings do not bind opposite G~C or C~G.
20 The specificity of polyamides 2 and 3 for sites which differ by a single A~T/T~A base pair results from small chemical changes. Replacing the Py/Py pair in 1 with a Py/Hp pairing as in 2, a single substitution of C3-OH for C3-H, destabilizes interaction with 5'-TGGTCA-3' by 191-fold, a free energy difference of 3.1 kcal mol-'. Interaction of 2 with 5'-TGGACA-3' is destabilized only 6-fold relative to 1, a free energy difference of 1.1 kcal mol-' . Similarly, replacing the Py/Py pair in 1 with Hp/Py as in 3 destabilizes interaction with S'-TGGACA-3'~by 2S2-fold, a free energy difference of 3.2 kcal mol-~. Interaction of 3 with S'TGG_TCA-3' is destabilized only b-fold relative to 1, a free energy difference of 1.0 kcal mol-1.
~ s The polyamides of this invention provide for coded targeting of predetermined DNA
sequences with affinity and specificity comparable to sequence-specific DNA
binding proteins.
I~p, Im, and Py polyamides complete the minor groove recognition code using three aromatic amino acids which combine to form four ring pairings (lm/Py, Py/Im, Hp/Py, and Py/Hp) which complement the four Watson-Crick base pairs, as shown in TABLE 2. There are a possible 240 to four base pair sequences which contain at least 1 A~T or T~A base pair and therefore can advantageously use an Hp/Py, or Py/Hp carboxamide binding. Polyamides binding to any of these sequences can be designed in accordance with the code of TABLE 2.
TABLE 2 Pairing code for minor groove recognition_* _ Pair G~C C~G T~A A~T
Im/Py -i- - - -PylIm - ~. - -Hp/Py - - ..f.
Py/Hp - - -* favored (+), disfavored (-) IS
For certain G~C rich sequences the affinity of polyamide~DNA complexes may be enhanced by substitution of an Im/~ pair for Im/Py at G~C and ~3/Im for PylIm at C~G. At A~T
and T~A base pairs, either a Py/~i, ~3/Py, Hp/~i, ~i/Hp, and (3/(3 may be used. The alternate aliphatic/aromatic amino acid pairing code is described in Table 3.
Za TABLE 3 Aliphatic/Aromatic substitrution for ring pairings*
Pair Substitution Py ...___..........R......_-........ .............................-.._.........
Iml Im/
Py/Im (3llm HpIPy Py/(3, ~/PY, Hpl(3, (3/(3 PYIHP PY/I~, ~IPY, ~IHP~ ~I~
_18_ U. S. Patent 5,578,444 describes numerous promoter region targeting sequences from which base pair sequences for targeting a polyamide can be identified.
PCT U.S. 97/003332 describes methods for synthesis of polyamides which are suitable for preparing polyamides of this invention. The use of ~3-aianine in place of a pyrrole amino acid in the synthetic methods provides aromatic/aliphatic pairing (Im/(3, (3/Im, Hp/(3, (3/Hp, Py/(3, and ~3/Py) and aliphatic/aliphatic pairing ((3/(3) substitution. The use of y-aminobutyric acid, or a substituted y-aminobutyric acid such as (R)-2,4 diaminobutyric acid, provides for preferred hairpin turns. The following examples illustrate the synthesis of polyamides of the present 1 o invention.
The process of designing a preferred polyamide molecule X1X2X3X4-y-XSX6X7Xg comprising eight aromatic amino acid residues of this invention is shown schematically in Figure 5. The polyamide design process provides a method for designing an eight carboxamide residue molecule comprising , four carboxamide binding pairs for detection and binding of a target six base pair 5'-V~NNNNW-3' sequence in the minor groove of double stranded DNA.
The design process identifies an appropriate polyamide ligand for recognition of a predetermined 6-bp, 5'-V~1\f~JNNW-3' sequence with subnanomolar affinity and >10-fold specificity versus mismatch sites. Trauger, J.W., Baird, E. E. Dervan, P.B. describes the recognition of DNA by 2o designed Iigands at subnanomolar concentrations. Nature 382, 559-561 (1996).
In order to prepare a polyamide molecule specific for an identified six base pair sequence of double stranded DNA, a user starts the 8-ring polyamide design process that implements the minor groove recognition pairing code summarized in Table 2 above. In the design process a 5'-VV1\I~~INNW-3' sequence was identified. In a preferred embodiment, the identified sequence was located within a gene promoter. U. S. Patent 5,578,444 describes numerous promoter region targeting sequences from which target six base pair sequences for targeting a polyamide can be identified. The identified sequence was then defined as 5'-WabcdW-3' in a stepwise process wherein a, b, c, and d, were sequentially and independently defined as A, G, C, or T. The 3o structure of the polyamide molecule was then correspondingly defined by sequentially chosing antiparallel carboxamide binding pairs according to the minor groove pairing code summarized in Table 2 above. Thus, if a was G, then X1 was defined as Im, and Xg was defined as Py. If a was C, then X 1 was defined as Py, and Xg was defined as Im. If a was T, then X I was defined as Hp, and Xg was defined as Py. If a was A, then Xl was defined as Py, and Xg was defined as Hp, Similarly,.b was defined as A, G, C, or T and corresponding carboxamide binding pairs were defined. According to the same rules, if b was G, then X2 was defined as Im, and X7 was ' defined as Py. If b was C, then X2 was defined as Py, and X7 was defined as Im. Likewise, if b was T, then X2 was defined as Hp, and X7 was defined as Py. If b was A, then X2 was defined as Py, and X7 was defined as Hp.
to The next step was to define c as A, G, C, or T and then define corresponding carboxamide binding pairs. Following the same rules, if c was G, then X3 was defined as Im, and X6 was defined as Py. If c was C, then X3 was defined as Py, and X6 was defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and X6 was defined as Py. If c was A, then X3 was defined as Py, and X6 was defined as Hp. Lastly, d was defined as A, G, C, or T and the last corresponding carboxamide binding pair was defined. According to above rules, if d was G, then X4 was defined as Im, and XS was defined as Py. If d was C, then X4 was defined as Py, and XS was defined as Im. If d was T, then X4 was defined as Hp, and XS was defined as Py. If d was A, then X4 was defined as Py, and XS was defined as Hp.
2o With all eight carboxamide residues that participate in binding pairs now defined, the designed polyamide X1X2X3X4-y-X5X6X7Xg suitable for binding to the identified sequence was synthesized using known techniques. Baird, E. E. & Dervan, P. B. describes the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chem. Soc. 118, 6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence was determined using a quantitative DNase footprint titration method for studying protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K., Methods Enzymol. 130, 132-181 (1986). If the affinity of the synthesized polyamide at the target site 3o was not subnanomolar affinity then adding a (3-alanine (process A) was considered in order to - optimize the exact positions of the binding pairs of aromatic amino acids.
If the affinity of the said polyamide at said target site was subnanomolar affinity then the sequence specificity of the polyamide versus mismatch sequences was determined. If the specificity versus mismatch sites was not > 10-fold specificity then adding a ~3-alanine (process A
schematically shown in Figure 6) was considered, in order to optimize the positions of the aromatic amino acids in relationship to the base pairs in the minor groove. Specificity of the polyamide molecule for the target identified sequence versus mismatch sequence sites of greater than 10-fold was considered a successful result of design process.
The 256 polyamide molecules comprising four carboxamide binding pairs that were designed using this method are useful for binding to the 256 target 5'-NNNN-3' core sequences, and are listed in Tables 4-11. A corresponding polyamide molecule was designed for each 1o DNA sequence (1-240) and (G1-G16) using the process outlined above and shown schematically in Figure 5.
If the synthesized polyamide molecule did not bind to the target identified sequence with subnanomolar affinity or if the synthesized. polyamide molecule did not exhibit a specificity for the target identified sequence versus mismatch sequence sites of greater than 10-fold, the option of substituting an aliphatic amino acid residues for one of the carboxamide residues was considered. The preferred aliphatic amino acid residue is (3-alanine. At least one aliphatic amino acid residue such as a ~i-alanine residue provided some flexibility to the central portion of the polyamide molecule, acting as a "spring" to permit optimization of the hydrogen bonding 2o between the carboxamide binding pairs and the nucleotide bases of the double stranded DNA.
In general, it was not found to be advantageous to replace either member of the terminal carboxamide binding pair, Xl/Xg, with ~3-alanine. Similarly, ~i-alanine was not substituted for members of the binding pair, X41X5, adjacent to the y hairpin residue. ~i-alanine residues were not substituted for N-methylimidazole residues. The use of (3-alanine in place of a pyrrole or 3-hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/(3, ~3lIm, Hp/(3, (3/Hp, Py/~, and (3/Py) and aliphatic/aliphatic pairing (~/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-alanine is 3o schematically illustrated in Figure 6. Selective placement of an aliphatic (3-alanine ((3) residue paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im) aromatic amino acid or another ~3-alanine residue is found to compensate for sequence composition effects to improve .....,.. ~ , . i ~ ..~~. , recognition and binding of the minor groove of DNA by pyrrole-imidazole polyamides of the present invention. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be reduced by replacement of an s aromatic amino acid with an aliphatic ~-alanine residue. In a polyamide molecule that comprises four binding pairs it is only beneficial to place ~3-alanine in positions X2, X3, Xb, and X~. No more than two (3-alanine residues may be placed within a single hairpin structure. No more than a single (3-residue may be placed within each individual polyamide subunit, e.g., if X2 is replaced with ~3-alanine, then X3 cannot be replaced.
~o These rules and others were implemented in the method schematically illustrated in Figure 6. This process is suitable for the refinement of the design polyamide comprising four binding pairs that has been designed by the method illustrated in Figure 5, but which lacks subnanomolar affinity or greater than 10-fold specificity at the identified target DNA sequence.
is As in the basic design method, the designed polyamides are synthesized and the affinity and specificity of binding to the target DNA were determined.
For a given polyamide molecule X1X2X3X4-y-XSXfX~Xg there are five possible outcomes for the process of substituting a ~i-alanine residue for an aromatic amino acid residue.
2o First, there may be no position at which it is possible to add a (3-alanine residue; in such case, a better binding affinity or selectivity can be sought in the design and synthesis of a polyamide with five or six carboxamide binding pairs, described below. Second, the process may result in a derivative which contains a single (3-alanine substitution (such derivatives are numbered according to the parent numbering scheme such that a single (3-derivative of compound 5 would 25 be called 5~3), which is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and at which point the process is deemed complete.
Third, the process of Figure 5 may result in a polyamide which contains a single (3-alanine substitution which is not sufficient to produce subnanomolar binding affinity and >10-3o fold specificity, but where there are no additional positions in which it is possible to substitute a (3-alanine residue, and in such a case a polyamide with five or six carboxamide binding pairs, should be designed and synthesized, as described below. Fourth, the process of Figure 5 may result in a polyamide that contains a single (3-alanine substitution that is not sufficient to produce subnanomolar binding affinity and >10-fold specificity, but where there is an additional position for (3-alanine substitution that does produce a polyamide with the criterion level of affinity and selectivity and therefore the design process is deemed complete. Polyamides that were designed by the process that produces polyamide molecules that contain two (3-alanine residues are labeled ~2 in Tables 12-19.
A fifth possibility is that substitution at a second position by the method illustrated in Figure G with a second (3-alanine residue is not sufficient to produce a polyamide having the 1o subnanomolar binding affinity and >10-fold specificity, and a polyamide with five or six carboxamide binding pairs, should be designed and synthesized, as described below. Tables 12-19 list polyamides corresponding to sequences 1-240 and G1-G16 which contain either one or two (3-alanine residues.
TABLE
4:
Figure 6 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a ~3-alanine residue in order to enhance the DNA
binding properties of certain eight carboxamide residue hairpin polyamide compounds.
Figure 7 schematically illustrates a method for the design of ten carboxamide residue hairpin polyamide compounds suitable for recognition of 7-by 5'-WNT12~1NNW-3' sequences in the t o minor groove of double stranded DNA.
Figure 8 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a (3-alanine residue in order to enhance the DNA
binding properties of certain tcn carboxamide residue hairpin polyamide compounds.
Figure 9 schematically illustrates a method for determining the position of an additional t 5 aromatic amino acid residue that should be replaced with a (3-alanine residue in order to enhance the DNA binding properties of certain ten carboxamide residue hairpin poiyamide compounds.
Figure 10 schematically illustrates a method for the design of twelve carboxamide residue hairpin polyamide compounds suitable for recognition of 8-by S'-VJhfIJNNW-3' sequences in the minor groove of double stranded DNA.
20 Figure 11 schematically illustrates a method for determining the position of an aromatic amino acid residue that should be replaced with a ~-alanine residue in order to enhance the DNA
binding properties of certain twelve carboxamide residue hairpin polyamide compounds.
DETAILED DESCRIPTION OF THE INVENTION
Within this application, unless otherwise stated, definitions of the terms and illustration of the techniques of this application may be found in any of several well-known references such as: Sambrook, J., e1 al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press (1989); Goeddel, D., ed., Gene Expression Technology, Methods in Enzymology, 185, Academic Press, San Diego, CA (1991); "Guide to Protein Purification" in Deutshcer, M.P., ed., Methods in Enzymology, Academic Press, San Diego, CA ( 1989); Innis, et al., PCR Protocols: A Guide to Methods and Applications, Academic Press, San Diego, CA
(1990); Freshney, R.L, Culture of Animal Cells: A Manual of Basic Technique, 2"d Ed., Alan Liss, Inc. New York, NY (1987); Murray, E.J., ed., Gene Transfer and Expression Protocols, pp.
109-128, The Humana Press Inc., Clifton, NJ and Lewin, B., Genes Vl, Oxford University Press, New York (1997).
For the purposes of this application, a promoter is a regulatory sequence of DNA- that is involved in the binding of RNA polymerase to initiate transcription of a gene.
A gene is a segment of DNA involved in producing a peptide, polypeptide or protein, including the coding region, non-coding regions preceding ("leader") and following ("trailer") the coding region, as well as intervening non-coding sequences ("introns") between individual coding segments ("exons"). Coding refers to the representation of amino acids, start and stop signals in a three base "triplet" code. Promoters are often upstream (" '5 to") the transcription initiation site of the corresponding gene. Other regulatory sequences of DNA in addition to promoters are known, including sequences involved with the binding of transcription factors, including response elements that are the DNA sequences bound by inducible factors. Enhancers comprise yet another group of regulatory sequences of DNA that can increase the utilization of promoters, and can function in either orientation (S'-3' or 3'-5') and in any location (upstream or downstream) relative to the promoter. Preferably, the regulatory sequence has a positive activity, i.e., binding of an endogeneous ligand (e.g. a transcription factor) to the regulatory sequence increases transcription, thereby resulting in increased expression of the corresponding target gene. In such a case, interference with transcription by binding a polyamide to a regulatory sequence would reduce or abolish expression of a gene.
The promoter may also include or be adjacent to a regulatory sequence known in the art as a silencer-. A silencer sequence generally has a negative regulatory effect on expression of the gene. In such a case, expression of a gene may be increased directly by using a poiyamide to prevent binding of a factor to a silencer regulatory sequence or indirectly, by using a polyamide to block transcription of a factor to a silencer regulatory sequence.
It is to be understood that the polyamides of this invention bind to double stranded DNA
in a sequence specific manner. The function of a segment of DNA of a given sequence, such as 5'-TATAAA-3', depends on its position relative to other functional regions in the DNA
sequence. In this case, if the sequence 5'-TATAAA-3' on the coding strand of DNA is 3o positioned about 30 base pairs upstream of the transcription start site, the sequence forms part of the promoter region (Lewin, Genes UI, pp. 831-835). On the other hand, if the sequence 5'-TATAAA-3' is downstream of the transcription start site in a coding region and in proper register with the reading frame, the sequence encodes the tyrosyl and lysyl amino acid residues (Lewin, Genes Vl, pp. 213-215).
While not being held to one hypothesis, it is believed that the binding of the polyamides of this invention modulate gene expression by altering the binding of DNA
binding proteins, such as RNA polymerase, transcription factors, TBF, TFIIIB and other proteins.
The effect on gene expression of polyamide binding to a segment of double stranded DNA is believed to be related to the function, e.g., promoter, of that segment of DNA.
to It is to be understood by one skilled in the art that the improved polyamides of the present invention may bind to any of the above-described DNA sequences or any other sequence having a desired effect upon expression of a gene. In addition, U.S. Patent No. 5,578,444 describes numerous promoter targeting sequences from which base pair sequences for targeting an improved polyamide of the present invention may be identified.
It is generally understood by those skilled in the art that the basic structure of DNA in a living cell includes both major and a minor groove. For the purposes of describing the present invention, the minor groove is the narrow groove of DNA as illustrated in common molecular 2o biology references such as Lewin, B., Genes vl, Oxford University Press, New York (1997).
To affect gene expression in a cell, which may include causing an increase or a decrease in gene expression, a effective quantity of one or more polyamide is contacted with the cell and internalized by the cell. The cell may be contacted in vivo or in vitro.
Effective extracellular concentrations of polyamides that can modulate gene expression range from about 10 nanomolar to about 1 micromolar. Gottesfeld, J.M., et al., Nature 387 202-205 (1997). To determine effective amounts and concentrations of polyamides in vitro, a suitable number of cells is plated on tissue culture plates and various quantities of one or more polyamide are added to separate wells. Gene expression following exposure to a polyamide can be monitored in the cells or 3o medium by detecting the amount of the protein gene product present as determined by various techniques utilizing specific antibodies, including ELISA and western blot.
Alternatively, gene expression following exposure to a polyamide can be monitored by detecting the amount of messenger RNA present as determined by various techniques, including northern blot and RT-PCR.
Similarly, to determine effective amounts and concentrations of polyamides for -in vivo administration, a sample of body tissue or fluid, such as plasma, blood, urine, cerebrospinal ~ fluid, saliva, or biopsy of skin, muscle, liver, brain or other appropriate tissue source is analyzed.
Gene expression following exposure to a polyamide can be monitored by detecting the amount ' of the protein gene product present as determined by various techniques utilizing specific antibodies, including ELISA and western blot. Alternatively, gene expression following exposure to a polyamide can be monitored by the detecting the amount of messenger RNA
present as determined by various techniques, including northern blot and RT-PCR.
The polyamides of this invention may be formulated into diagnostic and therapeutic compositions for in vivo or in vitro use. Representative methods of formulation may be found in Remington: The Science and Practice of Pharmacy, 19th ed., Mack Publishing Co., Easton, PA
(1995).
For in vivo use, the polyamides may be incorporated into a physiologically acceptable pharmaceutical composition that is administered to a patient in need of treatment or an animal for medical or research purposes. The polyamide composition comprises pharmaceutically acceptable earners, excipients, adjuvants, stabilizers, and vehicles. The composition may be in 2o solid, liquid, gel, or aerosol form. The polyamide composition of the present invention may be administered in various dosage forms orally, parentally, by inhalation spray, rectally, or topically. The term parenteral as used herein includes, subcutaneous, intravenous, intramuscular, intrasternal, infusion techniques or intraperitoneally.
The selection of the precise concentration, composition, and delivery regimen is influenced by, inter alia, the specific pharmacological properties of the particular selected compound, the intended use, the nature and severity of the condition being treated or diagnosed, the age, weight, gender, physical condition and mental acuity of the intended recipient as well as the route of administration. Such considerations are within the purview of the skilled artisan.
3o Thus, the dosage regimen may vary widely, but can be determined routinely using standard methods.
Polyamides of the present invention are also useful for detecting the presence of double stranded DNA of a specific -sequence for diagnostic or preparative purposes.
The sample containing the double stranded DNA can be contacted by polyamide linked to a solid substrate, thereby isolating DNA comprising a desired sequence. Alternatively, poIyamides linked to a suitable detectable marker, such as biotin, a hapten, a radioisotope or a dye molecule, can be contacted by a sample containing double stranded DNA.
The design of bifunctional sequence specific DNA binding molecules requires the integration of two separate entities: recognition and functional activity.
Polyamides that specifically bind with subnanomolar affinity to the minor groove of a predetermined sequence of double stranded DNA are linked to a functional molecule, providing the corresponding bifunctional conjugates useful in molecular biology, genomic sequencing, and human medicine.
Polyamides of this invention can be conjugated to a variety of functional molecules, which can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotides, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-a-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-~,-tocopheral, psoralen, EDTA, methidium, 2o acridine, Ni(II)~Gly-Gly-His, TO, Dansyl, pyrene, N-bromoacetamide, and gold particles. Such bifunctional polyamides are useful for DNA affinity capture, covalent DNA
modification, oxidative DNA cleavage, and DNA photocleavage. Such bifunctional polyamides are useful for DNA detection by providing a polyamide linked to a detectable label. Detailed instructions for synthesis of such bifunctional polyamides can be found in copending U.S.
provisional application 60/043,444, the teachings of which are incorporated by reference.
DNA complexed to a labeled polyamide can then be determined using the appropriate detection system as is well known to one skilled in the art. For example, DNA
associated with a polyamide linked to biotin can be detected by a streptavidin / alkaline phosphatase system.
The present invention also describes a diagnostic system, preferably in kit form, for assaying for the presence of the double stranded DNA sequence bound by the polyamide of this invention in a body sample, such brain tissue, cell suspensions or tissue sections, or body fluid samples such as CSF, blood, plasma or serum, where it is desirable to detect the presence, and preferably the amount, of the double stranded DNA sequence bound by the polyamide in the sample according to the diagnostic methods described herein.
The diagnostic system includes, in an amount sufficient to perform at least one assay, a specific polyamide as a separately packaged reagent. Instructions for use of the packaged reagents) are also typically included. As used herein, the term "package"
refers to a solid matrix or material such as glass, plastic (e.g., polyethylene, polypropylene or polycarbonate), paper, foil and the like capable of holding within fixed limits a polyamide of the present 1 o invention. Thus, for example, a package can be a glass vial used to contain milligram quantities of a contemplated polyamide or it can be a microliter plate well to which microgram quantities of a contemplated polyamide have been operatively affixed, i.e., linked so as to be capable of being bound by the target DNA sequence. "Instructions for use" typically include a tangible expression describing the reagent concentration or at least one assay method parameter such as the relative amounts of reagent and sample to be admixed, maintenance time periods for reagent or sample admixtures, temperature, buffer conditions and the like. A
diagnostic system of the present invention preferably also includes a detectable label and a detecting or indicating means capable of signaling the binding of the contemplated polyamide of the present invention to the target DNA sequence. As noted above, numerous detectable labels, such as biotin, and detecting or indicating means, such as enzyme-linked (direct or indirect) streptavidin, are well known in the art.
As used herein, "subnanomolar affinity" means binding that is characterized by a dissociation constant, Kd , of less than 1 nM, as measured by DNase I
footprint titration.
Preferably, polyamides of the present invention are characterized by subnanomolar binding affinity for the identified target DNA sequence. As used herein, the "selectivity" of the binding of a polyamide to a DNA sequence is the ratio of the dissociation constant, Kd , as measured by DNase I footprint titration of binding the polyamide to a mismatch DNA
sequence divided by the corresponding dissociation constant of the binding of the polyamide to the identified target 3o DNA sequence. Preferably, polyamides of the present invention are characterized by a selectivity of 5 or greater, more preferably a selectivity of greater that 10.
r The exemplary polyamide that illustrates the compositions and methods of the present invention is polyamide 3 of Figure 1, ImImHpPy-y-ImPyPyPy-~3-Dp. This polyamide was designed according to the method of the present invention to target the identified sequence 5'-WGGTCW-3'. See Table 5, below, Sequence No. 36 and the corresponding sequence of carboxamide binding pairs. Polyamide 3 binds an identified target sequence 5'-TGGTCA-3' with a dissociation constant, as measured by DNase I footprint titration, of 0.48 nM, i.e., with subnanomolar affinity as defined herein (see Table 1, below). The polyamide binds to the mismatch sequence 5'-TGGACA-3' with a dissociation contant of 37 nM, yielding a selectivity, as defined herein, of 77 (Table 1 ).
to Figure 1 shows representative structures of polyamides. ImImPyPy-y-ImPyPyPy-~3-Dp (1), ImImPyPy-y-ImHpPyPy-/3-Dp (2), and ImlmHpPy-y-ImPyPyPy-(3-Dp (3). (Hp = 3-hydroxy-N-methylpyrrole, Im = N-methylimidazole, Py = N-methylpyrrole, (3 = ~i-alanine, y = y-aminobutyric acid, Dp = Dimethylaminopropylamide). Polyamides were synthesized by solid phase methods using Boc-protected 3-methoxypyrrole, imidazole, and pyrrole aromatic amino acids, cleaved from the support by aminolysis, deprotected with sodium thiophenoxide, and purified by reversed phase HPLC. Baird, E. E. & Dervan, P. B. describes the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chern. Soc. 118, 6141-6146 (1996); also see PCT US 971003332. The identity and purity of the polyamides were 2o verified by'H NMR, analytical HPLC, and matrix-assisted laser-desorption ionization time-of flight mass spectrometry (MALDI-TOF MS-monoisotopic): 1 1223.6 {1223.6 calculated), 2 1239.6 (1239.6 calculated); 3 1239.6 (1239.6 calculated).
Figure 2 illustrates binding models for polyamides 1-3 in complex with 5'-TGGTCA-3' and 5'-TGGACA-3' (A~T and T~A in fourth position highlighted). Filled and unfilled circles represent imidazole and pyrrole rings respectively; circles containing an H
represent 3-hydroxypyrrole, the curved line connecting the polyamide subunits represents y-aminobutyric acid, the diamond represents (3-alanine, and the + represents the positively charged dimethylaminopropylamide tail group.
Figure 3 shows quantitative DNase I footprint titration experiments with polyamides 2 and 3 on the 3' 3~P labeled 250-by pJK6 EcoRIIPvuII restriction fragment. Lane 1, intact DNA;
lanes 2-11 DNase I digestion products in the presence of 100, 50, 20, 10, 5, 2, l, 0.5, 0.2, 0.1 nM
-I s-polyamide, respectively; lane 12, DNase I digestion products in the absence of polyamide; lane 13, adenine-specific chemical sequencing. Iverson, B. L. & Dervan, P. B.
describes an adenine-specific DNA chemical sequencing reaction. Methods ~nzymol. 15, 7823-7830 (1987). All reactions were done in a total volume of 400 p,L. A polyamide stock solution or Hz0 was added to an assay buffer containing radiolabeled restriction fragment, with the final solution conditions of 10 mM Tris-HC1, 10 mM KC1, 10 mM MgCh, 5 mM CaCl2, pH 7Ø Solutions were allowed to equilibrate for 4-12 h at 22 °C before initiation of footprinting reactions.
Footprinting reactions, separation of cleavage products, and data analysis were carried out as described. White, S., Baird, E. E. & Dervan, P. B. Effects of the A~T/T~A
degeneracy of to pyrrole-imidazole polyamide recognition in the minor groove of DNA.
Biochemistry 35, 12532-12537 (1996).
Figure 4 shows the structure and equilibrium dissociation constant for numerous compounds of the present invention. Polyamides are shown in complex with their respective 1s match site. Filled and unfilled circles represent imidazole (Im) and pyrrole (Py) rings, respectively; circles containing an H represent 3-hydroxypyrrole (Hp), the curved line connecting the polyamide subunits represents y-aminobutyric acid (y), the diamond represents ~3-alanine (~3), and the + represents the positively charged dimethylaminopropylamide tail group (Dp). The equilibrium dissociation constants are the average values obtained from three DNase 2o I footprint titration experiments. The standard deviation for each set is less than 15% of the reported number. Assays were earned out in the presence of 10 mM Tris~HCI, 10 mM KCI, 10 mM MgCl2, and 5 mM CaClz at pH 7.0 and 22°C.
Four-ring polyamide subunits, covalently coupled to form eight-ring hairpin structures, 2s bind specifically to 6-by target sequences at subnanomolar concentrations.
Trauger, J.W., Baird, E. E. & Dervan, P.B. describe the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996); Swalley, S. E., Baird, E. E. &
Dervan, P. B.
describe the discrimination of 5'-GGGG-3', S'-GCGC-3', and 5'-GGCC'3' sequences in the minor groove of DNA by eight-ring hairpin polyamides. J. Am. Chem. Soc. 119, 30 ( 1997). The DNA-binding affinities of three eight-ring hairpin polyamides shown in Figure 1 as compound 1, 2, and 3 containing pairings of Im/Py, Py/Im opposite G~C, C~G and either Py/Py, Hp/Py, or Py/Hp at a common single point opposite T~A and A~T has been determined.
Equilibrium dissociation constants (K~) for ImImPyPy-y-ImPyPyPy-(3-Dp 1, ImImPyPy-y-ImHpPyPy-~i-Dp 2, ImImHpPy-y-ImPyPyPy-~3-Dp 3 of Figure 1 are shown in Table 1.
3s Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K. describe a quantitative DNase footprint titration method for studying protein-DNA interactions. Methods Enzymol. 130, 132-181 {1986); The Kd values were determined by quantitative DNase I footprint titration experiments: on a 3' 32P-labeled 250-by DNA fragment containing the target sites, 5'-TGGACA-3' and 5'-TGGTCA-3' which differ by a single A~T base pair in the fourth position.
The DNase footprint gels are shown in Figure 3.
S
TABLE 1 Equilibrium dissociation constants%
Polyamidet 5'-TGG_TCA-3' 5'-TGGACA-3' KrelT
5'-T G G T C A-3' 5'-T G G 'A C A-3' 1 PyIPy + + 2.0 3'-A C C A G T-5' 3'-A C C T G T-5' K~ = 0.077 nM Kd = 0.15 nM
5'-T G G T C A-3' S'-T G G A. C A-3' 2 PyIHp + H + H a.of~
3'-A C C Fa G T-5' 3'-A C C T G T-5' Kd = 15 nM Kd = 0.83 nM
5'-T G G T C A-3' S'-T G G A' C A-3' H H
3 Hp/Py + +
3'-A C C 11 G T-5' 3'-A C C T G T-5' Kd = 0.48 nM K~ =37 nM
*The reported dissociation constants are the average values obtained from three DNase I footprint titration experiments. The standard deviation for each data set is less than 15% of the reported number. Assays were carried out in the presence of 10 mM Tris~HCI, 10 mM KCI, 10 mM MgCl2, and 5 mM CaCl2 at pI-i 7.0 and 22 °C.
Ring pairing opposite T~A and A~T in the fourth position.
Calculated as Kd(5'-TGGACA-3')/Kd(5'-TGGTCA-3').
Based on the pairing rules for polyamide-DNA complexes both of these sequences are a match for control polyamide 1 which places a Py/Py pairing opposite to A~T and T~A at both sites. It was determined that polyamide 1 (Py/Py) binds to 5'-TGGTCA-3' and 5'-TGGACA-3' within a factor of 2 (K~ = 0.077 or 0.15 nM respectively). In contrast, poiyamide 2 {Py/Hp) binds to 5'-TGGTCA-3' and 5'-TGGACA-3' with dissociation constants which differ by a factor of 18 (K~ = 15 nM and 0.83 nM respectively). By reversing the pairing in polyamide 3 (Hp/Py) the dissociation constants differ again in the opposite direction by a 15 factor of 77 (KD = 0.48 nM and 37 nM respectively). Control experiments performed on separate DNA fragments; reveal that neither a S'-TGGGCA-3' or a 5'-TGG_CCA-3' site is bound by polyamide 2 or 3 at concentrations < 100 nM, indicating that the Hp/Py and Py/Hp ring pairings do not bind opposite G~C or C~G.
20 The specificity of polyamides 2 and 3 for sites which differ by a single A~T/T~A base pair results from small chemical changes. Replacing the Py/Py pair in 1 with a Py/Hp pairing as in 2, a single substitution of C3-OH for C3-H, destabilizes interaction with 5'-TGGTCA-3' by 191-fold, a free energy difference of 3.1 kcal mol-'. Interaction of 2 with 5'-TGGACA-3' is destabilized only 6-fold relative to 1, a free energy difference of 1.1 kcal mol-' . Similarly, replacing the Py/Py pair in 1 with Hp/Py as in 3 destabilizes interaction with S'-TGGACA-3'~by 2S2-fold, a free energy difference of 3.2 kcal mol-~. Interaction of 3 with S'TGG_TCA-3' is destabilized only b-fold relative to 1, a free energy difference of 1.0 kcal mol-1.
~ s The polyamides of this invention provide for coded targeting of predetermined DNA
sequences with affinity and specificity comparable to sequence-specific DNA
binding proteins.
I~p, Im, and Py polyamides complete the minor groove recognition code using three aromatic amino acids which combine to form four ring pairings (lm/Py, Py/Im, Hp/Py, and Py/Hp) which complement the four Watson-Crick base pairs, as shown in TABLE 2. There are a possible 240 to four base pair sequences which contain at least 1 A~T or T~A base pair and therefore can advantageously use an Hp/Py, or Py/Hp carboxamide binding. Polyamides binding to any of these sequences can be designed in accordance with the code of TABLE 2.
TABLE 2 Pairing code for minor groove recognition_* _ Pair G~C C~G T~A A~T
Im/Py -i- - - -PylIm - ~. - -Hp/Py - - ..f.
Py/Hp - - -* favored (+), disfavored (-) IS
For certain G~C rich sequences the affinity of polyamide~DNA complexes may be enhanced by substitution of an Im/~ pair for Im/Py at G~C and ~3/Im for PylIm at C~G. At A~T
and T~A base pairs, either a Py/~i, ~3/Py, Hp/~i, ~i/Hp, and (3/(3 may be used. The alternate aliphatic/aromatic amino acid pairing code is described in Table 3.
Za TABLE 3 Aliphatic/Aromatic substitrution for ring pairings*
Pair Substitution Py ...___..........R......_-........ .............................-.._.........
Iml Im/
Py/Im (3llm HpIPy Py/(3, ~/PY, Hpl(3, (3/(3 PYIHP PY/I~, ~IPY, ~IHP~ ~I~
_18_ U. S. Patent 5,578,444 describes numerous promoter region targeting sequences from which base pair sequences for targeting a polyamide can be identified.
PCT U.S. 97/003332 describes methods for synthesis of polyamides which are suitable for preparing polyamides of this invention. The use of ~3-aianine in place of a pyrrole amino acid in the synthetic methods provides aromatic/aliphatic pairing (Im/(3, (3/Im, Hp/(3, (3/Hp, Py/(3, and ~3/Py) and aliphatic/aliphatic pairing ((3/(3) substitution. The use of y-aminobutyric acid, or a substituted y-aminobutyric acid such as (R)-2,4 diaminobutyric acid, provides for preferred hairpin turns. The following examples illustrate the synthesis of polyamides of the present 1 o invention.
The process of designing a preferred polyamide molecule X1X2X3X4-y-XSX6X7Xg comprising eight aromatic amino acid residues of this invention is shown schematically in Figure 5. The polyamide design process provides a method for designing an eight carboxamide residue molecule comprising , four carboxamide binding pairs for detection and binding of a target six base pair 5'-V~NNNNW-3' sequence in the minor groove of double stranded DNA.
The design process identifies an appropriate polyamide ligand for recognition of a predetermined 6-bp, 5'-V~1\f~JNNW-3' sequence with subnanomolar affinity and >10-fold specificity versus mismatch sites. Trauger, J.W., Baird, E. E. Dervan, P.B. describes the recognition of DNA by 2o designed Iigands at subnanomolar concentrations. Nature 382, 559-561 (1996).
In order to prepare a polyamide molecule specific for an identified six base pair sequence of double stranded DNA, a user starts the 8-ring polyamide design process that implements the minor groove recognition pairing code summarized in Table 2 above. In the design process a 5'-VV1\I~~INNW-3' sequence was identified. In a preferred embodiment, the identified sequence was located within a gene promoter. U. S. Patent 5,578,444 describes numerous promoter region targeting sequences from which target six base pair sequences for targeting a polyamide can be identified. The identified sequence was then defined as 5'-WabcdW-3' in a stepwise process wherein a, b, c, and d, were sequentially and independently defined as A, G, C, or T. The 3o structure of the polyamide molecule was then correspondingly defined by sequentially chosing antiparallel carboxamide binding pairs according to the minor groove pairing code summarized in Table 2 above. Thus, if a was G, then X1 was defined as Im, and Xg was defined as Py. If a was C, then X 1 was defined as Py, and Xg was defined as Im. If a was T, then X I was defined as Hp, and Xg was defined as Py. If a was A, then Xl was defined as Py, and Xg was defined as Hp, Similarly,.b was defined as A, G, C, or T and corresponding carboxamide binding pairs were defined. According to the same rules, if b was G, then X2 was defined as Im, and X7 was ' defined as Py. If b was C, then X2 was defined as Py, and X7 was defined as Im. Likewise, if b was T, then X2 was defined as Hp, and X7 was defined as Py. If b was A, then X2 was defined as Py, and X7 was defined as Hp.
to The next step was to define c as A, G, C, or T and then define corresponding carboxamide binding pairs. Following the same rules, if c was G, then X3 was defined as Im, and X6 was defined as Py. If c was C, then X3 was defined as Py, and X6 was defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and X6 was defined as Py. If c was A, then X3 was defined as Py, and X6 was defined as Hp. Lastly, d was defined as A, G, C, or T and the last corresponding carboxamide binding pair was defined. According to above rules, if d was G, then X4 was defined as Im, and XS was defined as Py. If d was C, then X4 was defined as Py, and XS was defined as Im. If d was T, then X4 was defined as Hp, and XS was defined as Py. If d was A, then X4 was defined as Py, and XS was defined as Hp.
2o With all eight carboxamide residues that participate in binding pairs now defined, the designed polyamide X1X2X3X4-y-X5X6X7Xg suitable for binding to the identified sequence was synthesized using known techniques. Baird, E. E. & Dervan, P. B. describes the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am.
Chem. Soc. 118, 6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence was determined using a quantitative DNase footprint titration method for studying protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K., Methods Enzymol. 130, 132-181 (1986). If the affinity of the synthesized polyamide at the target site 3o was not subnanomolar affinity then adding a (3-alanine (process A) was considered in order to - optimize the exact positions of the binding pairs of aromatic amino acids.
If the affinity of the said polyamide at said target site was subnanomolar affinity then the sequence specificity of the polyamide versus mismatch sequences was determined. If the specificity versus mismatch sites was not > 10-fold specificity then adding a ~3-alanine (process A
schematically shown in Figure 6) was considered, in order to optimize the positions of the aromatic amino acids in relationship to the base pairs in the minor groove. Specificity of the polyamide molecule for the target identified sequence versus mismatch sequence sites of greater than 10-fold was considered a successful result of design process.
The 256 polyamide molecules comprising four carboxamide binding pairs that were designed using this method are useful for binding to the 256 target 5'-NNNN-3' core sequences, and are listed in Tables 4-11. A corresponding polyamide molecule was designed for each 1o DNA sequence (1-240) and (G1-G16) using the process outlined above and shown schematically in Figure 5.
If the synthesized polyamide molecule did not bind to the target identified sequence with subnanomolar affinity or if the synthesized. polyamide molecule did not exhibit a specificity for the target identified sequence versus mismatch sequence sites of greater than 10-fold, the option of substituting an aliphatic amino acid residues for one of the carboxamide residues was considered. The preferred aliphatic amino acid residue is (3-alanine. At least one aliphatic amino acid residue such as a ~i-alanine residue provided some flexibility to the central portion of the polyamide molecule, acting as a "spring" to permit optimization of the hydrogen bonding 2o between the carboxamide binding pairs and the nucleotide bases of the double stranded DNA.
In general, it was not found to be advantageous to replace either member of the terminal carboxamide binding pair, Xl/Xg, with ~3-alanine. Similarly, ~i-alanine was not substituted for members of the binding pair, X41X5, adjacent to the y hairpin residue. ~i-alanine residues were not substituted for N-methylimidazole residues. The use of (3-alanine in place of a pyrrole or 3-hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/(3, ~3lIm, Hp/(3, (3/Hp, Py/~, and (3/Py) and aliphatic/aliphatic pairing (~/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-alanine is 3o schematically illustrated in Figure 6. Selective placement of an aliphatic (3-alanine ((3) residue paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im) aromatic amino acid or another ~3-alanine residue is found to compensate for sequence composition effects to improve .....,.. ~ , . i ~ ..~~. , recognition and binding of the minor groove of DNA by pyrrole-imidazole polyamides of the present invention. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be reduced by replacement of an s aromatic amino acid with an aliphatic ~-alanine residue. In a polyamide molecule that comprises four binding pairs it is only beneficial to place ~3-alanine in positions X2, X3, Xb, and X~. No more than two (3-alanine residues may be placed within a single hairpin structure. No more than a single (3-residue may be placed within each individual polyamide subunit, e.g., if X2 is replaced with ~3-alanine, then X3 cannot be replaced.
~o These rules and others were implemented in the method schematically illustrated in Figure 6. This process is suitable for the refinement of the design polyamide comprising four binding pairs that has been designed by the method illustrated in Figure 5, but which lacks subnanomolar affinity or greater than 10-fold specificity at the identified target DNA sequence.
is As in the basic design method, the designed polyamides are synthesized and the affinity and specificity of binding to the target DNA were determined.
For a given polyamide molecule X1X2X3X4-y-XSXfX~Xg there are five possible outcomes for the process of substituting a ~i-alanine residue for an aromatic amino acid residue.
2o First, there may be no position at which it is possible to add a (3-alanine residue; in such case, a better binding affinity or selectivity can be sought in the design and synthesis of a polyamide with five or six carboxamide binding pairs, described below. Second, the process may result in a derivative which contains a single (3-alanine substitution (such derivatives are numbered according to the parent numbering scheme such that a single (3-derivative of compound 5 would 25 be called 5~3), which is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and at which point the process is deemed complete.
Third, the process of Figure 5 may result in a polyamide which contains a single (3-alanine substitution which is not sufficient to produce subnanomolar binding affinity and >10-3o fold specificity, but where there are no additional positions in which it is possible to substitute a (3-alanine residue, and in such a case a polyamide with five or six carboxamide binding pairs, should be designed and synthesized, as described below. Fourth, the process of Figure 5 may result in a polyamide that contains a single (3-alanine substitution that is not sufficient to produce subnanomolar binding affinity and >10-fold specificity, but where there is an additional position for (3-alanine substitution that does produce a polyamide with the criterion level of affinity and selectivity and therefore the design process is deemed complete. Polyamides that were designed by the process that produces polyamide molecules that contain two (3-alanine residues are labeled ~2 in Tables 12-19.
A fifth possibility is that substitution at a second position by the method illustrated in Figure G with a second (3-alanine residue is not sufficient to produce a polyamide having the 1o subnanomolar binding affinity and >10-fold specificity, and a polyamide with five or six carboxamide binding pairs, should be designed and synthesized, as described below. Tables 12-19 list polyamides corresponding to sequences 1-240 and G1-G16 which contain either one or two (3-alanine residues.
TABLE
4:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WGWNNW-3' DNA aromatic amino acid sequence sequence 1) 5' G T T T W-3' ImHpHpHp-y-Pypypypy -W
2) 5'-W G T T A W-3' ImHpF~IpPy-y-HpPyPyPy 3) 5'-W G T T G W-3' ImHpHpIm-y-PyPyPyPy 4 ) 5' G T T C W-3' ImHpHpPy-y-ImPyPyPy -W
5) 5'-W G T A T W-3' ImHpPyHp-y-pyHpPyPy 6 ) 5' G T A A W-3 ' ImHpPyPy-y-HpHpPypy -W
7 ) 5' G T A G W-3 ' ImHpPyIm-y-pygppypy -W
8) 5' G T A C W-3' ImHpPyPy-y-ImHpPyPy -W
2) 5'-W G T T A W-3' ImHpF~IpPy-y-HpPyPyPy 3) 5'-W G T T G W-3' ImHpHpIm-y-PyPyPyPy 4 ) 5' G T T C W-3' ImHpHpPy-y-ImPyPyPy -W
5) 5'-W G T A T W-3' ImHpPyHp-y-pyHpPyPy 6 ) 5' G T A A W-3 ' ImHpPyPy-y-HpHpPypy -W
7 ) 5' G T A G W-3 ' ImHpPyIm-y-pygppypy -W
8) 5' G T A C W-3' ImHpPyPy-y-ImHpPyPy -W
9) 5'-W G T G T W-3' ImHpImHp-y-Pypypypy 10) 5'-W G T G A W-3' ImHpImPy-y-HpPyPyPy 11) 5' G T G G W-3 ' ImHpImIm-y-PyPyPyPy -W
12) 5' G T G C W-3' ImHpImPy-y-ImpyPypy -W
13) 5' G T C T W-3' ImHpPyHp-y-PyImPyPy -W
14) 5' G T C A W-3' ImHpPyPy-y-HpImPyPy -W
15) 5' G T C G W-3' ImHpPyIm-y-PyImPyPy -W
16) 5' G T C C W-3' ImHpPyPy-y-ImImPyPy -W
17) 5' G A T T W-3' ImPyHpHp-y-PypyHpPy -W
18 ) 5' G A T A W-3 ' ImPyHpPy-y-HpPyHpPy -W
19) 5' G A T G W-3' ImPyHpIm-y-PyPyHpPy -W
20) 5'-W G A T C W-3' ImPyHpPy-y-ImPyHpPy 21) 5'-W G A A T W-3' ImPyPyHp-y-PyHpHpPy 22) 5'-W G A A A W-3' ImPyPyPy-y-HpHpHpPy 23) 5'-W G A A G W-3' ItriPyPyIm-y-PyHpHpPy 24) 5' G A A C W-3' ImPyPyPy-y-ImHpHpPy -W
25) 5' G A G T W-3' ImPyImHp-y-PyPyHpPy -W
26) 5'-W G A G A W-3' ImPyImPy-y-HpPyHpPy 27) 5'-W G A G G W-3' ImPyImIm-y-Pypygppy 28) 5' G A G C W-3' ImPyImPy-y-ImPyHpPy -W
29) 5'-W G A C T W-3' ImPyPyHp-y-PyImHpPy 30) 5'-W G A C A W-3' ImPyPyPy-y-HpImHpPy 31) 5' G A C G W-3' ImPyPyIm-y-PyImHpPy - -W
32) 5'-W G A C C W-3' ImPyPyPy-y-ImImHpPy WO 98/37067 PCTlUS98/01714 'TABLE
5:
8-ring Hairpin Polyamides for recognition of 6-by S'-WGSNNW-3' DNA aromatic amino acid sequence sequence 33) 5'-W G G T TW-3' ImImHpHp-y-pyPypypy 34) 5'-W G G T AW-3' ImImHpPy-y-HpPyPyPy 35) 5' G G T GW-3' ImImHpIm-y-PyPyPyPy -W
3 6 ) 5 G G T CW- 3 ' ImImHpPy-y- ImPyPyPy ' -W
37) 5'-W G G A TW-3' ImImPyHp-y-PyHpPyPy 38) 5'-W G G A AW-3' ImImPyPy-y-HpHpPyPy 39) 5' G G A GW-3' ImImPyIm-y-PyHpPyPy -W
40) 5' G G A CW-3' ImImPyPy-y-ImHpPyPy -W
41) 5'-W G G G TW-3' ImImImHp-y-PyPypypy 42) 5'-W G G G AW-3' ImImImPy-y-HppyPypy 43) 5'-W G G C TW-3' ImImPyHp-y-PyImPyPy 44) 5' G G C AW-3' ImImPyPy-y-HpImPyPy -W
45) 5'-W G C T TW-3' ImPyHpHp-y-PyPyImPy 46) 5'-W G C T AW-3' ImPyHpPy-y-HpPyImPy 47) 5' G C T GW-3' ImPyHpIm-y-PyPyImPy -W
48) 5'-W G C T CW-3' ImPyHpPy-y-ImPyImPy 49) 5'-W G C A TW-3' ImPyPyHp-y-PyHpImPy 50) 5'-W G C A AW-3' ImPyPyPy-y-HpHpImPy 51) 5' G C A GW-3' ImPyPyIm-y-PyHpImPy -W
52) 5'-W G C A CW-3' ImPyPyPy-y-ImHpImPy 53) 5'-W G C G TW-3' ImPyImHp-y-PypyImPy 54) 5'-W G C G AW-3' ImPyImPy-y-HpPyImPy 55) 5'-W G C C TW-3' ImPyPyHp-y-pyImImPy 56) 5'-W G C C AW-3' ImPyPyPy-y-HpImImPy G1) 5'-W G G G GW-3' ImImImIm-y-PyPypypy G2) 5'-W G G G CW-3' ImImImPy-y-ImPyPyPy G3) 5'-W G G C GW-3' ImImPyIm-y-PyImPyPy G4) 5'-W G G C CW-3' ImImPyPy-y-ImImPyPy G5) 5'-W G C G GW-3' ImPyImIm-y-PyPyImPy G6) 5'-W G C G CW-3' ImPyImPy-y-ImPyImPy G7) 5' G C C GW-3' ImPyPyIm-y-PyImImPy -W
G8) 5'-W G C C CW-3' ImPyPyPy-y-ImImImPy TABLE :
6 8-ring Hairpin Polyamides for recognition of 6-by 5'-WTWNNW-3' DNA aromatic amino acid sequence sequence 57) 5'-W TT T T W-3' HpHpHpHp-y-PYPyPyPy 5 8 ) 5 ' TT T A W- 3 ' HpHpHpPy-y-HpPypypy -W
59) 5'-W TT T G W-3' HpHpHpIm-y-PyPypypy 60) 5'-W TT T C W-3' HpHpHpPy-y-ImPyPypy 61) 5'-W TT A T W-3' HpHpPYHp-y-PyHpPyPy 62) 5'-W TT A A W-3' HpHpPYPy-y-HpHpPYPy 63) 5'-W TT A G W-3' HpHpPyIm-y-PyHpPyPy 64) 5'-W TT A C W-3' HpHpPyPy-y-ImHpPYPy 65) 5' -W TT G T W-3' HpHpImHp-y-PyPypypY
66) 5' -W TT G A W-3' HpHpImPy-y-HpPYPypy 67) 5'-W TT G G W-3' HpHpImIm-y-PYPypyPy 6 8 ) 5 ' TT G C W-3 ' HpHpImPy-y- ImPyPyPy -W
69) 5'-W TT C T W-3' HpHpPyHp-y-PyImPYPy 70) 5' -W TT C A W-3' HpHpPYPy-y-HpImPYPy 71 ) 5 ' TT C G W- 3 ' HpHpPyIm-y-PyImPyPy -W
72) 5'-W TT C C W-3' HpHpPyPy-y-ImImPYPy 73) 5'-W TA T T W-3' HpPYHpHp-y-PypyHpPy 74) 5' -W TA T A W-3' HpPyHpPy-y-HpPyHpPy 75) 5'-W TA T G W-3' HpPyHpIm-y-PyPyHpPy 76) 5' -W TA T C W-3' HpPyHppy-y-ImPyHpPy 77) 5'-W TA A T W-3' HpPyPYHp-y-PYHpHpPy 78) 5'-W TA A A W-3' HpPyPyPy-y-HpHpHpPy 79) 5' -W TA A G W-3' HppyPYIm-y-PYHpHpPy 80) 5' -W TA A C W-3' HpPYPYPy-y-ImHpHpPy 81) 5' -W TA G T W-3' HpPyImHp-y-PyPyHpPy 82) 5'-W TA G A W-3' HpPyImPy-y-HpPyHpPy 83) 5'-W TA G G W-3' HpPYImIm-y-PyPYHpPy 84) 5'-W TA G C W-3' HpPyImPy-y-ImPyHpPy 85) 5'-W TA C T W-3' HpPyPyHp-y-PYImHpPy 86) 5'-W TA C A W-3' Hppypypy_y_Hpl~ppy 87) 5'-W TA C G W-3' HpPyPYIm-y-PyImHpPy 88) 5' -W TA C C W-3' HpPyPyPy-y-ImImHpPy TABLE
7:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WTSNNW-3' DNA aromatic amino acid sequence sequence 89 ) 5' T G T T W-3 ' HpImHpHp-y-PyPyPyPy -W
90) 5' T G T A W-3' HpImHpPy-y-HpPyPyPy -W
91) 5'-W T G T G W-3' HpImHpIm-y-PyPyPyPy 92) 5'-W T G T C W-3' HpImHpPy-y-ImPyPyPy 93) 5'-W T G A T W-3' HpImPyHp-y-PyHpPyPy 94) 5'-W T G A A W-3' HpImPyPy-y-HpHpPyPy 95) 5'-W T G A G W-3' HpImPyIm-y-PyHpPyPy 96) 5'-W T G A C W-3' HpImPyPy-y-ImHpPyPy 97) 5'-W T G G T W-3' HpImImHp-y-PyPyPyPy 98) 5'-W T G G A W-3' HpImImPy-y-HpPyPyPy 99) 5'-W T G C T W-3' HpImPyHp-y-PyImPyPy 100) 5' T G C A W-3' HpImPyPy-y-HpImPyPy -W
101) 5' T G G G W-3' HpIm2mIm-y-PyPyPyPy -W
102 ) 5' T G G C W-3 ' HpImImPy-y-ImPyPyPy -W
103) 5'-W T G C G W-3' HpImPyIm-y-PyImPyPy 104) 5'-W T G C C W-3' HpImPyPy-y-ImImPyPy 105) 5'-W T C T T W-3' HpPyHpHp-y-PyPyImPy 106) 5'-W T C T A W-3' HpPyHpPy-y-HpPyImPy 107) 5'-W T C T G W-3' HpPyHpIm-y-PyPyImPy 108) 5' T C T C W-3' HpPyHpPy-y-ImPyImPy -W
109) 5'-W T C A T W-3' HpPyPyHp-y-PyHpImPy 110) 5' T C A A W-3' HpPyPyPy-y-HpHpImPy -W
lIl) 5'-W T C A G W-3' HpPyPyIm-y-PyHpImPy 112) 5'-W T C A C W-3' HpPyPyPy-y-ImHpImPy 113) 5' T C G T W-3' HpPyImHp-y-PyPyImPy -W
114) 5' T C G A W-3' HpPyImPy-y-HpPyImPy -W
115) 5' T C C T W-3' HpPyPyHp-y-PyImImPy -W
116) 5' T C C A W-3' HpPyPyPy-y-HpImImPy -W
117) 5'-W T C G G W-3' HpPyImIm-y-PyPyImPy 118) 5'-W T C G C W-3' HpPyImPy-y-ImPyImPy 119 ) 5 ' T C C G W- 3 ' HpPyPyIm-y-PyImImPy -W
12 0 5' T C C C W- 3 ' HpPyPyPy-y- ImImImPy ) -W
8:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WAWNNW-3' DNA aromatic amino acid sequence sequence 121 ) 5 A T T T W- 3 ' PyHpHpHp-y- Pypypygp ' -W
122) 5' A T T A W-3' PyHpHpPy-y-HpPyPyHp -W
123) 5'-W A T T G W-3' PyHpHpIm-y-PyPyPyHp 124) 5'-W A T T C W-3' PyHpHpPy-y-ImPyPyHp 125) 5'-W A T A T W-3' PyHpPyHp-y-PyHpPyHp 126) 5'-W A T A A W-3' PyHpPyPy-y-HpHpPyHp 127) 5'-W A T A G W-3' pyHppylm-y-pyHppyHp 128) 5' A T A C W-3' PyHpPyPy-y-ImFipPyHp -W
129) 5'-W A T G T W-3' PyHpImHp-y-PyPyPyHp 130) 5'-W A T G A W-3' PyHpImPy-y-HpPyPyHp 131) 5' A T G G W-3' PyHpImIm-y-PypypyHp -W
132) 5'-W A T G C W-3' PyHpImPy-y-ImPyPyHp 233) 5'-W A T C T W-3' PyHpPyHp-y-PyImPyHp 134) 5'-W A T C A W-3' PyHpPyPy-y-HpImPyHp 135) 5' A T C G W-3' PyHpPyIm-y-PyImPyHp -W
136) 5'-W A T C C W-3' PyHpPyPy-y-ImImPyHp 137) 5'-W A A T T W-3' PyPyFlpHp-y-PyPyHpHp 138) 5' A A T A W-3' PyPyHpPy-y-HpPyHpHp -W
139) 5'-W A A T G W-3' PyPyHpIm-y-pypyHpHp 140) 5' A A T C W-3' PyPyHpPy-y-ImPyHpHp -W
141) 5'-W A A A T W-3' PyPyPyHp-y-PyHpHpHp 142) 5'-W A A A A W-3' PyPyPyPy-y-HpHpHpHp 143) 5'-W A A A G W-3' PyPypylm-y-pyHpHpHp 144) 5' A A A C W-3' PyPyPyPy-y-ImHpHpHp -W
145) 5'-W A A G T W-3' PypyImHp-y-PyPyHpHp 146) 5'-W A A G A W-3' PyPyImPy-y-HpPyHpHp 147) 5'-W A A G G W-3' PyPyImIm-y-PypyHpHp 14 8 ) 5 A A G C W- 3 ' PyPyImPy-y- ImPyHpI~Ip ' -W
149) 5' A A C T W-3' pypypyHp_y_pyl~pHp -W
150) 5' A A C A W-3' PyPyPyPy-y-HpImApHp -W
151) 5'-W A A C G W-3' PyPyPyIm-y-PyImHpHp 152) 5'-W A A C C W-3' Pypypypy-y-ImImHpHp TABLE
9:
8-ring-Hairpin Polyamides for recognition of 6-by 5'-WASNNW-3' DNA aromatic amino acid sequence sequence 153) 5' A GT T W-3' PyImHpHp-y-PyPyPyHp -W
154) 5' A GT A W-3' PyImHpPy-y-HpPyPyHp -W
155) 5'-W A GT G W-3' PyImHpIm-y-PyPyPyHp 156) 5'-W A GT C W-3' PyImHpPy-y-ImPyPyHp 157 ) 5' A GA T W-3' PyImPyHp-y-PyHpPyHp -W
158) 5' A GA A W-3' PyImPyPy-y-HpHpPyHp -W
159) 5' A GA G W-3' PyImPyIm-y-PyHpPyHp -W
160) 5' A GA C W-3' PyImPyPy-y-ImHpPyHp -W
161) 5' A GG T W-3' PyImImHp-y-PyPyPyHp -W
162) 5' A GG A W-3' PyImImPy-y-HpPyPyHp -W
163) 5'-W A GC T W-3' PyImPyHp-y-PyImPyHp 164) 5' A GC A W-3' PyImPyPy-y-HpImPyHp -W
165) 5' A GG G W-3' PyImImIm-y-PyPyPyHp -W
166) 5' A GG C W-3' PyImImPy-y-ImPyPyHp -W
167) 5'-W A GC G W-3' PyImPyIm-y-PyImPyHp 16 8 ) 5 A GC C W- 3 ' PyImPyPy-y- ImImPyHp ' -W
169) 5' A CT T W-3' PyPyHpHp-y-PyPyImHp -W
170) 5' A CT A W-3' PyPyHpPy-y-HpPyImHp -W
171) 5' A CT G W-3' PyPyHpIm-y-PyPyImHp -W
172) 5'-W A CT C W-3' PyPyHpPy-y-ImPyImHp 173 ) 5' A CA T W-3 ' PyPyPyHp-y-PyHpImHp -W
174) 5' A CA A W-3' PyPyPyPy-y-HpHpImHp -W
175) 5' A CA G W-3' PyPyPyIm-y-PyHpImHp -W
176) 5'-W A CA C W-3' PyPyPyPy-y-ImHpImHp 177) 5' A CG T W-3' PyPyImHp-y-PyPyImHp -W
178) 5' A CG A W-3' PyPyImPy-y-HpPyImHp -W
179) 5' A CC T W-3' PyPyPyHp-y-PyImImHp -W
180) 5'-W A CC A W-3' PyPyPyPy-y-HpImImHp 181) 5' A CG G W-3' PyPyImIm-y-PyPyImHp -W
182) 5'-W A CG C W-3' PyPyImPy-y-ImPyImHp 183) 5' A CC G W-3' PyPyPyIm-y-PyImImHp -W
184) 5'-W A CC C W-3' PyPyPyPy-y-ImImImHp 'FABLE
10:
8-ring -Hairpin Polyamides for recogmhon of 6-by 5'-WCWNNW-3' DNA aromatic amino acid sequence sequence 185) 5'-W CT T T W-3' PyHpHpHp-y-Pypypylm 186} 5'-W CT T A W-3' PyHpHpPy-y-HpPypyIm 187) 5'-W CT T G W-3' PyHpHpIm-y-PyPyPyIm 18 8 ) 5 ' CT T C W- 3 ' PyHpHpPy-y- ImPyPyIm -W
189) 5' CT A T W-3' PyHpPyHp-y-PyHpPyIm -W
190) 5' CT A A W-3' pyHppypy-y-HpHpPyIm -W
191) 5' CT A G W-3' PyHpPyIm-y-pyHpPyIm -W
192} 5' CT A C W-3' PyHpPyPy-y-ImHpPyIm -W
193) 5'-W CT G T W-3' PyHpImHp-y-pypypylm 194) 5'-W CT G A W-3' PYHpImPy-y-HpPyPyIm 195) 5' CT G G W-3' PYHpImIm-y-Pypypylm -W
196) 5' CT G C W-3' PyHpImPy-y-ImPyPyIm -W
197) 5'-W CT C T W-3' PyHpPyHp-y-PyImPyIm 198) 5' CT C A W-3' PyHpPyPy-y-HpImPyIm -W
199) 5'-W CT C G W-3' PyHpPyIm-y-pyImPyIm 200) 5'-W CT C C W-3' PyHpPyPy-y-ImImPyIm 201) 5' CA T T W-3' PyPyHpHp-y-PypyHpIm -W
202) 5'-W CA T A W-3' PyPyHpPy-y-HpPyHpIm 203} 5'-W CA T G W-3' PyPyHpIm-y-PypyHplm 204) 5'-W CA T C W-3' PYPYHpPY-Y-ImPyHpIm 205) 5' CA A T W-3' PyPyPyHp-y-PyHpHpIm -W
206) 5'-W CA A A W-3' Pypypypy-y-HpHpHpIm 207) 5'-W CA A G W-3' PyPyPyIm-y-PYHpHpIm 208) 5' CA A C W-3' PyPypypy-y-ImHpHpIm -W
209) 5'-W CA G T W-3' PyPyImHp-y-PypyHplm 210) 5' CA G A W-3' PyPyImPy-y-HpPyHpIm -W
211) 5' CA G G W-3' PyPyImIm-y-PyPyHpIm -W
212) 5'-W CA G C W-3' PyPyImPy-y-ImPyHpIm 213) 5'-W CA C T W-3' PyPyPyHp-y-pyImHpIm 214) 5' CA C A W-3' Pypypypy-y-HpImHpIm -W
215) 5' CA C G W-3' PyPypylm-y-PyImHpIm -W
216) 5' CA C C W-3' pypypypy-y-ImImHpIm -W
WO 981370b7 PCT/US98/01714 TABLE
11:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WCSNNW-3' DNA aromatic amino acid sequence sequence 217) 5'-WC G T T W-3' PyImHpHp-y-PyPyPyIm 218) 5'-W~C G T A W-3' PyImHpPy-y-HpPyPyIm 219) 5'-WC G T G W-3' PyImHpIm-y-PyPyPyIm 220) 5'-WC G T C W-3' PyImHpPy-y-ImPyPyIm 221) 5'-WC G A T W-3' PyImPyHp-y-PyHpPyIm 222) 5'-WC G A A W-3' PyImPyPy-y-HpHpPyIm 223) 5'-WC G A G W-3' PyImPyIm-y-PyHpPyIm 224) 5'-WC G A C W-3' PyImPyPy-y-ImHpPyIm 225) 5' C G G T W-3' PyImImHp-y-PyPyPyIm -W
226) 5'-WC G G A W-3' PyImImPy-y-HpPyPyIm 227) 5'-WC G C T W-3' PyImPyHp-y-PyImPyIm 228) 5' C G C A W-3' PyImPyPy-y-HpImPyIm -W
229) 5'-WC C T T W-3' PyPyHpHp-y-PyPyImIm 230) 5' C C T A W-3' PyPyHpPy-y-HpPyImIm -W
231) 5' C C T G W-3' PyPyHpIm-y-PyPyImIm -W
232) 5' C C T C W-3' PyPyHpPy-y-ImPyImIm -W
233) 5'-WC C A T W-3' PyPyPyHp-y-PyHpImIm 234) 5'-WC C A A W-3' PyPyPyPy-y-HpHpImIm 235) 5' C C A G W-3' PyPyPyIm-y-PyHpImIm -W
236) 5'-WC C A C W-3' PyPyPyPy-y-ImHpImIm 237) 5'-WC C G T W-3' PyPyImFip-y-PyPyImIm 238) 5' C C G A W-3' PyPyImPy-y-HpPyImIm -W
239) 5'-WC C C T W-3' PyPyPyHp-y-PyImImIm 240) 5' C C C A W-3' PyPyPyPy-y-HpImImIm -W
G9) 5'-WC G G G W-3' PyImImIm-y-PyPyPyIm G10) 5' C G G C W-3' PyImImPy-y-ImPyPyIm -W
G11) 5' C G C G W-3' PyImPyIm-y-PyImPyIm -W
G12) 5'-WC G C C W-3' PyImPyPy-y-ImImPyIm G13) 5'-WC C G G W-3' PyPyImIm-y-PyPyImIm G14) 5' C C G C W-3' PyPyImPy-y-ImPyImIm -W
G15) 5'-WC C C G W-3' PyPyPyIm-y-PyImImIm G16) 5' C C C C W-3' PyPyPyPy-y-ImImImIm -W
TABLE 12:
8-ring Hairpin Polyamides for recognition of 6-by S'-WGWNNW-3' with included.
(3-substitutions DNA aromatic amino acid sequence sequence 3~i) 5' GT TG W-3' ImHp-~i-Im-y-Pypypypy -W
S 7~3) 5'-W GT AG W-3' ImHp-~3-Im-y-PyHppyPy 9(3) 5' GT GT W-3' Im-~3-ImHp-y-pypypypy -W
10(3) 5' GT GA W-3' Im-~3-ImPy-y-HpPyPyPy -W
I1~3} 5' GT GG W-3' Im-~3-ImIm-y-PyPypypy -W
12(3) 5' GT GC W-3' Im-(3-ImPy-y-ImPyPyPy -W
15(3) 5' GT CG W-3' ImHp-(3-Im-y-PyImPyPy -W
19(3) 5' GA TG W-3' ImPy-~3-Im-y-PyPyHpPy -W
23(3) 5' GA AG W-3' ImPy-~3-Im-y-PyHpHpPy -W
253) 5' GA GT W-3' Im-p-ImHp-y-PypyHppy -W
26(3) 5' GA GA W-3' Im-p-ImPy-y-HpPyHpPy -W
1S 27(3) 5' GA GG W-3' Im-(3-Imlm-y-PyPyHpPy -W
28~i) 5' GA GC W-3' Im-(3-ImPy-y-ImPyHpPy -W
31 5'-W GA GG W-3' R) ImPy-(3- Im-y-pyImHpPy TABLE
13: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WGSNNW-3' with (3-substitutions inchzded.
DNA aromatic amino acid sequence sequence 35(3) 5' G G T G W-3' ImIm-(3-Im-y-PyPyPyPy -W
393) 5' G G A G W-3' ImIm-~-Im-y-PyHpPyPy -W
45(3) 5' G C T T W-3' ImPyHpHp-y-Py-(3-ImPy -W
46(3) 5' G C T A W-3' ImPyIipPy-y-Hp-(3-ImPy -W
47(3) 5' G C T G W-3' ImPyI-IpIm-y-Py-(3-ImPy -W
47(32) 5' G C T G W-3' ImPy-~3-Im-y-Py-(3-ImPy -W
48(3) 5' G C T C W-3' ImPyHpPy-y-Im-(3-ImPy -W
49(3) 5' G C A T W-3' ImPyPyHp-y-Py-(3-ImPy -W
50(3) 5' G C A A W-3 T ImPyPyPy-y-Hp-(3-ImPy -W
513) 5'-W G C A G W-3' ImPyPyIm-y-Py-(3-ImPy 5132) 5' G C A G W-3' ImPy-(3-Im-y-Py-(3-ImPy -W
i5 523) 5' G C A C W-3' ImPyPyPy-y-Im-(3-ImPy -W
533) 5' G C G T W-3' ImPyImHp-y-Py-(3-ImPy -W
53~i2) 5' G C G T W-3' Im-~3-ImHp-y-Py-~3-ImPy -W
543) 5' G C G A W-3' ImPyImPy-y-Hp-R-ImPy -W
54(32) 5' G C G A W-3' Im-p-ImPy-y-Hp-(3-ImPy -W
G3 (3) 5' G G C G W-3' Imlm-~3-Im-y-PyImPyPy -W
G5(3) 5' G C G G W-3' ImPyImIm-y-Py-(3-ImPy -W
G5~i2) 5' G C G G W-3' Im-(3-ImIm-y-Py-(3-ImPy -W
G6~) 5' G C G C W-3' ImPyImPy-y-Im-(3-ImPy -W
G6(32) 5' G C G C W-3' Im-p-ImPy-y-Im-~3-ImPy -W
G7 (3) 5' G C C G W-3' ImPy-~3-Im-y-PyImImPy -W
..__r... _ , , , TABL>14: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WTWNNW-3' with (3-substitutions includ d e DNA quenc e .
se aromatic amino acid sequence 59(3) 5' TT T G W-3' HpHp-(3-Im-y-pypypypy -W
633) 5' TT A G W-3' HpHp-~-Im--W -p y yHppypy 65(3) 5' TT G T W-3' _ _ -W Hp ~ Imp-Y-PYPYPYPY
663) 5' TT G A W-3' Hp-p-ImPy-y-HpPYPyPy -W
673) 5' TT G G W-3' Hp-(3-ImIm-y-pypypypY
-W
68(3) 5' TT G C W-3' -W Hp- ~3- ImPy-y- ImPyPyPy 71(3) 5' TT C G W-3' HpHp-(3-Im-y-PyTmPyPy -W
75(3) 5' TA T G W-3' Hppy_(3-Im-y-pYpyHppy -W
79(3) 5' TA A G W-3' HpPy-(3-Im-y-pyHpHpPy -W
81(3) 5' TA G T W-3' Hp-~i-ImHp-y-PypyHpPy -W
82(3) 5' TA G A W-3' Hp-(3-ImP
-W Y_Y_HPPYHPPY
83(3) 5' TA G G W-3' Hp-J3-ImIm-y-pypygpPy -W
843) 5'-W TA G C W-3' Hp-~3- ImPy-y- ImPyHpPy 87(3) 5' TA C G W-3' HpPy-(3-Im-y-PyImHpPy -W
TABLE 15:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WTSNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 913) 5' T G T G W-3' Hplm-~3-Im-y-PyPyPyPy -W
95(3) 5' T G A G W-3' HpIm-(3-Im-y-PyHpPyPy -W
103(3) 5' T G C G W-3' HpIm-(3-Im-y-PyImPyPy -W
105(3) 5' T C T T W-3' HpPyHpHp-y-Py-~-ImPy -W
106(3) 5' T C T A W-3' HpPyHpPy-y-Hp-(~-ImPy -W
107(3) 5' T C T G W-3' HpPyHpIm-y-Py-(3-ImPy -W
107~i2) 5' T C T G W-3' HpPy-(3-Im-y-Py-(3-ImPy -W
108(3) 5' T C T C W-3' HpPyHpPy-y-Im-(3-ImPy -W
109(3) 5' T C A T W-3' HpPyPyHp-y-Py-(3-ImPy -W
110R) 5' T C A A W-3' HpPyPyPy-y-Hp-p-ImPy -W
111(3} 5' T C A G W-3' HpPyPyIm-y-Py-p-ImPy -W
111(32) 5' T C A G W-3' HpPy-(3-Im-y-Py-(3-ImPy -W
1123) 5' T C A C W-3' HpPyPyPy-y-Im-(3-ImPy -W
113(3) 5' T C G T W-3' HpPyImHp-y-Py-~3-ImPy -W
113(32) 5' T C G T W-3' Hp-(3-ImHp-y-Py-(3-ImPy -W
114(3) 5' T C G A W-3' HpPyImPy-y-Hp-~3-ImPy -W
114(32) 5' T C G A W-3' Hp-(3-ImPy-y-Hp-(3-ImPy -W
1173) 5' T C G G W-3' HpPyImIm-y-Py--ImPy -W
117(32) 5' T C G G W-3' Hp-(3-Imlm-y-Py-(3-ImPy -W
118(3) 5' T C G C W-3' HpPyImPy-y-Im-~3-ImPy -W
118(32) 5' T C G C W-3' Hp-(3-ImPy-y-Im-p-ImPy -W
119(3) 5' T C C G W-3' HpPy-~-Im-y-PyImImPy -W
..~................~...... ~ . ~ ~ ,.» , 'TABLE 16: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WAWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 123(3) 5' A T TG W-3' pygp_~3_Im_y-pypypyHp -W
127(3) 5' A T AG W-3' PyHp-~3-Im-y-PyHpPyHp -W
1293) 5' A T GT W-3' Py-(3-ImHp-y-PyPyPyHp -W
1303) 5' A T GA W-3' Py-~3-ImPy-y-HpPyPyHp -W
131(3) 5' A T GG W-3' Py-(3-ImIm-y-Pypypygp -W
132j3) 5' A T GC W-3' p -W y-p-ImPy-y-ImPyPyHp 1353) 5' A T CG W-3' PyHp-(3-Im-y-PyImPyHp -W
139~i} 5' A A TG W-3' PyPy-(3-Im-y-PyPyHpHp -W
143(3) 5' A A AG W-3' PyPy-~3-Im-y-PyHpHpHp -W
145(3) 5' A A GT W-3' Py-(3-ImHp-y-PypyHpHp -W
146(3) 5' A A GA W-3' Py-~-ImPy-y-HpPyHpHp -W
IS 147p) 5' A A GG W-3' Py-(3-Imlm-y-PyPyHpHp -W
1480 5' A A GC W-3' Py-p-ImPy-y-ImPyHpHp -W
151(3) 5' A A CG W-3' PyPy-~3-Im-y-PyImHpHp -W
_3~,_ 'TABLE
I 7: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WASNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 155(3) 5' A G T G W-3' Pylm-(3-Im-y-PyPyPyHp -W
159(3) 5' A G A G W-3' PyIm-(3-Im-y-PyHpPyHp -W
167~i) 5' A G C G W-3' PyIm-~i-Im-y-PyImPyHp -W
169~i) 5'-W A C T T W-3' PyPyHpHp-y-Py-(3-ImHp 170~i) 5' A C T A W-3' PyPyHpPy-y-Hp-(3-ImHp -W
1713) 5' A C T G W-3' PyPyHpIm-y-Py-(3-ImHp -W
171(32) 5' A C T G W-3' PyPy-p-Im-y-Py-(3-ImHp -W
172(3) 5' A C T C W-3' PyPyHpPy-y-Im-(3-ImF3p -W
173(3) 5' A C A T W-3' PyPyPyHp-y-Py-(3-ImHp -W
1743) 5' A C A A W-3' PyPyPyPy-y-Hp-R-ImHp -W
1753) 5' A C A G W-3' PyPyPyIm-y-Py-~3-ImHp -W
17532) 5' A C A G W-3' Pypy-(3-Im-y-Py-(3-ImHp -W
176(3) 5' A C A C W-3' PyPypyPy-y-Im-(3-ImHp -W
1770 5' A C G T W-3' PyPyImHp-y-Py-(3-ImHp -W
177(32) 5' A C G T W-3' Py-(3-ImHp-y-Py-(3-ImHp -W
178(3) 5' A C G A W-3' PyPyImPy-y-Hp-(3-ImHp -W
178(32) 5' A C G A W-3' Py-(3-ImPy-y-Hp-/3-ImHp -W
1813) 5' A C G G W-3' PyPyImIm-y-Py-(3-ImHp -W
181(32) 5' A C G G W-3' py-(3-Imlm-y-Py-(3-ImHp -W
182(3) 5' A C G C W-3' PyPyImPy-y-Im-R-ImHp -W
182(32) 5' A C G C W-3' Py-(3-ImPy-y-Im-(3-ImHp -W
18332) 5' A C C G W-3' Pypy-~i-Im-y-PyImImHp -W
~... . .
I AI3LP;
I 8: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WCWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 185(3) 5' C T T TW-3' PyHpHpHp-y-Pypy-(3-Im -W
186(3) 5''-WC T T AW-3' PyHpHpPy-y-HpPy-(3-Im 1873) 5' C T T GW-3' PyHpHpIm-y-Pypy-(3-Im -W
187(32) 5' C T T GW-3' p H
-W Y P-~-Im-y-PyPy-(3-Im 188(3) 5' C T T CW-3' pyHpHpPy-y-ImPy-(3-Im -W
189(3) 5' C T A TW-3' PyHpPyHp-y-PyHp-(3-Im -W
1903) 5' C T A AW-3' PyHpPyPy-y-HpHp-~i-Im -W
191(3) 5' C T A GW-3' PyHpPyim-y-PyHp-/3-Im -W
191(32) 5' C T A GW-3' PyHp-(3-Im-y-PyHp-~3-Im -W
192(3) 5' C T A CW-3' PyHpPyPy-y-ImHp-J3-Im -W
193(3) 5' C T G TW-3' PyHpImHp-y-PyPy-~3-Im -W
1932) 5' C T G TW-3' Py-~i-ImHp-y-Pypy-(3-Im -W
194(3) 5' C T G AW-3' PyHpImPy-y-HpPy-(3-Im -W
194(32) 5' C T G AW-3' Py--ImPy-y-HpPy-(3-Im -W
195p) 5' C T G GW-3' PyHpImIm-y-Pypy-~3-Im -W
1952) 5' C T G GW-3' Py-(3-ImIm-y-PyPy-~-Im -W
196(3) 5' C T G CW-3' PyHpImPy-y-ImPy-(3-Im -W
196(32) 5' C T G CW-3' Py-p-ImPy-y-ImPy-(3-Im -W
197(3) 5' C T C TW-3' PyHpPyHp-y-PyIm-(3-Im -W
198(3) 5' C T C AW-3' PyHpPyPy-y-HpIm-(3-Im -W
199(3) 5' C T C GW-3' PyHpPyIm-y-PyIm-(3-Im -W
19932) 5' C T C GW-3' PyHp-(3-Im-y-Pylm-p-Im -W
200(3) 5' C T C CW-3' PyHpPyPy-y-ImIm-(3-Im -W
201(3) 5' C A T TW-3' PyPyHpHp-y-PyPy-~3-Im -W
202(3) 5' C A T AW-3' PyPyHpPy-y-HpPy-~3-Im -W
203~i) 5' C A T GW-3' PyPyHpIm-y-PyPy-~-Im -W
203~i2) 5' C A T GW-3' p p -W Y Y-~-Im-y-PyPy-(3-Im 2043) 5' C A T CW-3' PyPyHpPy-y-ImPy-p-Im -W
205(3) 5' C A A TW-3' PyPyPyHp-y-PyHp-(3-Im -W
2063) 5' C A A AW-3' PyPypypy-y-HpHp-p-Im -W
TABLE 18 (cont}:
8-ring Hairpin Polyamides for 6-by 5'-WCWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 207(3) 5' C A A G W-3' PypyPyIm-y-PyHp-(3-Im -W
207(32) 5' C A A G W-3' PyPy-(3-Im-y-PyHp-(3-Tm -W
2083) 5' C A A C W-3' PyPypyPy-y-ImHp-(3-Im -W
209(3) 5' C A G T W-3' PypyImHp-y-PyPy-~-Im -W
209(32) 5' C A G T W-3' Py-p-ImHp-y-PyPy-(3-Im -W
210(3) 5' C A G A W-3' PyPyImPy-y-HpPy-p-Im -W
210(32) 5' C A G A W-3' Py-p-ImPy-y-HpPy-p-Im -W
211(3) 5' C A G G W-3' PyPyImIm-y-Pypy-(3-Im -W
211(32) 5' C A G G W-3' Py-(3-Imlm-y-PyPy-R-Im -W
212(3) 5' C A G C W-3' PyPyImPy-y-ImPy-(3-Im -W
21232) 5' C A G C W-3' Py-[3-ImPy-y-ImPy-(3-Im -W
213(3) 5' C A C T W-3' PyPyPyHp-y-Pylm-R-Im -W
2143) 5' C A C A W-3' PyPyPyPy-y-HpIm-p-Im -W
2153) 5' C A C G W-3' PyPyPyIm-y-PyIm-~3-Im -W
215(32) 5' C A C G W-3' PyPy-(3-Im-y-PyIm-~-Im -W
216(3) 5' C A C C W-3' PyPyPyPy-y-ImIm-~i-Im -W
1A13Lt:
ly: ~-nng Hairpin Polyamides for recognition of 6-by 5'-WCSNNW-3' with ~3-substitutions included .
DNA aromatic amino acid sequence sequence 217(3) 5' CG T T W-3' PyImHpHp-y-PyPy-(3-Im -W
218(3) 5' CG T A W-3' PyImHpPy-y-HpPy-~-Im -W
219(3) 5' CG T G W-3' PyImHpIm-y-Pypy-(3-Im -W
219(32) 5' CG T G W-3' Pylm-p-Im-y-PyPy-~i-Im -W
220(3) 5' CG T C W-3' PyImHpPy-y-ImPy-(3-Im -W
2210 5' CG A T W-3' PyImPyHp-y-PyHp-~3-Im -W
222(3) 5' CG A A W-3' PyImPYPy-y-HpHp-~3-Im -W
223(3) 5' CG A G W-3' PyImPyIm-y-PyHp-p-Im -W
2232) 5' CG A G W-3' PyIm-~3-Im-y-PyHp-~i-Im -W
224(3) 5' CG A C W-3' PyImPyPy-y-ImHp-~-Im -W
2253) 5' CG G T W-3' PyImImHp-Y-Pypy-~3-Im -W
226(3) 5' CG G A W-3' PyImImPy-Y-HpPy-J3-Im -W
227(3) 5' CG C T W-3' PyImPyHp-y-PyIm-~3-Im -W
228(3) 5' CG C A W-3' PyImPyPy-y-HpIm-(3-Im -W
2293) 5' CC T T W-3' PyPyHpHp-y-Py-(3-ImIm -W
2303) 5' CC T A W-3' PyPyHpPy-y-Hp-p-ImIm -W
2313) 5' CC T G W-3' PyPyHpIm-y-Py-~3-ImIm -W
231(32) 5' CC T G W-3' p p ~~
-W Y Y-t'-Im-y-Py-~3-ImIm 232(3) 5' CC T C W-3' PyPyHpPy-y-Im-~3-ImIm -W
2333) 5' CC A T W-3' PyPyPyHp-y-Py-(3-ImIm -W
234(3) 5' CC A A W-3' PyPypypy-y-Hp-R-ImIm -W
235~i) 5' CC A G W-3' PyPyPyIm-y-Py-p-Imlm -W
235(32) 5' CC A G W-3' p 'p -W Y Y-~-Im-y-Py-~3-Imlm 236(3) 5' CC A C W-3' PyPyPyPy-y-Im-~3-ImIm -W
2370 5' CC G T W-3' PyPyImHp-y-Py-p-ImIm -W
2372) 5' CC G T W-3' Py-(3-ImHp-Y-Py-~-Imlm -W
2383) 5' CC G A W-3' PyPyImPy-y-Hp-(3-ImIm -W
238(32) 5' CC G A W-3' Py-~3-ImPy-y-Hp-~3-ImIm -W
G9~3) 5' CG G G W-3' PyImImIm-y-pypy-~3-Im -W
G10(3) 5' CG G C W-3' PyImImPy-Y-ImPy-(3-Im -W
TABLE 19 (cont): 8-ring Hairpin Poiyamides for recognition of 6-by 5'-WCSNNW-3' with (3-substitutions -included.
DNA sequence aromatic amino acid sequence 611(3) 5' -W C G C G W-3' PyImPyIm-y-PyIm-~3-Im 611(32)5' -W C G C G W-3' Pylm-[3-Im-y-Pylm-/3-Im G12R) 5' -W C G C C W-3' PyImPyPy-'y-ImIm-~3-Im 613(3) 5' -W C C G G W-3' PyPyImIm-y-Py-~3-Imlm 613(32)5' -W C C G G W-3' Py-(3-ImIm-y-Py-~3-ImIm G14~3) 5' -W C C G C W-3' PyPyImPy-y-Im-(3-ImIm G14~2)5' -W C C G C W-3' Py-(3-ImPy-y-Im-(3-Imlm 615(3) 5' -W C C C G W-3' PyPy-(3-Im-y-PyImImim If the process described above of designing a preferred polyamide molecule y-XSX6X~Xg comprising eight aromatic aminoacid residues does not produce a selective polyamide that binds to the target identified DNA sequence with subnanomolar affinity and with a selectivity over mismatch sequences of greater than a factor of ten, a polyamide molecule X 1 X2X3X4X5-y-X6X~XgX9X 1 p having five carboxamide binding pairs can be designed that is 2o selective for a seven base pair identified target 5'-WNI~I~~1NNW-3' sequence. The design and synthesis of the five binding pair polyamide is similar to that of the four binding pair polyamide X1X2X3X4-y-XSX6X~Xg described above.
The polyamide design process, shown schematically in Figure 7 provides a method for designing a ten carboxamide residue molecule comprising five carboxamide binding pairs for selective detection and binding of a target seven base pair 5'- -3' sequence in the minor groove of double stranded DNA. The design process identifies an appropriate polyamide ligand for recognition of a predetermined seven base pair, 5'-VVI'11~TNNNVV-3' sequence with subnanomolar affinity and >10-fold specificity versus mismatch sites. Trauger, J.W., Baird, E.
3o E. Dervan, P.B. describes the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (/996).
In order to prepare a polyamide molecule specific for an identified seven base pair sequence of double stranded DNA, a user starts the 10-ring hairpin design process that implements the minor groove recognition pairing code summarized in Table 2 above. In the . design process a 5'-WNNNNNW-3' sequence was identified. In a preferred embodiment, the identified sequence was located within a gene promoter. The identified sequence was then defined as S'-WabcdeW-3' in a stepwise process wherein a, b, c, d,and e, were sequentially and independently defined as A, G, C, or T. The structure of the polyamide molecule was then s correspondingly defined by sequentially chosing antiparallel carboxamide binding pairs according to the minor groove pairing code summarized in Table 2 above. Thus, if a was G, then X 1 was defined as Im, and X 1 p was defined as Py. If a was C, then X 1 was defined as Py, and X 1 p was defined as Im. If a was T, then X 1 was def ned as Hp, and X I p was defined as Py. If a was A, then X 1 was defined as Py, and X 1 p was defined as Hp.
Similarly, b was defined as A, G, C, or T and corresponding carboxamide binding pairs were defined. According to the same rules, if b was G, then X2 was defined as Im, and X9 was defined as Py. If b was C, then X2 was defined as Py, and X9 was defined as Im. Likewise, if b was T, then X~ was defined as Hp, and X9 was defined as Py. If b was A, then X2 was defined ~ 5 as Py, and X9 was defined as Hp.
The next step was to define c as A, G, C, or T and then define corresponding carboxamide binding pairs. Following the same rules, if c was G, then X3 was defined as Im, and Xg was defined as Py. If c was C, then X3 was defned as Py, and Xg was defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and Xg was defined as Py. If c was A, then X3 was defined as Py, and Xg was defined as Hp. Similarly, d was defined as A, G, C, or T and the corresponding carboxamide binding pair was defined. According to the above rules, if d was G, then X4 was defined as Im, and X~ was defined as Py. If d was C, then X4 was defined as Py, and X~ was defined as Im. If d was T, then X4 was defined as Hp, and X~
was defined as 25 Py. If d was A, then X4 was defined as Py, and X~ was defined as Hp.
Finally, a was defined as - A, G, C, or T and the corresponding carboxamide binding pair was defined.
According to the above rules, if a was G, then XS was defined as Im, and X6 was defined as Py.
If a was C, then XS was defined as Py, and X6 was defined as Im. If a was T, then XS was defined as Hp, and X6 was defined as Py. If a was A, then XS was defined as Py, and X6 was defined as Hp.
With all ten carboxamide residues that participate in the binding pairs now defined, the designed polyamide X1X2X3X4X5-y-X6X~XgX9Xlp suitable for binding to the identified sequence was synthesized using known techniques. Baird, E. E. & Dervan, P. B.
describes~the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids: J. Am.
Chem. Soc. 118, 6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence was determined using a quantitative DNase footprint titration method for studying protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K., Methods Enzymol. 130, 132-181 {1986). If the affinity of the synthesized polyamide at the target site was not subnanomolar affinity then substituting at least one (3-alanine residue for a pyrrole or 3-1o hydroxypyrrole residue was considered in order to optimize the exact positions of the binding pairs of aromatic amino acids. If the affinity of the polyamide at the target site was subnanomolar affinity then the sequence specificity of the polyamide versus mismatch sequences was determined. If the specificity versus mismatch sites was not >
10-fold specificity then adding a (3-alanine (shown schematically in Figure 8) was considered, in order to optimize the positions of the aromatic amino acids in relationship to the base pairs in the minor groove.
Specificity of the polyamide molecule for the target identified sequence versus mismatch sequence sites of greater than 10-fold was considered a successful result of design process.
The 1024 polyamide molecules comprising five carboxamide binding pairs that were 2o designed using this method are useful for binding to the 1024 target S'-NNMVN-3' core sequences, and are listed in Tables 20-S 1. A corresponding polyamide molecule was designed for each DNA sequence (241-1232) and {G17-G48) using the process outlined above and shown schematically in Figure 7.
If the synthesized polyamide molecule did not bind to the target identified sequence with subnanomolar affinity or if the synthesized polyamide molecule did not exhibit a specificity for the target identified sequence versus mismatch sequence sites of greater than 10-fold, the option of substituting an aliphatic amino acid residue for one of the carboxamide residues was considered. The preferred aliphatic amino acid residue is /3-alanine. At least one aliphatic 3o amino acid residue such as a (3-alanine residue provided some flexibility to the central portion of the polyamide molecule, acting as a "spring" to permit optimization of the hydrogen bonding between the carboxamide binding pairs and the nucleotide bases of the double stranded DNA.
In general, it was not found to be advantageous to replace either member of the terminal carboxamide binding pair, X1/X10, with (3-alanine. Similarly, ~3-alanine was not substituted for members of the binding pair, XS/X6, adjacent to the y hairpin residue. (3-alanine residues were not substituted for N-mcthylimidazole residues. The use of (3-alanine in place of a pyrrole or 3-hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/~, ~3/Im, Hp/(3, (i/Hp, Py/(3, and ~3/Py) and aliphatic/aliphatic pairing (~i/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-alanine is schematically illustrated in Figure 8. Selective placement of an aliphatic ~-alanine (~i) residue to paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im) aromatic amino acid or another (3-alanine residue is found to compensate for sequence composition effects to improve recognition and binding of the minor groove of DNA by pyrrole-imidazole polyamides of the present invention. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be reduced by replacement of an aromatic amino acid with an aliphatic (3-alanine residue. In a polyamide molecule that comprises five binding pairs it is only beneficial to place (3-alanine in positions X2, X3, X4, X~, Xg, and X9. No more than two ~3-alanine residues may be placed within a single hairpin structure. No more than a single ~3-residue may be placed within each individual polyamide subunit, e.g., if X2 2o is replaced with (3-alanine, X3 or X4 cannot be replaced as well.
These rules and others were implemented in the method schematically illustrated in Figure 8. This process is suitable for the refinement of the design polyamide comprising five binding pairs that has been designed by the method illustrated in Figure 7, but which lacks subnanomolar affinity or greater than 10-fold specificity at the identified target DNA sequence.
As in the basic design method, the designed polyamides are synthesized and the affinity and specificity of binding to the target DNA were determined.
As discussed above, for a given 10-ring polyamide molecule there are six possible outcomes for the process of substituting a ~3-alanine residue for an aromatic amino acid residue.
First, there may be no position at which it is possible to add a (3-alanine residue; in such case, a better binding affinity or selectivity can be sought in the design and synthesis of a polyamide with four or six carboxamide binding pairs, described below. Second, the process may result in a derivative which contains a single (3-alanine substitution (such derivatives are numbered according to the parent numbering scheme such that a single (3-derivative of compound 5 would be called 5[3), which is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and at which point the process is deemed complete.
Third, the process of Figure 8 may result in a polyamide which contains a single j3-alanine substitution which is not sufficient to produce subnanomolar binding affinity and >IO-fold specificity, but where there are no additional positions in which it is possible to substitute a ~3-alanine residue, and in such a case a paired (3-alanine residue should be added as described in Figure 9 and text below. Fourth, the process of Figure 7 may result in a polyamide that contains a single ~3-alanine substitution that is not sufficient to produce subnanomolar binding affinity and >10-fold specificity, but where there is an additional position for ~3-alanine substitution that does produce a polyamide with the criterion level of affinity and selectivity.
Tables 52-83 list polyamide compounds 241(3-12323 and G17~3 -G48~, corresponding to DNA
sequences 241-1232 and G17 - G48, that contain one or two (3-alanine residues.
A fifth possibility is that substitution at a second position by the method illustrated in Figure 9 with a paired ~3-alanine residue is not sufficient to produce a polyamide having the 2o subnanomolar binding affinity and >10-fold specificity, and a polyamide with four or six carboxamide binding pairs, should be designed and synthesized, as described below. Finally, the design process may result in a polyamide that has a paired (3-alanine substitution that is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and therefore the.
design process is deemed complete. Tables 52-83 list polyamide compounds 241 (3-1232(3 and G17~3 -G48~3, corresponding to DNA sequences 241-1232 and G17 - G48, that contain one or two (3-alanine residues. In addition, Tables 52-83 list polyamides corresponding to sequences (241-1232) and (G17-G48) labeled (241(3p-1232(3p) and (G17(3p-G48(3p) that contain paired ~3/~
residues added by the process described in Figure 9.
TABLE 20:10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGWNNW-3' DNA aromatic amino acid sequence sequence 241) 5'-W G GT T T W-3' ImImHpHpHp-y-PyPypypypy S 242) 5'-W G GT T A W-3' ImImHpHpPy-y-HpPypypypy 243} 5'-W G GT T G W-3' ImImHpHpIm-y-PyPyPyPyPy 244) 5'-W G GT T C W-3' ImImHpHpPy-y-ImPyPyPypy 245) 5'-W G GT A T W-3' ImImHpPyHp-y-PyHpPyPyPy 246) 5'-W G GT A A W-3' ImImHpPyPy-y-HpHpPyPyPy 247} 5'-W G GT A G W-3' ImImHpPyIm-y-PyHpPyPyPy 248) 5'-W G GT A C W-3' ImImHpPyPy-y-ImHpPyPyPy 249) 5'-W G GT G T W-3' ImImHpImHp-y-PyPyPypypy 250) 5'-W G GT G A W-3' ImImHpImPy-y-HpPyPyPyPy 251) 5'-W G GT G G W-3' ImImHpImIm-y-pypypypypy 252) 5'-W G GT G C W-3' ImImHpImPy-y-ImPypyPypy 253) 5'-W G GT C T W-3' ImImHpPyHp-y-pyImPyPyPy 254) 5'-W G GT C A W-3' ImImHpPyPy-y-HpImPyPyPy 255) 5'-W G GT C G W-3' ImImHpPyIm-y-PyImPyPyPy 256) 5'-W G GT C C W-3' ImImHpPyPy-y-ImImPyPyPy 257) 5'-W G GA T T W-3' ImImPyHpHp-y-PyPyHpPyPy 258) 5'-W G GA T A W-3' ImImPyHpPy-y-HpPyHpPyPy 259) 5'-W G GA T G W-3' ImImPyHpIm-y-PyPyHpPyPy 260) 5'-W G GA T C W-3' ImImPyHpPy-y-ImPyHpPyPy 261) 5'-W G GA A T W-3' ImImPyPyHp-y-PyHpHpPyPy 262) 5'-W G GA A A W-3' ImImPyPyPy-y-HpHpHpPyPy 263) 5'-W G GA A G W-3' ImZmPyPyIm-y-PyHpHpPyPy 264) 5'-W G GA A C W-3' ImImPyPyPy-y-ImHpHpPyPy 265) 5'-W G GA G T W-3' ImImPyImHp-y-PyPyHpPyPy 266) 5'-W G GA G A W-3' ImImPyimPy-y-HpPyHpPyPy 267) 5'-W G GA G G W-3' ImImPyImIm-y-PyPyHpPyPy 268) 5'-W G GA G C W-3' ImImPyImPy-y-ImPyHpPyPy 269) 5'-W G GA C T W-3' ImImPyPyHp-y-PyImHpPyPy 270) 5'-W G GA C A W-3' ImImPyPyPy-y-HpImHpPyPy 271) 5'-W G GA C G W-3' ImImPyPyIm-y-PyImHpPyPy 272) 5'-W G GA C C W-3' ImImPyPyPy-y-ImImHpPyPy TABLE
21:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGSNNW-3' DNA aromatic amino acid sequence sequence 273) 5' G GG T T W-3' ImImImHpHp-y-PyPyPyPyPy -W
274) 5' G GG T A W-3' ImImImHpPy-y-HppyPyPyPy ~W
275) 5' G GG T G W-3' ImImImHpIm-y-PyPyPyPyPy -W
276) 5' G GG T C W-3' ImImImHpPy-y-ImPyPyPyPy -W
277 ) 5' G GG A T W-3' ImImImPyHp-y-PyHpPyPyPy -W
278) 5' G GG A A W-3' ImImImPyPy-y-HpHpPypyPy -W
279) 5' G GG A G W-3' ImImImPyIm-y-PyHppyPyPy -W
2 8 0 5 ' G GG A C W- 3 ImImImPyPy-y- ImHpPyPypy ) -W ' 281) 5' G GG G T W-3' ImImImImHp-y-PyPyPyPyPy -W
282) 5' G GG G A W-3' ImImImImPy-y-HpPyPyPyPy -W
283) 5' G GG C T W-3' ImImImPyHp-y-PyImPyPyPy -W
284) 5' G GG C A W-3' ImImImPypy-y-HpImPyPyPy -W
285) 5' G GC T T W-3' ImImPyHpHp-y-PyPyImPyPy -W
286) 5' G GC T A W-3' ImImPyHpPy-y-HpPyImPyPy -W
287) 5' G GC T G W-3' ImImPyHpIm-y-PyPyImPyPy -W
288) 5' G GC T C W-3' ImImPyHpPy-y-ImPyImPyPy -W
289) 5' G GC A T W-3' ImImPyPyHp-y-PyHpImPyPy -W
290) 5' G GC A A W-3' ImImPyPyPy-y-HpHpImPyPy -W
291) 5' G GC A G W-3' ImImPyPyIm-y-PyHpImPyPy -W
292) 5' G GC A C W-3' ImImPyPyPy-y-ImHpImPyPy -W
293) 5' G GC G T W-3' ImImpyImHp-y-PyPyImPyPy -W
294) 5' G GC G A W-3' ImImPyImPy-y-HpPyImPyPy -W
295) 5' G GC C T W-3' ImImPyPyHp-y-PyImImPyPy -W
296) 5' G GC C A W-3' ImImPyPyPy-y-HpImImPyPy -W
G17 ) 5' G GG G G W-3 ' ImImImImIm-y-PyPyPyPyPy -W
G18) 5' G GG G C W-3' ImImImImPy-y-ImPypyPypy -W
Gl9) 5' G GG C G W-3' ImImImPyIm-y-PyImPyPyPy -W
G20) 5' G GG C C W-3' ImImImPypy-y-ImImPyPyPy -W
G21) 5' G GC G G W-3' ImImPyImIm-y-PyPyImPyPy -W
G22) 5' G GC G C W-3' ImImPyImPy-y-ImPyImPyPy -W
G23) 5' G GC C G W-3' ImImPyPyIm-y-PyImImPyPy -W
G24) 5'-W G GC C C W-3' ImImPyPyPy-y-ImImImPypy '/'ABLE
22:
10-ring Hairpin Polyamides for recognition of ?-by 5'-WGTWNNW-3' DNA aromatic amino acid sequence sequence 297) 5'-W GT T T T W-3' ImHpHpHpHp-y-pypypypypY
298) 5'-W GT T T A W-3' ImHpHpHpPy-y-HpPyPyPyPy 299) 5'-W GT T T G W-3' ImHpHpHpIm-y-pypypypypY
300) 5'-W GT T T C W-3' ImHpHpHpPy-y-ImPYPyPyPy 301) 5'-W GT T A T W-3' ImHpHpPyHp-y-pyHpPyPYPy 302) 5'-W GT T A A W-3' ImHpHpPyPy-y-HpHpPYPyPy 303) 5'-W GT T A G W-3' ImHpHpPyIm-y-PyHpPyPyPy 304) 5'-W GT T A C W-3' ImHpHpPyPy-y-ImHpPyPYPy 305) 5'-W GT T G T W-3' ImHpHpImHp-y-PyPYPyPYPy 3 0 6 5 ' GT T G A W- 3 ImHpHp ImPy-y-HpPyPyPyPy ) -W ' 307) 5'-W GT T G G W-3' ImHpHpImIm-y-PyPyPypypy 308) 5'-W GT T G C W-3' ImHpHpImPy-y-ImPyPyPyPy 309) 5'-W GT T C T W-3' ImHpHpPyHp-y-PyImPYPYPy 310) 5'-W GT T C A W-3' ImHpHpPyPy-y-HpImPyPyPy 311) 5' GT T C G W-3' ImHpHpPyim-y-PyImPYPYPy -W
312 ) 5 ' GT T C C W- 3 ImHpHpPyPy-y- ImImPyPyPy -W ' 313) 5' GT A T T W-3' ImHpPyHpHp-y-PyPyHpPyPy -W
3 14) 5'-W GT A T A W-3' ImHpPyHpPy-y-HpPyHpPyPy 315) 5' GT A T G W-3' ImHppyHpIm-y-PyPyHpPyPy -W
316) 5' GT A T C W-3' ImHpPyHpPy-y-ImPyHpPyPy -W
317) 5' GT A A T W-3' ImHpPyPyHp-y-PyHpHpPyPy -W
318) 5' GT A A A W-3' ImHpPyPypy-y-HpHpHpPyPy -W
319) 5' GT A A G W-3' ImHpPYPyIm-y-PyHpHpPyPy -W
3 2 0 5 ' GT A A C W- 3 ImHpPyPyPy-y- ImHpHpPyPy ) -W ' 321) 5' GT A G T W-3' I,~ppYl~p_y_pypyHppypY
-W
322) 5' GT A G A W-3' ImHpPyImPy-y-HpPyHpPyPy -W
323) 5'-W GT A G G W-3' ImHpPyImIm-y-PypyHpPyPy 324 ) 5 ' GT A G C W-3 ' ImHpPyImPy-y- ImPyHpPyPy -W
325) 5' GT A C T W-3' ImHpPyPyHp-y-PyImHpPYPy -W
326) 5' GT A C A W-3' ImHpPyPYPy-y-HpImHpPyPy -W
327) 5' GT A C G W-3' ImHpPyPYIm-y-PyImHpPyPy -W
328) 5' GT A C C W-3' ImApPyPyPy-y-ImImHpPyPy -W
TABLE
23:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTSNNW-3' DIVA aromatic amino acid sequence sequence 329) 5' G T G T T W-3' ImHpImHpHp-y-PyPyPyPyPy -W
330) 5' G T G T A W-3' ImHpImHpPy-y-HpPyPyPyPy -W
331) 5' G T G T G W-3' ImHpImHpIm-y-PyPyPyPyPy -W
332) 5'-W G T G T C W-3' ImHpImHpPy-y-ImPyPyPyPy 333) 5'-W G T G A T W-3' ImHpImPyHp-y-PyHpPyPyPy 334) 5'-W G T G A A W-3' ImHpImPyPy-y-HpHpPyPyPy 335) 5'-W G T G A G W-3' ImHpImPyIm-y-PyHpPyPyPy 336) 5' G T G A C W-3' ImHpImPyPy-y-ImHpPyPyPy -W
337) 5'-W G T G G T W-3' ImHpImImHp-y-PyPyPyPyPy 338) 5'-W G T G G A W-3' ImHpImImPy-y-HpPyPyPyPy 339) 5'-W G T G C T W-3' ImHpImPyHp-y-PyImPyPyPy 340) 5'-W G T G C A W-3' ImHpImPyPy-y-HpImPyPyPy 341) 5'-W G T G G G W-3' ImHpImImIm-y-PyPyPyPyPy 342) 5' G T G G C W-3' ImHpImImPy-y-ImPyPyPyPy -W
343) 5'-W G T G C G W-3' ImHpImPyIm-y-PyImPyPyPy 344) 5'-W G T G C C W-3' ImHpImPyPy-y-ImImPyPyPy 345) 5' G T C T T W-3' ImHpPyHpHp-y-PyPyImPyPy -W
346) 5'-W G T C T A W-3' ImHpPyHpPy-y-HpPyImPyPy 347) 5'-W G T C T G W-3' ImHpPyHpIm-y-PyPyImPyPy 348) 5'-W G T C T C W-3' ImHpPyHpPy-y-ImPyImPyPy 349) 5'-W G T C A T W-3' ImHpPyPyHp-y-PyHpImPyPy 350) 5' G T C A A W-3' ImHpPyPyPy-y-HpHpImPyPy -W
351) 5' G T C A G W-3' ImHpPyPyIm-y-PyHpImPyPy -W
352) 5'-W G T C A C W-3' ImHpPyPyPy-y-ImHpImPyPy 353) 5'-W G T C G T W-3' ImHpPyImHp-y-PyPyImPyPy 354) 5' G T C G A W-3' ImHpPyImPy-y-HpPyImPyPy -W
355) 5' G T C C T W-3' ImHpPyPyHp-y-PyImImPyPy -W
356) 5'-W G T C C A W-3' ImHpPyPyPy-y-HpImImPyPy 357) 5'-W G T C G G W-3' ImHpPyImIm-y-PyPyImPyPy 358) 5'-W G T C G C W-3' ImHpPyImPy-y-ImPyImPyPy 359) 5'-W G T C C G W-3' ImHpPyPyIm-y-PyImImPyPy 3 6 0 5 ' G T C C C W- 3 ImApPyPyPy-y- ImImImPyPy ) -W ' TABLE
24:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGAWNNW-3' DNA aromatic amino acid sequence sequence 361) 5' G A TT T W-3' ImPyHpHpHp-y-PyPyPyHppy -W
362) 5' G A TT A W-3' ImPyHpHpPy-y-HpPyPyHpPy -W
363) 5'-W G A TT G W-3' ImPyHpHpIm-y-PyPyPyHpPy 364} 5'-W G A TT C W-3' ImPyHpHpPy-y-ImPyPyHpPy 365) 5' G A TA T W-3' ImPylipPyHp-y-pyHpPyHpPy -W
366) 5' G A TA A W-3' ImPyHpPyPy-y-HpHpPyHpPy -W
367) 5'-W G A TA G W-3' ImPyHpPyIm-y-PyHpPyHpPy 368) 5'-W G A TA C W-3' ImPyHpPyPy-y-ImHpPyHpPy 369) 5' G A TG T W-3' ImPyHpImHp-y-PyPypygppy -W
370) 5' G A TG A W-3' ImPyHpImPy-y-HpPyPyHpPy -W
371) 5' G A TG G W-3' ImPyHpImIm-y-PyPyPyHpPy -W
372) 5'-W G A TG C W-3' ImPyHpImPy-y-ImPyPyHpPy 373 ) 5' G A TC T W-3' ImPyHpPyHp-y-PyImPyHpPy -W
374) 5' G A TC A W-3' ImPyHpPyPy-y-HpImPyHpPy -W
375) 5' G A TC G W-3' ImPyHpPyIm-y-PyImPyHpPy -W
37 6 5 ' G A TC C W- 3 ImPyHpPyPy-y- ImImPyHpPy ) -W ' 377) 5'-W G A AT T W-3' ImPyPyHpHp-y-PyPyHpHpPy 378) 5' G A AT A W-3' ImPyPyHpPy-y-HpPyHpHpPy -W
379) 5'-W G A AT G W-3' ImPyPyHpIm-y-PyPyHpHpPy 3 8 0 5 ' G A AT C W- 3 ImPyPyHpPy-y- ImPyHpHpPy ) -W ' 3 81 5 ' G A AA T W- 3 ImPyPyPyHp -y- PyHpHpHpPy ) -W ' 382) 5'-W G A AA A W-3' ImPyPyPyPy-y-HpHpHpHpPy 3 83 5 ' G A AA G W-3 ' IrriPyPypylm-y-PyHpHpHpPy ) -W
384) 5' G A AA C W-3' ImPyPyPyPy-y-ImllpHpHpPy -W
385) 5' G A AG T W-3' ImPyPyImHp-y-PyPyHpHpPy -W
386) 5'-W G A AG A W-3' ImPyPyImpy-y-HpPyHpHpPy 387) 5'-W G A AG G W-3' ImPyPyImIm-y-PyPyHpHpPy 388) 5' G A AG C W-3' ImPyPyImPy-y-ImPyHpHpPy -W
389) 5'-W G A AC T W-3' ImPyPyPyHp-y-PyImHpHpPy 390) 5' G A AC A W-3' ImPyPyPypy-y-HpImHpHpPy -W
391) 5'-W G A AC G W-3' ImPyPypyIm-y-PyImHpHpPy 392) 5' G A AC C W-3' ImPyPyPyPy-y-ImImHpHpPy -W
TABLE
25:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' DNA aromatic amino acid sequence sequence 393) 5'-W G AG T T W-3' ImPyImHpHp-y-PyPyPyHpPy 394) 5'-W G AG T A W-3' ImPyImHpPy-y-HpPyPyHpPy 395) 5'-W G AG T G W-3' ImPyImHpIm-y-PyPyPyHpPy 396) 5'-W G AG T C W-3' ImPyImHpPy-y-ImPyPyHpPy 397) 5'-W G AG A T W-3' imPyImPyHp-y-PyHpPyHpPy 398) 5'-W G AG A A W-3' ImPyImPyPy-y-HpHpPyHpPy 399) 5'-W G AG A G W-3' ImPyImPyIm-y-PyHpPyHpPy 400) 5'-W G AG A C W-3' ImPyImPyPy-y-ImHpPyHpPy 401) 5'-W G AG G T W-3' ImPyImImHp-y-PyPyPyHpPy 402) 5'-W G AG G A W-3' ImPyImImPy-y-HpPyPyHpPy 403) 5'-W G AG C T W-3' ImPyImPyHp-y-PyImPyHpPy 404) 5' G AG C A W-3' ImPyImPyPy-y-HpImPyHpPy -W
405) 5'-W G AG G G W-3' ImPyImImIm-y-PyPyPyHpPy 406) 5' G AG G C W-3' ImPyImImPy-y-ImPyPyHpPy -W
407) 5'-W G AG C G W-3' ImPyImPyIm-y-PyImPyHpPy 408) 5'-W G AG C C W-3' ImPyImPyPy-y-ImImPyHpPy 409) 5' G AC T T W-3' ImPyPyHpHp-y-PyPyImHpPy -W
4 10) 5'-W G AC T A W-3' ImPyPyHpPy-y-HpPyImHpPy 411) 5'-W G AC T G W-3' ImPyPyHpIm-y-PyPyImHpPy 412) 5'-W G AC T C W-3' ImPyPyHpPy-y-ImPyImHpPy 413) 5' G AC A T W-3' ImPyPyPyHp-y-PyHpImHpPy -W
414) 5'-W G AC A A W-3' ImPyPyPyPy-y-HpHpImHpPy 415) 5'-W G AC A G W-3' ImPyPyPyIm-y-PyHpImHpPy 416) 5'-W G AC A C W-3' ImPyPyPyPy-y-ImHpImHpPy 417) 5'-W G AC G T W-3' ImPyPyImAp-y-PyPyImHpPy 418) 5'-W G AC G A W-3' ImPyPyImPy-y-HpPyImHpPy 419) 5'-W G AC C T W-3' ImPyPyPyHp-y-PyImImHpPy 420) 5' G AC C A W-3' ImPyPyPyPy-y-HpimImHpPy -W
421) 5' G AC G G W-3' ImPyPyImIm-y-PyPyImHpPy -W
422) 5'-W G AC G C W-3' ImPyPyImPy-y-ImPyImHpPy 423) 5'-W G AC C G W-3' ImPyPyPyIm-y-PyImImHpPy 424) 5'-W G AC C C W-3' ImPyPyPyPy-y-ImImImHpPy TABLE
26:
10-ring Hairpin Poiyamides for recognition of 7-by 5'-WGCWNNW-3' DNA aromatic amino acid sequence sequence 425) 5'-W G CT T T W-3' ImPyHpHpHp-y-PyPyPyImpy S 426) 5'-W G CT T A W-3' ImPyHpHpPy-y-HpPyPyImPy 427) 5'-W G CT T G W-3' ImPyHpHpIm-y-PyPyPyImPy 428) 5' -W G CT T C W-3' ImPyHpHpPy-y-ImPyPyImPy 429) 5'-W G CT A T W-3' ImPyHpPyHp-y-PyHpPyImPy 430) 5'-W G CT A A W-3' ImPyHpPyPy-y-HpHpPyImPy 431) 5' -W G CT A G W-3' ImPyHpPyIm-y-PyHpPyImPy 432) 5' -W G CT A C W-3' ImPyHpPyPy-y-ImHpPyImPy 433) 5' -W G CT G T W-3' ImPyHpImHp-y-PyPyPyImpy 434) 5'-W G CT G A W-3' ImPyHpImPy-y-HpPyPyImPy 435) 5'-W G CT G G W-3' ImPyHpImIm-y-PyPyPyImPy 436) 5'-W G CT G C W-3' ImPyHpImpy-y-ImPyPyImPy 437) 5' -W G CT C T W-3' ImPyHpPyHp-y-PyImPyImPy 438) 5' -W G CT C A W-3' ImPyHpPyPy-y-HpImPyImPy 439) 5' -W G CT C G W-3' ImPyHpPyIm-y-PyImPyImPy 440) 5' -W G CT C C W-3' ImPyHpPyPy-y-ImImPyImPy 441) 5' -W G CA T T W-3' ImPyPyHpHp-y-PyPyHpImPy 442) 5'-W G CA T A W-3' ImPyPyHpPy-y-HpPyHpImPy 443 ) 5' -W G CA T G W-3' ImPyPyHpIm-y-PyPyHpImPy 444) 5'-W G CA T C W-3' ImPyPyHpPy-y-ImPyHpImPy 445) 5' -W G CA A T W-3' ImPyPyPyHp-y-PyApHpImPy 446) 5'-W G CA A A W-3' ImPyPyPyPy-y-HpHpHpImPy 447) 5'-W G CA A G W-3' ImpyPyPyIm-y-PyHpHpImPy 4 4 8 5 ' G CA A C W- 3 ImPyPyPypy-y- ImHpHpImPy ) -W ' 449) 5' -W G CA G T W-3' ImPyPyImHp-y-PyPyHpImPy 450) 5' -W G CA G A W-3' ImPyPyImPy-y-HpPyHpImPy 4 51 5 ' G CA G G W- 3 ImPyPyImIm-y-PyPyHpImPy ) -W ' 452) 5' -W G CA G C W-3' ImPyPyImPy-y-ImPyFipImPy 453) 5' -W G CA C T W-3' ImPyPyPyHp-y-PyImHpImPy 454) 5'-W G CA C A W-3' ImPyPyPyPy-y-HpImHpImPy 455) 5' -W G CA C G W-3' ImPyPyPyIm-y-PyImHpImPy 456) 5'-W G CA C C W-3' ImPyPyPyPy-y-ImImHpImPy TABLE
27:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' DNA aromatic amino acid sequence sequence 457) 5'-W G C G T T W-3' ImPyImHpHp-y-PyPyPyImPy 458) 5'-W G C G T A W-3' ImPyImHpPy-y-HpPyPyImPy 459) 5' G C G T G W-3' ImPyImHpIm-y-PyPyPyImPy -W
460) 5'-W G C G T C W-3' ImPyImHpPy-y-ImPyPyImPy 46I) 5'-W G C G A T W-3' ImPyImPyHp-y-PyHpPyImPy 462) 5'-W G C G A A W-3' ImPyImPyPy-y-HpHpPyImPy 463) 5'-W G C G A G W-3' ImPyImPyIm-y-PyHpPyImPy 464) 5'-W G C G A C W-3' ImPyImPyPy-y-ImHpPyImPy 465) 5'-W G C G G T W-3' ImPyImImHp-y-PyPyPyImPy 466) 5'-W G C G G A W-3' ImPyImImPy-y-HpPyPyImPy 467) 5'-W G C G C T W-3' ImPyImPyHp-y-PyImPyImPy 468) 5'-W G C G C A W-3' ImPyImPyPy-y-HpImPyImPy 469) 5'-W G C C T T W-3' ImPyPyHpHp-y-PyPyImImPy 470) 5'-W G C C T A W-3' ImPyPyHpPy-y-HpPyImImPy 471) 5'-W G C C T G W-3' ImPyPyHpIm-y-PyPyImImPy 472) 5'-W G C C T C W-3' ImPyPyHpPy-y-ImPyImImPy 473) 5'-W G C C A T W-3' ImPyPyPyHp-y-PyHpImImPy 474) 5'-W G C C A A W-3' ImPyPyPyPy-y-HpHpImImPy 475) 5'-W G C C A G W-3' ImPyPyPyIm-y-PyHpImImPy 47 6 5' G C C A C W- 3 ImPyPyPyPy-y- ImHpImImPy ) -W ' 477) 5'-W G C C G T W-3' ImPyPyImHp-y-PyPyImImPy 478) 5'-W G C C G A W-3' ImPyPyImPy-y-HpPyImImPy 479) 5' G C C C T W-3' Ir~iPyPyPyHp-y-PyImImImPy -W
480) 5' G C C C A W-3' ImPyPyPyPy-y-HpImImImPy -W
G25) 5' G C G G G W-3' ImPyImImIm-y-PyPyPyImPy -W
G26) 5' G C G G C W-3' ImPyImImPy-y-ImPyPyImPy -W
G27) 5'-W G C G C G W-3' ImPyImPyIm-y-PyImPyImPy G28) 5' G C G C C W-3' ImPyImPyPy-y-ImImPyImPy -W
G29) 5' G C C G G W-3' ImPyPyImIm-y-PyPyImImPy -W
G30) 5'-W G C C G C W-3' ImPyPyImPy-y-ImPyImImPy G31) 5' G C C C G W-3' ImPyPyPyIm-y-PyImImImPy -W
G32) 5' G C C C C W-3' ImPyPyPyPy-y-ImImImImPy -W
TABLE 28:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGWNNW-3' DNA aromatic amino acid sequence sequence 481) 5'-W C G T T T W-3' PyImHpHpHp-y-PyPypypylm 482) 5' C G T T A W-3' PyImHpHppy-y-HpPyPyPyIm =W
483) 5'-W C G T T G W-3' PyImHpHpIm-y-PyPypypylm 484) 5'-W C G T T C W-3' PyImHpHpPy-y-ImPyPyPyIm 485) 5' C G T A T W-3' PyImHpPyHp-y-pyHpPyPyIm -W
486) 5'-W C G T A A W-3' PyImHpPyPy-y-HpHpPyPyIm 487) 5' C G T A G W-3' PyImHpPyIm-y-PyHpPyPyIm -W
488) 5'-W C G T A C W-3' PyImHpPyPy-y-ImHpPyPyIm 489) 5'-W C G T G T W-3' PyImHpImHp-y-PyPypypylm 490) 5' C G T G A W-3' PyImHpImPy-y-HpPyPyPyIm -W
491) 5' C G T G G W-3' PyImHpImIm-y-PyPyPyPyIm -W
492) 5' C G T G C W-3' PyImHpImPy-y-ImPyPyPyIm -W
493} 5' C G T C T W-3' PyImHpPyHp-y-PyImPyPyIm -W
494) 5'-W C G T C A W-3' PyImHpPyPy-y-HpImPyPyIm 495) 5'-W C G T C G W-3' PyImHpPyIm-y-PyImPyPyIm 496) 5' C G T C C W-3' PyImHpPyPy-y-ImImPypyIm -W
497) 5'-W C G A T T W-3' PyImPyHpHp-y-PyPyHpPyIm 498) 5' C G A T A W-3' PyImPyHpPy-y-HpPyHpPyIm -W
499) 5' C G A T G W-3' PyImPyHpIm-y-PyPyHpPyIm -W
500) 5' C G A T C W-3' PyImPyHpPy-y-ImPyHpPyIm -W
501) 5'-W C G A A T W-3' PyImPyPyHp-y-PyHpHpPyIm 502) 5'-W C G A A A W-3' PyImPyPyPy-y-HpHpHpPyIm 503) 5'-W C G A A G W-3' PyImPyPyIm-y-PyHpHpPyIm 504) 5'-W C G A A C W-3' PyImPyPyPy-y-ImHpHpPyIm 505) 5'-W C G A G T W-3' PyImPyImHp-y-PyPyHpPyIm 506) 5'-W C G A G A W-3' PyImPyImPy-y-HpPyHpPyIm 507) 5'-W C G A G G W-3' PyImPyImIm-y-PyPyHpPyIm 508) 5' C G A G C W-3' PyImPyImPy-y-ImPyHpPyIm -W
509) 5' C G A C T W-3' PyImPyPyHp-y-PyImHpPyIm -W
510) 5' C G A C A W-3' PyImPyPyPy-y-HpImHpPyIm -W
511) 5' C G A C G W-3' PyImPyPyIm-y-PyImHpPyIm -W
512) 5' C G A C C W-3' PyImPyPyPy-y-ImImHpPyIm -W
TABLE
29:
10-ring Hairpin Polyanudes for recognition of 7-by 5'-WCGSNNW-3' DNA aromatic amino acid sequence sequence 513) 5'-W C G G T TW-3' PyImImHpHp-y-PyPyPyPyIm 514) 5'-W C G G T AW-3' PyImImHpPy-y-HppyPypylm 515) 5' C G G T GW-3' PyImImHpIm-y-pypypypylm -W
516) 5'-W C G G T CW-3' PyImImHpPy-y-ImPyPyPyIm 517) 5'-W C G G A TW-3' PyImImPyHp-y-PyHpPyPyIm 518) 5' C G G A AW-3' PyImImPyPy-y-HpHpPyPyIm -W
519) 5' C G G A GW-3' PyImImPyIm-y-PyHpPyPyIm -W
520) 5'-W C G G A CW-3' PyImImPyPy-y-ImHpPyPyIm 521) 5' C G G G TW-3' PyImImImHp-y-PyPyPyPyIm -W
522) 5'-W C G G G AW-3' PyImImImPy-y-HpPyPyPyIm 523) 5' C G G C TW-3' PyImImPyHp-y-PyImPyPyIm -W
524) 5'-W C G G C AW-3' PyImImPyPy-y-HpImPyPyIm 525) 5'-W C G C T TW-3' PyImPyHpHp-y-PyPyImPyIm 526) 5' C G C T AW-3' PyImPyHpPy-y-HpPyImPyIm -W
527) 5'-W C G C T GW-3' PyImPyHpIm-y-PyPyImPyIm 528) 5' C G C T CW-3' PyImPyHpPy-y-ImPyImPyIm -W
529) 5' C G C A TW-3' PyImPyPyHp-y-PyHpImPyIm -W
530) 5'-W C G C A AW-3' PyImPypyPy-y-HpHpImPyIm 531) 5' C G C A GW-3' PyImPyPyIm-y-PyHpImPyIm -W
532) 5'-W C G C A CW-3' PyImPyPyPy-y-ImHpImPyIm 533) 5'-W C G C G TW-3' PyImPyImHp-y-PyPyImPyIm 534) 5'-W C G C G AW-3' PyImPyImPy-y-HpPyImPyIm 535) 5'-W C G C C TW-3' PyImPyPyAp-y-PyImImPyIm 536) 5'-W C G C C AW-3' PyImPyPyPy-y-HpImImPyIm G33) 5'-W C G G G GW-3' PyImImImIm-y-PyPyPyPyIm G34) 5'-W C G G G CW-3' PyImImImPy-y-ImPyPyPyIm G35) 5' C G G C GW-3' PyImImPyIm-y-PyImPyPyim -W
G36) 5'-W C G G C CW-3' PyImImPyPy-y-ImImPyPyIm G37) 5'-W C G C G GW-3' PyImPyImIm-y-PyPyImPyIm G38) 5' C G C G CW-3' PyImPyImPy-y-ImPyImPyIm -W
G39) 5' C G C C GW-3' PyImPyPyIm-y-PyImImPyim -W
G40) 5' C G C C CW-3' PyImPyPyPy-y-ImImImPyim -W
TABLE
30:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' DNA aromatic amino acid sequence sequence 537) 5'-W C TT T T W-3' PyHpHpHpHp-y-PyPypypyIm 538) 5'-W C TT T A W-3' PyHpHpHpPy-y-IipPyPyPyIm 539) 5'-W C TT T G W-3' PyHpHpHpIm-y-PyPyPyPyIm 540) 5'-W C TT T C W-3' PyHpHpHpPy-y-ImPyPyPyIm 541) 5'-W C TT A T W-3' PyHpHpPyHp-y-PyHpPyPyIm 542) 5'-W C TT A A W-3' PyHpHpPyPy-y-HpHpPyPyIm 543) 5'-W C TT A G W-3' PyHpHppyIm-y-PyHpPyPyIm 544) 5'-W C TT A C W-3' PyHpHpPyPy-y-ImHpPyPyIm 545) 5'-W C TT G T W-3' PyHpHpImHp-y-PyPyPypylm 546) 5'-W C TT G A W-3' PyHpHpImPy-y-HpPyPyPyIm 547) 5'-W C TT G G W-3' PyHpHpImIm-y-PyPyPypylm 548) 5'-W C TT G C W-3' PyHpHpImPy-y-ImpyPyPyIm 549) 5'-W C TT C T W-3' PyHpHpPyHp-y-PyImpyPyIm 550) 5'-W C TT C A W-3' PyHpHpPyPy-y-HpImPyPyIm 551) 5'-W C TT C G W-3' PyHpHpPyIm-y-pylmpyPyIm 552) 5'-W C TT C C W-3' PyHpHppyPy-y-ImImPyPyIm 553 ) 5' -W C TA T T W-3' PyHpPyHpHp-y-PyPyHpPyIm 554) 5'-W C TA T A W-3' PyHpPyHpPy-y-HpPyHpPyIm 555) 5'-W C TA T G W-3' PyHpPyHpIm-y-PyPyHpPyIm 556) 5'-W C TA T C W-3' PyHpPyHpPy-y-ImPyHppyIm 557) 5'-W C TA A T W-3' PyHpPyPyHp-y-PyHpHpPyIm 558) 5'-W C TA A A W-3' PyHpPyPyPy-y-HpHpHpPyIm 559) 5'-W C TA A G W-3' PyHpPyPyIm-y-PyHpHpPyIm 560) 5'-W C TA A C W-3' PyHpPyPyPy-y-ImHpHpPyIm 561) 5'-W C TA G T W-3' PyHppyImHp-y-PyPyHpPyIm 562) 5'-W C TA G A W-3' PyHpPyImpy-y-HpPyHpPyIm 563) 5'-W C TA G G W-3' PyHpPyImIm-y-PyPyHpPyIm 564) 5' -W C TA G C W-3' PyHpPyImPy-y-ImPyHpPyIm 565) 5'-W C TA C T W-3' PyHpPyPyHp-y-PyImHpPyIm 566) 5' -W C TA C A W-3' PyHpPyPyPy-y-HpImHpPyIm 567) 5'-W C TA C G W-3' PyHpPyPyIm-y-PyImHpPyIm 568) 5' -W C TA C C W-3' PyHpPyPyPy-y-ImImHpPyIm TABLE
31:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTSNNW-3' DIVA aromatic amino acid sequence sequence 569) 5'-W CT G T T W-3' PyHpImHpHp-y-PyPyPyPyIm 570) -5'-W CT G T A W-3' PyIipImHpPy-y-HpPyPyPyIm 571) 5'-W CT G T G W-3' PyHpImHpIm-y-PyPyPyPyIm 572) 5'-W CT G T C W-3' PyHpImHpPy-y-ImPyPyPyIm 573) 5'-W CT G A T W-3' PyHpImPyHp-y-PyHpPyPyIm 574) 5'-W CT G A A W-3' PyHpImPyPy-y-HpHpPyPyIm 575) 5' -W CT G A G W-3' PyHpImPyIm-y-PyHpPyPyIm 576) 5'-W CT G A C W-3' PyHpImPyPy-y-ImHpPyPyIm 577) 5'-W CT G G T W-3' PyHpImImHp-y-PyPyPyPyIm 578) 5'-W CT G G A W-3' PyHpImImPy-y-HpPyPyPyIm 579) 5'-W CT G C T W-3' PyHpImPyHp-y-PyImPyPyIm 580) 5'-W CT G C A W-3' PyHpImPyPy-y-HpImPyPyIm 581) 5'-W CT ~GG G W-3' PyHpImImIm-y-PyPyPyPyIm 582) 5'-W CT G G C W-3' PyHpImImPy-y-ImPyPyPyIm 583) 5'-W CT G C G W-3' PyHpImPyIm-y-PyImPyPyIm 584) 5'-W CT G C C W-3' PyHpImPyPy-y-ImImPyPyIm 585) 5' -W CT C T T W-3' PyHpPyHpHp-y-PyPyImPyIm 586) 5'-W CT C T A W-3' PyHpPyHpPy-y-HpPyImPyIm 587) 5'-W CT C T G W-3' PyHpPyHpIm-y-PyPyImPyIm 588) 5' -W CT C T C W-3' PyHpPyHpPy-y-ImPyImPyIm 589) 5'-W CT C A T W-3' PyHpPyPyHp-y-PyHpImPyIm 590) 5'-W CT C A A W-3' PyHpPyPyPy-y-HpHpImPyIm 591) 5' -W CT C A G W-3' PyHpPyPyIm-y-PyHpImPyIm 592) 5'-W CT C A C W-3' PyHpPyPyPy-y-ImHpImPyIm 593) 5'-W CT C G T W-3' PyHpPyImHp-y-PyPyImPyIm 594) 5' -W CT C G A W-3' PyHpPyImPy-y-HpPyImPyIm 595) 5'-W CT C C T W-3' PyHpPyPyHp-y-PyImImPyIm 596) 5'-W CT C C A W-3' PyHpPyPyPy-y-HpImImPyIm 597) 5'-W CT C G G W-3' PyHpPyImIm-y-PyPyImPyIm 598) 5'-W CT C G C W-3' PyHpPyImPy-y-ImPyImPyIm 599) 5' -W CT C C G W-3' PyHpPyPyIm-y-PyImImPyIm 600) 5'-W CT C C C W-3' PyHpPyPyPy-y-ImImImPyIm TABLE
32:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCAWNNW-3' DNA aromatic amino acid sequence sequence 601) 5'-W C A T T TW-3' PypyHpHpHp-y-PyPyPyHpIm 602) '5'-W C A T T AW-3' PyPyHpHpPy-y-HpPyPyHpIm 603) 5'-W C A T T GW-3' PypyHpHpIm-y-PyPyPyHpIm 604) 5'-W C A T T CW-3' PyPyHpHppy-y-ImPyPyHpIm 605) 5' C A T A TW-3' PyPyHpPyHp-y-PyHpPyHpIm -W
606) 5'-W C A T A AW-3' pypyHpPyPy-y-HpHpPyHpIm 607) 5'-W C A T A GW-3' PyPyHpPyIm-y-PyHpPyHpIm 608) 5' C A T A CW-3' PyPyHpPyPy-y-ImHppyHpIm -W
609) 5' C A T G TW-3' PyPyHpImHp-y-PyPyPyHpIm -W
610) 5'-W C A T G AW-3' PyPyHpImPy-y-HpPypyHpIm 611) 5' C A T G GW-3' PyPyHpImIm-y-PypypyHpIm -W
612) 5' C A T G CW-3' PyPyHpImpy-y-ImPyPyHpIm -W
613) 5'-W C A T C TW-3' pyPyHpPyHp-y-PyImPyHpIm 614) 5' C A T C AW-3' PyPyHpPyPy-y-HpImPyHpIm -W
615) 5' C A T C GW-3' PypyHpPyIm-y-PyImPyHpIm -W
616) 5' C A T C CW-3' PyPyHpPyPy-y-ImImPyHpIm -W
617) 5' C A A T TW-3' PyPyPyHplip-y-pyPyHpHpIm -W
618) 5' C A A T AW-3' PyPyPyHpPy-y-HpPyHpHpIm -W
619) 5' C A A T GW-3' PyPyPyHpIm-y-PypyHpHpIm -W
620) 5'-W C A A T CW-3' PyPypyHpPy-y-ImPyHpHpIm 621) 5'-W C A A A TW-3' PypypypyHp-y-PyHpHpHpIm 622) 5'-W C A A A AW-3' PyPypypypy-y-HpHpHpHpIm 623) 5'-W C A A A GW-3' PyPyPypylm-y-PyHpHpHpIm 624) 5' C A A A CW-3' pyPyPypypy-y-I~pgpHpIm -W
625) 5'-W C A A G TW-3' PyPyPyImHp-y-pyPyHpHpIm 626) 5'-W C A A G AW-3' PypypylmPy-y-HpPyHpHpIm 627) 5'-W C A A G GW-3' PyPyPyImIm-y-PyPyHpHpIm 628) 5'-W C A A G CW-3' PyPypyImPy-y-ImPyHpHpIm 629) 5' C A A C TW-3' PyPypypygp-y-pyl~pHpIm -W
630) 5' C A A C AW-3' pyPypypypy-y-HpImHpHpIm -W
631) 5' C A A C GW-3' PyPypypyim-y-PyImHpHpIm -W
632) 5'-W C A A C CW-3' PyPypypypy-y-ImImHpHpIm TABLE 10-ring 33: Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' DNA aromatic amino acid sequence sequence 633) 5' -W CA G T T W-3' PyPyImHpHp-y-PyPyPyHpIm 634) ~5' CA G T A W-3' PyPyImHpPy-y-HpPyPyHpIm -W
635) 5' -W CA G T G W-3' PyPyImHpIm-y-PyPyPyHpIm 636) 5'-W CA G T C W-3' PyPyImHpPy-y-ImPyPyHpIm 637) 5'-W CA G A T W-3' PyPyImPyHp-y-PyHpPyHpIm 638) 5'-W CA G A A W-3' PyPyImPyPy-y-HpHpPyHpIm 639) 5' -W CA G A G W-3' PyPyImPyIm-y-PyHpPyHpIm 640) 5' -W CA G A C W-3' PyPyImPyPy-y-ImHpPyHpIm 641) 5' -W CA G G T W-3' PyPyImImHp-y-PyPyPyHpIm 642) 5'-W CA G G A W-3' PyPyImImPy-y-HpPyPyHpIm 643) 5'-W CA G C T W-3' PyPyImPyHp-y-PyImPyHpIm 644) 5' -W CA G C A W-3' PyPyImPyPy-y-HpImPyHpIm 645) 5'-W CA G G G W-3' PyPyImImIm-y-PyPyPyHpIm 646) 5' -W CA G G C W-3' PyPyImImPy-y-ImPyPyHpIm 647) 5'-W CA G C G W-3' PyPyImPyIm-y-PyImPyHpIm 648) 5'-W CA G C C W-3' PyPyImPyPy-y-ImImPyHpIm 649) 5' -W CA C T T W-3' PyPyPyHpFip-y-PyPyImHpIm 650) 5' -W CA C T A W-3' PyPyPyHpPy-y-HpPyImHpIm 651) 5' -W CA C T G W-3' PyPyPyHpIm-y-PyPyImHpIm 652) 5'-W CA C T C W-3' PyPyPyHpPy-y-ImPyimHpim 653) 5'-W CA C A T W-3' PyPyPyPyHp-y-PyHpImHpIm 654) 5' -W CA C A A W-3' PyPyPyPyPy-y-HpHpImHpIm 655) 5'-W CA C A G W-3' ~PyPyPyPyIm-y-PyHpImHpIm 656) 5'-W CA C A C W-3' PyPyPyPyPy-y-ImHpImHpIm 657 5' -W CA C G T W-3' PyPyPyImHp-y-PyPyImHpIm ) 658) 5' -W CA C G A W-3' PyPyPyImPy-y-HpPyImHpIm 659) 5' -W CA C C T W-3' PyPyPyPyHp-y-PyImImHpIm 660) 5' -W CA C C A W-3' PyPyPyPyPy-y-HpImImHpIm 661) 5' -W CA C G G W-3' PyPyPyImIm-y-PyPyImHpIm 662) 5'-W CA C G C W-3' PyPyPyImPy-y-ImPyImHpIm 663) 5'-W CA C C G W-3' PyPyPyPyIm-y-PyImImHpIm 664) 5' -W CA C C C W-3' PyPyPyPyPy-y-ImImImHpIm 'TABLE
34:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCWNNW-3' DNA aromatic anuno acid sequence sequence 665) 5'-W C C T T TW-3' PyPyHpHpHp-y-PyPypylmim 666) ~5'-W C C T T AW-3' PyPyHpHpPy-y-HpPyPyImIm 667) 5'-W C C T T GW-3' PyPyHpHpIm-y-PypypylmIm 668) 5' C C T T CW-3' PyPyHpHpPy-y-ImPyPyImIm -W
669) 5'-W C C T A TW-3' PyPyHpPyHp-y-PyHpPyImIm 670) 5'-W C C T A AW-3' PyPyHpPyPy-y-HpHpPyImIm 671) 5'-W C C T A GW-3' PyPyHpPyIm-y-PyHpPyImIm 672) 5'-W C C T A CW-3' PypyHpPyPy-y-ImHpPyImIm 673) 5'-W C C T G TW-3' PyPyHpImHp-y-PyPypyImlm 674) 5'-W C C T G AW-3' PyPyHpImPy-y-HpPyPyImIm 675) 5'-W C C T G GW-3' PyPyHpImIm-y-PyPypyImIm 676) 5' C C T G CW-3' PyPyHpImPy-y-ImPyPyImIm -W
677) 5'-W C C T C TW-3' PyPyHpPyHp-y-PyImPyImIm 678) 5'-W C C T C AW-3' PyPyHpPyPy-y-HpImPyImIm 679) 5'-W C C T C GW-3' PyPyHpPyIm-y-PyImPyImIm 680) 5'-W C C T C CW-3' PyPyHpPyPy-y-ImImPyImIm 681) 5'-W C C A T TW-3' PyPypyHpHp-y-PyPyHpImIm 682) 5' C C A T AW-3' PyPyPyHpPy-y-HpPyHpImIm -W
683) 5'-W C C A T GW-3' PyPyPyHpIm-y-PyPyHpImIm 684) 5'-W C C A T CW-3' PyPyPyHpPy-y-ImPyHpImIm 685) 5'-W C C A A TW-3' PyPyPyPyHp-y-PyHpHpImIm 2S 686) 5'-W C C A A AW-3' PyPyPyPyPy-y-HpHpHpImIm 687) 5'-W C C A A GW-3' PyPypypylm-y-pyHpHpImIm 688) 5'-W C C A A CW-3' PyPyPyPyPy-y-ImHpHpImIm 689) 5'-W C C A G TW-3' PyPyPyImHp-y-PyPyHpImIm 690) 5'-W C C A G AW-3' PyPyPyImPy-y-HpPyHpImIm 691) 5'-W C C A G GW-3' PyPyPyImIm-y-PyPyHpImIm 692) 5' C C A G CW-3' PyPyPyImPy-y-ImPyHpImIm -W
693) 5'-W C C A C TW-3' PyPyPyPyHp-y-PyImHpImIm 694) 5'-W C C A C AW-3' PyPyPyPyPy-y-HpImHpImIm 695) 5'-W C C A C GW-3' pyPypypylm-y-pyImHpImIm 696) 5' C C A C CW-3' PyPyPyPypy-y-ImImHpImIm -W
WO 98!37067 PCT/US98/01714 TABLE
35:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' DNA aromatic amino acid sequence sequence 697) 5'-W C CG T T W-3' PyPyImHpHp-y-PyPypyImIm 698) ~5' C CG T A W-3' PyPyImHpPy-y-HpPyPyImIm -W
699) 5' C CG T G W-3' PyPyImHpIm-y-PyPyPyImIm -W
700) 5' C CG T C W-3' PyPyImHppy-y-ImPyPyImIm -W
701) 5' C CG A T W-3' PyPyImPyHp-y-PyHpPyImIm -W
702) 5' C CG A A W-3' PyPyImPyPy-y-HpHpPyImIm -W
703) 5'-W C CG A G W-3' PyPyImPyIm-y-PyHpPyImIm 704) 5' C CG A C W-3' PyPyImPyPy-y-ImHpPyImIm -W
705) 5' C CG G T W-3' PyPyImImHp-y-PyPyPyImIm -W
706) 5' C CG G A W-3' PyPyImImPy-y-HpPyPyImIm -W
707) 5' C CG C T W-3' PyPyImPyHp-y-PyImPyImIm -W
708) 5' C CG C A W-3' PyPyImPyPy-y-HpImPyImIm -W
709) 5' C CC T T W-3' PyPyPyHpHp-y-PyPyImImIm -W
710) 5' C CC T A W-3' PyPyPyHpPy-y-HpPyImImIm -W
711) 5' C CC T G W-3' PyPyPyHpIm-y-PyPyImImIm -W
712) 5' C CC T C W-3' PyPyPyHpPy-y-ImPyImImIm -W
713) 5' C CC A T W-3' PypyPyPyHp-y-PyHpImImIm -W
714) 5' C CC A A W-3' PyPyPyPyPy-y-HpHpImImIm -W
715) 5' C CC A G W-3' PyPyPyPyIm-y-PyHpImImIm -W
716) 5' C CC A C W-3' PyPyPyPyPy-y-ImHpImImIm -W
717 ) 5' C CC G T W-3' PyPyPyImHp-y-PyPyImImIm -W
718 ) 5' C CC G A W-3 ' PyPyPyImPy-y-HpPyImImIm -W
719) 5' C CC C T W-3' PyPyPyPyHp-y-PyImImImIm -W
720) 5' C CC C A W-3' PyPyPyPypy-y-HpImImImIm -W
G41) 5' C CG G G W-3' PyPyImImIm-y-PyPyPyImIm -W
G42) 5'-W C CG G C W-3' PyPyImImPy-y-ImPyPyImIm G43) 5' C CG C G W-3' PyPyImPyIm-y-PyImPyImIm -W
G44) 5' C CG C C W-3' PyPyImPyPy-y-ImImPyImIm -W
G45) 5' C CC G G W-3' PyPyPyImIm-y-PyPyImImIm -W
G46) 5' C CC G C W-3' PyPyPyImPy-y-ImPyImImIm -W
G47) 5'-W C CC C G W-3' PyPyPyPyIm-y-PyImImImIm G48) 5'-W C CC C C W-3' PyPyPyPyPy-y-ImImImImIm TABLE
5:
8-ring Hairpin Polyamides for recognition of 6-by S'-WGSNNW-3' DNA aromatic amino acid sequence sequence 33) 5'-W G G T TW-3' ImImHpHp-y-pyPypypy 34) 5'-W G G T AW-3' ImImHpPy-y-HpPyPyPy 35) 5' G G T GW-3' ImImHpIm-y-PyPyPyPy -W
3 6 ) 5 G G T CW- 3 ' ImImHpPy-y- ImPyPyPy ' -W
37) 5'-W G G A TW-3' ImImPyHp-y-PyHpPyPy 38) 5'-W G G A AW-3' ImImPyPy-y-HpHpPyPy 39) 5' G G A GW-3' ImImPyIm-y-PyHpPyPy -W
40) 5' G G A CW-3' ImImPyPy-y-ImHpPyPy -W
41) 5'-W G G G TW-3' ImImImHp-y-PyPypypy 42) 5'-W G G G AW-3' ImImImPy-y-HppyPypy 43) 5'-W G G C TW-3' ImImPyHp-y-PyImPyPy 44) 5' G G C AW-3' ImImPyPy-y-HpImPyPy -W
45) 5'-W G C T TW-3' ImPyHpHp-y-PyPyImPy 46) 5'-W G C T AW-3' ImPyHpPy-y-HpPyImPy 47) 5' G C T GW-3' ImPyHpIm-y-PyPyImPy -W
48) 5'-W G C T CW-3' ImPyHpPy-y-ImPyImPy 49) 5'-W G C A TW-3' ImPyPyHp-y-PyHpImPy 50) 5'-W G C A AW-3' ImPyPyPy-y-HpHpImPy 51) 5' G C A GW-3' ImPyPyIm-y-PyHpImPy -W
52) 5'-W G C A CW-3' ImPyPyPy-y-ImHpImPy 53) 5'-W G C G TW-3' ImPyImHp-y-PypyImPy 54) 5'-W G C G AW-3' ImPyImPy-y-HpPyImPy 55) 5'-W G C C TW-3' ImPyPyHp-y-pyImImPy 56) 5'-W G C C AW-3' ImPyPyPy-y-HpImImPy G1) 5'-W G G G GW-3' ImImImIm-y-PyPypypy G2) 5'-W G G G CW-3' ImImImPy-y-ImPyPyPy G3) 5'-W G G C GW-3' ImImPyIm-y-PyImPyPy G4) 5'-W G G C CW-3' ImImPyPy-y-ImImPyPy G5) 5'-W G C G GW-3' ImPyImIm-y-PyPyImPy G6) 5'-W G C G CW-3' ImPyImPy-y-ImPyImPy G7) 5' G C C GW-3' ImPyPyIm-y-PyImImPy -W
G8) 5'-W G C C CW-3' ImPyPyPy-y-ImImImPy TABLE :
6 8-ring Hairpin Polyamides for recognition of 6-by 5'-WTWNNW-3' DNA aromatic amino acid sequence sequence 57) 5'-W TT T T W-3' HpHpHpHp-y-PYPyPyPy 5 8 ) 5 ' TT T A W- 3 ' HpHpHpPy-y-HpPypypy -W
59) 5'-W TT T G W-3' HpHpHpIm-y-PyPypypy 60) 5'-W TT T C W-3' HpHpHpPy-y-ImPyPypy 61) 5'-W TT A T W-3' HpHpPYHp-y-PyHpPyPy 62) 5'-W TT A A W-3' HpHpPYPy-y-HpHpPYPy 63) 5'-W TT A G W-3' HpHpPyIm-y-PyHpPyPy 64) 5'-W TT A C W-3' HpHpPyPy-y-ImHpPYPy 65) 5' -W TT G T W-3' HpHpImHp-y-PyPypypY
66) 5' -W TT G A W-3' HpHpImPy-y-HpPYPypy 67) 5'-W TT G G W-3' HpHpImIm-y-PYPypyPy 6 8 ) 5 ' TT G C W-3 ' HpHpImPy-y- ImPyPyPy -W
69) 5'-W TT C T W-3' HpHpPyHp-y-PyImPYPy 70) 5' -W TT C A W-3' HpHpPYPy-y-HpImPYPy 71 ) 5 ' TT C G W- 3 ' HpHpPyIm-y-PyImPyPy -W
72) 5'-W TT C C W-3' HpHpPyPy-y-ImImPYPy 73) 5'-W TA T T W-3' HpPYHpHp-y-PypyHpPy 74) 5' -W TA T A W-3' HpPyHpPy-y-HpPyHpPy 75) 5'-W TA T G W-3' HpPyHpIm-y-PyPyHpPy 76) 5' -W TA T C W-3' HpPyHppy-y-ImPyHpPy 77) 5'-W TA A T W-3' HpPyPYHp-y-PYHpHpPy 78) 5'-W TA A A W-3' HpPyPyPy-y-HpHpHpPy 79) 5' -W TA A G W-3' HppyPYIm-y-PYHpHpPy 80) 5' -W TA A C W-3' HpPYPYPy-y-ImHpHpPy 81) 5' -W TA G T W-3' HpPyImHp-y-PyPyHpPy 82) 5'-W TA G A W-3' HpPyImPy-y-HpPyHpPy 83) 5'-W TA G G W-3' HpPYImIm-y-PyPYHpPy 84) 5'-W TA G C W-3' HpPyImPy-y-ImPyHpPy 85) 5'-W TA C T W-3' HpPyPyHp-y-PYImHpPy 86) 5'-W TA C A W-3' Hppypypy_y_Hpl~ppy 87) 5'-W TA C G W-3' HpPyPYIm-y-PyImHpPy 88) 5' -W TA C C W-3' HpPyPyPy-y-ImImHpPy TABLE
7:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WTSNNW-3' DNA aromatic amino acid sequence sequence 89 ) 5' T G T T W-3 ' HpImHpHp-y-PyPyPyPy -W
90) 5' T G T A W-3' HpImHpPy-y-HpPyPyPy -W
91) 5'-W T G T G W-3' HpImHpIm-y-PyPyPyPy 92) 5'-W T G T C W-3' HpImHpPy-y-ImPyPyPy 93) 5'-W T G A T W-3' HpImPyHp-y-PyHpPyPy 94) 5'-W T G A A W-3' HpImPyPy-y-HpHpPyPy 95) 5'-W T G A G W-3' HpImPyIm-y-PyHpPyPy 96) 5'-W T G A C W-3' HpImPyPy-y-ImHpPyPy 97) 5'-W T G G T W-3' HpImImHp-y-PyPyPyPy 98) 5'-W T G G A W-3' HpImImPy-y-HpPyPyPy 99) 5'-W T G C T W-3' HpImPyHp-y-PyImPyPy 100) 5' T G C A W-3' HpImPyPy-y-HpImPyPy -W
101) 5' T G G G W-3' HpIm2mIm-y-PyPyPyPy -W
102 ) 5' T G G C W-3 ' HpImImPy-y-ImPyPyPy -W
103) 5'-W T G C G W-3' HpImPyIm-y-PyImPyPy 104) 5'-W T G C C W-3' HpImPyPy-y-ImImPyPy 105) 5'-W T C T T W-3' HpPyHpHp-y-PyPyImPy 106) 5'-W T C T A W-3' HpPyHpPy-y-HpPyImPy 107) 5'-W T C T G W-3' HpPyHpIm-y-PyPyImPy 108) 5' T C T C W-3' HpPyHpPy-y-ImPyImPy -W
109) 5'-W T C A T W-3' HpPyPyHp-y-PyHpImPy 110) 5' T C A A W-3' HpPyPyPy-y-HpHpImPy -W
lIl) 5'-W T C A G W-3' HpPyPyIm-y-PyHpImPy 112) 5'-W T C A C W-3' HpPyPyPy-y-ImHpImPy 113) 5' T C G T W-3' HpPyImHp-y-PyPyImPy -W
114) 5' T C G A W-3' HpPyImPy-y-HpPyImPy -W
115) 5' T C C T W-3' HpPyPyHp-y-PyImImPy -W
116) 5' T C C A W-3' HpPyPyPy-y-HpImImPy -W
117) 5'-W T C G G W-3' HpPyImIm-y-PyPyImPy 118) 5'-W T C G C W-3' HpPyImPy-y-ImPyImPy 119 ) 5 ' T C C G W- 3 ' HpPyPyIm-y-PyImImPy -W
12 0 5' T C C C W- 3 ' HpPyPyPy-y- ImImImPy ) -W
8:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WAWNNW-3' DNA aromatic amino acid sequence sequence 121 ) 5 A T T T W- 3 ' PyHpHpHp-y- Pypypygp ' -W
122) 5' A T T A W-3' PyHpHpPy-y-HpPyPyHp -W
123) 5'-W A T T G W-3' PyHpHpIm-y-PyPyPyHp 124) 5'-W A T T C W-3' PyHpHpPy-y-ImPyPyHp 125) 5'-W A T A T W-3' PyHpPyHp-y-PyHpPyHp 126) 5'-W A T A A W-3' PyHpPyPy-y-HpHpPyHp 127) 5'-W A T A G W-3' pyHppylm-y-pyHppyHp 128) 5' A T A C W-3' PyHpPyPy-y-ImFipPyHp -W
129) 5'-W A T G T W-3' PyHpImHp-y-PyPyPyHp 130) 5'-W A T G A W-3' PyHpImPy-y-HpPyPyHp 131) 5' A T G G W-3' PyHpImIm-y-PypypyHp -W
132) 5'-W A T G C W-3' PyHpImPy-y-ImPyPyHp 233) 5'-W A T C T W-3' PyHpPyHp-y-PyImPyHp 134) 5'-W A T C A W-3' PyHpPyPy-y-HpImPyHp 135) 5' A T C G W-3' PyHpPyIm-y-PyImPyHp -W
136) 5'-W A T C C W-3' PyHpPyPy-y-ImImPyHp 137) 5'-W A A T T W-3' PyPyFlpHp-y-PyPyHpHp 138) 5' A A T A W-3' PyPyHpPy-y-HpPyHpHp -W
139) 5'-W A A T G W-3' PyPyHpIm-y-pypyHpHp 140) 5' A A T C W-3' PyPyHpPy-y-ImPyHpHp -W
141) 5'-W A A A T W-3' PyPyPyHp-y-PyHpHpHp 142) 5'-W A A A A W-3' PyPyPyPy-y-HpHpHpHp 143) 5'-W A A A G W-3' PyPypylm-y-pyHpHpHp 144) 5' A A A C W-3' PyPyPyPy-y-ImHpHpHp -W
145) 5'-W A A G T W-3' PypyImHp-y-PyPyHpHp 146) 5'-W A A G A W-3' PyPyImPy-y-HpPyHpHp 147) 5'-W A A G G W-3' PyPyImIm-y-PypyHpHp 14 8 ) 5 A A G C W- 3 ' PyPyImPy-y- ImPyHpI~Ip ' -W
149) 5' A A C T W-3' pypypyHp_y_pyl~pHp -W
150) 5' A A C A W-3' PyPyPyPy-y-HpImApHp -W
151) 5'-W A A C G W-3' PyPyPyIm-y-PyImHpHp 152) 5'-W A A C C W-3' Pypypypy-y-ImImHpHp TABLE
9:
8-ring-Hairpin Polyamides for recognition of 6-by 5'-WASNNW-3' DNA aromatic amino acid sequence sequence 153) 5' A GT T W-3' PyImHpHp-y-PyPyPyHp -W
154) 5' A GT A W-3' PyImHpPy-y-HpPyPyHp -W
155) 5'-W A GT G W-3' PyImHpIm-y-PyPyPyHp 156) 5'-W A GT C W-3' PyImHpPy-y-ImPyPyHp 157 ) 5' A GA T W-3' PyImPyHp-y-PyHpPyHp -W
158) 5' A GA A W-3' PyImPyPy-y-HpHpPyHp -W
159) 5' A GA G W-3' PyImPyIm-y-PyHpPyHp -W
160) 5' A GA C W-3' PyImPyPy-y-ImHpPyHp -W
161) 5' A GG T W-3' PyImImHp-y-PyPyPyHp -W
162) 5' A GG A W-3' PyImImPy-y-HpPyPyHp -W
163) 5'-W A GC T W-3' PyImPyHp-y-PyImPyHp 164) 5' A GC A W-3' PyImPyPy-y-HpImPyHp -W
165) 5' A GG G W-3' PyImImIm-y-PyPyPyHp -W
166) 5' A GG C W-3' PyImImPy-y-ImPyPyHp -W
167) 5'-W A GC G W-3' PyImPyIm-y-PyImPyHp 16 8 ) 5 A GC C W- 3 ' PyImPyPy-y- ImImPyHp ' -W
169) 5' A CT T W-3' PyPyHpHp-y-PyPyImHp -W
170) 5' A CT A W-3' PyPyHpPy-y-HpPyImHp -W
171) 5' A CT G W-3' PyPyHpIm-y-PyPyImHp -W
172) 5'-W A CT C W-3' PyPyHpPy-y-ImPyImHp 173 ) 5' A CA T W-3 ' PyPyPyHp-y-PyHpImHp -W
174) 5' A CA A W-3' PyPyPyPy-y-HpHpImHp -W
175) 5' A CA G W-3' PyPyPyIm-y-PyHpImHp -W
176) 5'-W A CA C W-3' PyPyPyPy-y-ImHpImHp 177) 5' A CG T W-3' PyPyImHp-y-PyPyImHp -W
178) 5' A CG A W-3' PyPyImPy-y-HpPyImHp -W
179) 5' A CC T W-3' PyPyPyHp-y-PyImImHp -W
180) 5'-W A CC A W-3' PyPyPyPy-y-HpImImHp 181) 5' A CG G W-3' PyPyImIm-y-PyPyImHp -W
182) 5'-W A CG C W-3' PyPyImPy-y-ImPyImHp 183) 5' A CC G W-3' PyPyPyIm-y-PyImImHp -W
184) 5'-W A CC C W-3' PyPyPyPy-y-ImImImHp 'FABLE
10:
8-ring -Hairpin Polyamides for recogmhon of 6-by 5'-WCWNNW-3' DNA aromatic amino acid sequence sequence 185) 5'-W CT T T W-3' PyHpHpHp-y-Pypypylm 186} 5'-W CT T A W-3' PyHpHpPy-y-HpPypyIm 187) 5'-W CT T G W-3' PyHpHpIm-y-PyPyPyIm 18 8 ) 5 ' CT T C W- 3 ' PyHpHpPy-y- ImPyPyIm -W
189) 5' CT A T W-3' PyHpPyHp-y-PyHpPyIm -W
190) 5' CT A A W-3' pyHppypy-y-HpHpPyIm -W
191) 5' CT A G W-3' PyHpPyIm-y-pyHpPyIm -W
192} 5' CT A C W-3' PyHpPyPy-y-ImHpPyIm -W
193) 5'-W CT G T W-3' PyHpImHp-y-pypypylm 194) 5'-W CT G A W-3' PYHpImPy-y-HpPyPyIm 195) 5' CT G G W-3' PYHpImIm-y-Pypypylm -W
196) 5' CT G C W-3' PyHpImPy-y-ImPyPyIm -W
197) 5'-W CT C T W-3' PyHpPyHp-y-PyImPyIm 198) 5' CT C A W-3' PyHpPyPy-y-HpImPyIm -W
199) 5'-W CT C G W-3' PyHpPyIm-y-pyImPyIm 200) 5'-W CT C C W-3' PyHpPyPy-y-ImImPyIm 201) 5' CA T T W-3' PyPyHpHp-y-PypyHpIm -W
202) 5'-W CA T A W-3' PyPyHpPy-y-HpPyHpIm 203} 5'-W CA T G W-3' PyPyHpIm-y-PypyHplm 204) 5'-W CA T C W-3' PYPYHpPY-Y-ImPyHpIm 205) 5' CA A T W-3' PyPyPyHp-y-PyHpHpIm -W
206) 5'-W CA A A W-3' Pypypypy-y-HpHpHpIm 207) 5'-W CA A G W-3' PyPyPyIm-y-PYHpHpIm 208) 5' CA A C W-3' PyPypypy-y-ImHpHpIm -W
209) 5'-W CA G T W-3' PyPyImHp-y-PypyHplm 210) 5' CA G A W-3' PyPyImPy-y-HpPyHpIm -W
211) 5' CA G G W-3' PyPyImIm-y-PyPyHpIm -W
212) 5'-W CA G C W-3' PyPyImPy-y-ImPyHpIm 213) 5'-W CA C T W-3' PyPyPyHp-y-pyImHpIm 214) 5' CA C A W-3' Pypypypy-y-HpImHpIm -W
215) 5' CA C G W-3' PyPypylm-y-PyImHpIm -W
216) 5' CA C C W-3' pypypypy-y-ImImHpIm -W
WO 981370b7 PCT/US98/01714 TABLE
11:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WCSNNW-3' DNA aromatic amino acid sequence sequence 217) 5'-WC G T T W-3' PyImHpHp-y-PyPyPyIm 218) 5'-W~C G T A W-3' PyImHpPy-y-HpPyPyIm 219) 5'-WC G T G W-3' PyImHpIm-y-PyPyPyIm 220) 5'-WC G T C W-3' PyImHpPy-y-ImPyPyIm 221) 5'-WC G A T W-3' PyImPyHp-y-PyHpPyIm 222) 5'-WC G A A W-3' PyImPyPy-y-HpHpPyIm 223) 5'-WC G A G W-3' PyImPyIm-y-PyHpPyIm 224) 5'-WC G A C W-3' PyImPyPy-y-ImHpPyIm 225) 5' C G G T W-3' PyImImHp-y-PyPyPyIm -W
226) 5'-WC G G A W-3' PyImImPy-y-HpPyPyIm 227) 5'-WC G C T W-3' PyImPyHp-y-PyImPyIm 228) 5' C G C A W-3' PyImPyPy-y-HpImPyIm -W
229) 5'-WC C T T W-3' PyPyHpHp-y-PyPyImIm 230) 5' C C T A W-3' PyPyHpPy-y-HpPyImIm -W
231) 5' C C T G W-3' PyPyHpIm-y-PyPyImIm -W
232) 5' C C T C W-3' PyPyHpPy-y-ImPyImIm -W
233) 5'-WC C A T W-3' PyPyPyHp-y-PyHpImIm 234) 5'-WC C A A W-3' PyPyPyPy-y-HpHpImIm 235) 5' C C A G W-3' PyPyPyIm-y-PyHpImIm -W
236) 5'-WC C A C W-3' PyPyPyPy-y-ImHpImIm 237) 5'-WC C G T W-3' PyPyImFip-y-PyPyImIm 238) 5' C C G A W-3' PyPyImPy-y-HpPyImIm -W
239) 5'-WC C C T W-3' PyPyPyHp-y-PyImImIm 240) 5' C C C A W-3' PyPyPyPy-y-HpImImIm -W
G9) 5'-WC G G G W-3' PyImImIm-y-PyPyPyIm G10) 5' C G G C W-3' PyImImPy-y-ImPyPyIm -W
G11) 5' C G C G W-3' PyImPyIm-y-PyImPyIm -W
G12) 5'-WC G C C W-3' PyImPyPy-y-ImImPyIm G13) 5'-WC C G G W-3' PyPyImIm-y-PyPyImIm G14) 5' C C G C W-3' PyPyImPy-y-ImPyImIm -W
G15) 5'-WC C C G W-3' PyPyPyIm-y-PyImImIm G16) 5' C C C C W-3' PyPyPyPy-y-ImImImIm -W
TABLE 12:
8-ring Hairpin Polyamides for recognition of 6-by S'-WGWNNW-3' with included.
(3-substitutions DNA aromatic amino acid sequence sequence 3~i) 5' GT TG W-3' ImHp-~i-Im-y-Pypypypy -W
S 7~3) 5'-W GT AG W-3' ImHp-~3-Im-y-PyHppyPy 9(3) 5' GT GT W-3' Im-~3-ImHp-y-pypypypy -W
10(3) 5' GT GA W-3' Im-~3-ImPy-y-HpPyPyPy -W
I1~3} 5' GT GG W-3' Im-~3-ImIm-y-PyPypypy -W
12(3) 5' GT GC W-3' Im-(3-ImPy-y-ImPyPyPy -W
15(3) 5' GT CG W-3' ImHp-(3-Im-y-PyImPyPy -W
19(3) 5' GA TG W-3' ImPy-~3-Im-y-PyPyHpPy -W
23(3) 5' GA AG W-3' ImPy-~3-Im-y-PyHpHpPy -W
253) 5' GA GT W-3' Im-p-ImHp-y-PypyHppy -W
26(3) 5' GA GA W-3' Im-p-ImPy-y-HpPyHpPy -W
1S 27(3) 5' GA GG W-3' Im-(3-Imlm-y-PyPyHpPy -W
28~i) 5' GA GC W-3' Im-(3-ImPy-y-ImPyHpPy -W
31 5'-W GA GG W-3' R) ImPy-(3- Im-y-pyImHpPy TABLE
13: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WGSNNW-3' with (3-substitutions inchzded.
DNA aromatic amino acid sequence sequence 35(3) 5' G G T G W-3' ImIm-(3-Im-y-PyPyPyPy -W
393) 5' G G A G W-3' ImIm-~-Im-y-PyHpPyPy -W
45(3) 5' G C T T W-3' ImPyHpHp-y-Py-(3-ImPy -W
46(3) 5' G C T A W-3' ImPyIipPy-y-Hp-(3-ImPy -W
47(3) 5' G C T G W-3' ImPyI-IpIm-y-Py-(3-ImPy -W
47(32) 5' G C T G W-3' ImPy-~3-Im-y-Py-(3-ImPy -W
48(3) 5' G C T C W-3' ImPyHpPy-y-Im-(3-ImPy -W
49(3) 5' G C A T W-3' ImPyPyHp-y-Py-(3-ImPy -W
50(3) 5' G C A A W-3 T ImPyPyPy-y-Hp-(3-ImPy -W
513) 5'-W G C A G W-3' ImPyPyIm-y-Py-(3-ImPy 5132) 5' G C A G W-3' ImPy-(3-Im-y-Py-(3-ImPy -W
i5 523) 5' G C A C W-3' ImPyPyPy-y-Im-(3-ImPy -W
533) 5' G C G T W-3' ImPyImHp-y-Py-(3-ImPy -W
53~i2) 5' G C G T W-3' Im-~3-ImHp-y-Py-~3-ImPy -W
543) 5' G C G A W-3' ImPyImPy-y-Hp-R-ImPy -W
54(32) 5' G C G A W-3' Im-p-ImPy-y-Hp-(3-ImPy -W
G3 (3) 5' G G C G W-3' Imlm-~3-Im-y-PyImPyPy -W
G5(3) 5' G C G G W-3' ImPyImIm-y-Py-(3-ImPy -W
G5~i2) 5' G C G G W-3' Im-(3-ImIm-y-Py-(3-ImPy -W
G6~) 5' G C G C W-3' ImPyImPy-y-Im-(3-ImPy -W
G6(32) 5' G C G C W-3' Im-p-ImPy-y-Im-~3-ImPy -W
G7 (3) 5' G C C G W-3' ImPy-~3-Im-y-PyImImPy -W
..__r... _ , , , TABL>14: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WTWNNW-3' with (3-substitutions includ d e DNA quenc e .
se aromatic amino acid sequence 59(3) 5' TT T G W-3' HpHp-(3-Im-y-pypypypy -W
633) 5' TT A G W-3' HpHp-~-Im--W -p y yHppypy 65(3) 5' TT G T W-3' _ _ -W Hp ~ Imp-Y-PYPYPYPY
663) 5' TT G A W-3' Hp-p-ImPy-y-HpPYPyPy -W
673) 5' TT G G W-3' Hp-(3-ImIm-y-pypypypY
-W
68(3) 5' TT G C W-3' -W Hp- ~3- ImPy-y- ImPyPyPy 71(3) 5' TT C G W-3' HpHp-(3-Im-y-PyTmPyPy -W
75(3) 5' TA T G W-3' Hppy_(3-Im-y-pYpyHppy -W
79(3) 5' TA A G W-3' HpPy-(3-Im-y-pyHpHpPy -W
81(3) 5' TA G T W-3' Hp-~i-ImHp-y-PypyHpPy -W
82(3) 5' TA G A W-3' Hp-(3-ImP
-W Y_Y_HPPYHPPY
83(3) 5' TA G G W-3' Hp-J3-ImIm-y-pypygpPy -W
843) 5'-W TA G C W-3' Hp-~3- ImPy-y- ImPyHpPy 87(3) 5' TA C G W-3' HpPy-(3-Im-y-PyImHpPy -W
TABLE 15:
8-ring Hairpin Polyamides for recognition of 6-by 5'-WTSNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 913) 5' T G T G W-3' Hplm-~3-Im-y-PyPyPyPy -W
95(3) 5' T G A G W-3' HpIm-(3-Im-y-PyHpPyPy -W
103(3) 5' T G C G W-3' HpIm-(3-Im-y-PyImPyPy -W
105(3) 5' T C T T W-3' HpPyHpHp-y-Py-~-ImPy -W
106(3) 5' T C T A W-3' HpPyHpPy-y-Hp-(~-ImPy -W
107(3) 5' T C T G W-3' HpPyHpIm-y-Py-(3-ImPy -W
107~i2) 5' T C T G W-3' HpPy-(3-Im-y-Py-(3-ImPy -W
108(3) 5' T C T C W-3' HpPyHpPy-y-Im-(3-ImPy -W
109(3) 5' T C A T W-3' HpPyPyHp-y-Py-(3-ImPy -W
110R) 5' T C A A W-3' HpPyPyPy-y-Hp-p-ImPy -W
111(3} 5' T C A G W-3' HpPyPyIm-y-Py-p-ImPy -W
111(32) 5' T C A G W-3' HpPy-(3-Im-y-Py-(3-ImPy -W
1123) 5' T C A C W-3' HpPyPyPy-y-Im-(3-ImPy -W
113(3) 5' T C G T W-3' HpPyImHp-y-Py-~3-ImPy -W
113(32) 5' T C G T W-3' Hp-(3-ImHp-y-Py-(3-ImPy -W
114(3) 5' T C G A W-3' HpPyImPy-y-Hp-~3-ImPy -W
114(32) 5' T C G A W-3' Hp-(3-ImPy-y-Hp-(3-ImPy -W
1173) 5' T C G G W-3' HpPyImIm-y-Py--ImPy -W
117(32) 5' T C G G W-3' Hp-(3-Imlm-y-Py-(3-ImPy -W
118(3) 5' T C G C W-3' HpPyImPy-y-Im-~3-ImPy -W
118(32) 5' T C G C W-3' Hp-(3-ImPy-y-Im-p-ImPy -W
119(3) 5' T C C G W-3' HpPy-~-Im-y-PyImImPy -W
..~................~...... ~ . ~ ~ ,.» , 'TABLE 16: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WAWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 123(3) 5' A T TG W-3' pygp_~3_Im_y-pypypyHp -W
127(3) 5' A T AG W-3' PyHp-~3-Im-y-PyHpPyHp -W
1293) 5' A T GT W-3' Py-(3-ImHp-y-PyPyPyHp -W
1303) 5' A T GA W-3' Py-~3-ImPy-y-HpPyPyHp -W
131(3) 5' A T GG W-3' Py-(3-ImIm-y-Pypypygp -W
132j3) 5' A T GC W-3' p -W y-p-ImPy-y-ImPyPyHp 1353) 5' A T CG W-3' PyHp-(3-Im-y-PyImPyHp -W
139~i} 5' A A TG W-3' PyPy-(3-Im-y-PyPyHpHp -W
143(3) 5' A A AG W-3' PyPy-~3-Im-y-PyHpHpHp -W
145(3) 5' A A GT W-3' Py-(3-ImHp-y-PypyHpHp -W
146(3) 5' A A GA W-3' Py-~-ImPy-y-HpPyHpHp -W
IS 147p) 5' A A GG W-3' Py-(3-Imlm-y-PyPyHpHp -W
1480 5' A A GC W-3' Py-p-ImPy-y-ImPyHpHp -W
151(3) 5' A A CG W-3' PyPy-~3-Im-y-PyImHpHp -W
_3~,_ 'TABLE
I 7: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WASNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 155(3) 5' A G T G W-3' Pylm-(3-Im-y-PyPyPyHp -W
159(3) 5' A G A G W-3' PyIm-(3-Im-y-PyHpPyHp -W
167~i) 5' A G C G W-3' PyIm-~i-Im-y-PyImPyHp -W
169~i) 5'-W A C T T W-3' PyPyHpHp-y-Py-(3-ImHp 170~i) 5' A C T A W-3' PyPyHpPy-y-Hp-(3-ImHp -W
1713) 5' A C T G W-3' PyPyHpIm-y-Py-(3-ImHp -W
171(32) 5' A C T G W-3' PyPy-p-Im-y-Py-(3-ImHp -W
172(3) 5' A C T C W-3' PyPyHpPy-y-Im-(3-ImF3p -W
173(3) 5' A C A T W-3' PyPyPyHp-y-Py-(3-ImHp -W
1743) 5' A C A A W-3' PyPyPyPy-y-Hp-R-ImHp -W
1753) 5' A C A G W-3' PyPyPyIm-y-Py-~3-ImHp -W
17532) 5' A C A G W-3' Pypy-(3-Im-y-Py-(3-ImHp -W
176(3) 5' A C A C W-3' PyPypyPy-y-Im-(3-ImHp -W
1770 5' A C G T W-3' PyPyImHp-y-Py-(3-ImHp -W
177(32) 5' A C G T W-3' Py-(3-ImHp-y-Py-(3-ImHp -W
178(3) 5' A C G A W-3' PyPyImPy-y-Hp-(3-ImHp -W
178(32) 5' A C G A W-3' Py-(3-ImPy-y-Hp-/3-ImHp -W
1813) 5' A C G G W-3' PyPyImIm-y-Py-(3-ImHp -W
181(32) 5' A C G G W-3' py-(3-Imlm-y-Py-(3-ImHp -W
182(3) 5' A C G C W-3' PyPyImPy-y-Im-R-ImHp -W
182(32) 5' A C G C W-3' Py-(3-ImPy-y-Im-(3-ImHp -W
18332) 5' A C C G W-3' Pypy-~i-Im-y-PyImImHp -W
~... . .
I AI3LP;
I 8: 8-ring Hairpin Polyamides for recognition of 6-by 5'-WCWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 185(3) 5' C T T TW-3' PyHpHpHp-y-Pypy-(3-Im -W
186(3) 5''-WC T T AW-3' PyHpHpPy-y-HpPy-(3-Im 1873) 5' C T T GW-3' PyHpHpIm-y-Pypy-(3-Im -W
187(32) 5' C T T GW-3' p H
-W Y P-~-Im-y-PyPy-(3-Im 188(3) 5' C T T CW-3' pyHpHpPy-y-ImPy-(3-Im -W
189(3) 5' C T A TW-3' PyHpPyHp-y-PyHp-(3-Im -W
1903) 5' C T A AW-3' PyHpPyPy-y-HpHp-~i-Im -W
191(3) 5' C T A GW-3' PyHpPyim-y-PyHp-/3-Im -W
191(32) 5' C T A GW-3' PyHp-(3-Im-y-PyHp-~3-Im -W
192(3) 5' C T A CW-3' PyHpPyPy-y-ImHp-J3-Im -W
193(3) 5' C T G TW-3' PyHpImHp-y-PyPy-~3-Im -W
1932) 5' C T G TW-3' Py-~i-ImHp-y-Pypy-(3-Im -W
194(3) 5' C T G AW-3' PyHpImPy-y-HpPy-(3-Im -W
194(32) 5' C T G AW-3' Py--ImPy-y-HpPy-(3-Im -W
195p) 5' C T G GW-3' PyHpImIm-y-Pypy-~3-Im -W
1952) 5' C T G GW-3' Py-(3-ImIm-y-PyPy-~-Im -W
196(3) 5' C T G CW-3' PyHpImPy-y-ImPy-(3-Im -W
196(32) 5' C T G CW-3' Py-p-ImPy-y-ImPy-(3-Im -W
197(3) 5' C T C TW-3' PyHpPyHp-y-PyIm-(3-Im -W
198(3) 5' C T C AW-3' PyHpPyPy-y-HpIm-(3-Im -W
199(3) 5' C T C GW-3' PyHpPyIm-y-PyIm-(3-Im -W
19932) 5' C T C GW-3' PyHp-(3-Im-y-Pylm-p-Im -W
200(3) 5' C T C CW-3' PyHpPyPy-y-ImIm-(3-Im -W
201(3) 5' C A T TW-3' PyPyHpHp-y-PyPy-~3-Im -W
202(3) 5' C A T AW-3' PyPyHpPy-y-HpPy-~3-Im -W
203~i) 5' C A T GW-3' PyPyHpIm-y-PyPy-~-Im -W
203~i2) 5' C A T GW-3' p p -W Y Y-~-Im-y-PyPy-(3-Im 2043) 5' C A T CW-3' PyPyHpPy-y-ImPy-p-Im -W
205(3) 5' C A A TW-3' PyPyPyHp-y-PyHp-(3-Im -W
2063) 5' C A A AW-3' PyPypypy-y-HpHp-p-Im -W
TABLE 18 (cont}:
8-ring Hairpin Polyamides for 6-by 5'-WCWNNW-3' with (3-substitutions included.
DNA aromatic amino acid sequence sequence 207(3) 5' C A A G W-3' PypyPyIm-y-PyHp-(3-Im -W
207(32) 5' C A A G W-3' PyPy-(3-Im-y-PyHp-(3-Tm -W
2083) 5' C A A C W-3' PyPypyPy-y-ImHp-(3-Im -W
209(3) 5' C A G T W-3' PypyImHp-y-PyPy-~-Im -W
209(32) 5' C A G T W-3' Py-p-ImHp-y-PyPy-(3-Im -W
210(3) 5' C A G A W-3' PyPyImPy-y-HpPy-p-Im -W
210(32) 5' C A G A W-3' Py-p-ImPy-y-HpPy-p-Im -W
211(3) 5' C A G G W-3' PyPyImIm-y-Pypy-(3-Im -W
211(32) 5' C A G G W-3' Py-(3-Imlm-y-PyPy-R-Im -W
212(3) 5' C A G C W-3' PyPyImPy-y-ImPy-(3-Im -W
21232) 5' C A G C W-3' Py-[3-ImPy-y-ImPy-(3-Im -W
213(3) 5' C A C T W-3' PyPyPyHp-y-Pylm-R-Im -W
2143) 5' C A C A W-3' PyPyPyPy-y-HpIm-p-Im -W
2153) 5' C A C G W-3' PyPyPyIm-y-PyIm-~3-Im -W
215(32) 5' C A C G W-3' PyPy-(3-Im-y-PyIm-~-Im -W
216(3) 5' C A C C W-3' PyPyPyPy-y-ImIm-~i-Im -W
1A13Lt:
ly: ~-nng Hairpin Polyamides for recognition of 6-by 5'-WCSNNW-3' with ~3-substitutions included .
DNA aromatic amino acid sequence sequence 217(3) 5' CG T T W-3' PyImHpHp-y-PyPy-(3-Im -W
218(3) 5' CG T A W-3' PyImHpPy-y-HpPy-~-Im -W
219(3) 5' CG T G W-3' PyImHpIm-y-Pypy-(3-Im -W
219(32) 5' CG T G W-3' Pylm-p-Im-y-PyPy-~i-Im -W
220(3) 5' CG T C W-3' PyImHpPy-y-ImPy-(3-Im -W
2210 5' CG A T W-3' PyImPyHp-y-PyHp-~3-Im -W
222(3) 5' CG A A W-3' PyImPYPy-y-HpHp-~3-Im -W
223(3) 5' CG A G W-3' PyImPyIm-y-PyHp-p-Im -W
2232) 5' CG A G W-3' PyIm-~3-Im-y-PyHp-~i-Im -W
224(3) 5' CG A C W-3' PyImPyPy-y-ImHp-~-Im -W
2253) 5' CG G T W-3' PyImImHp-Y-Pypy-~3-Im -W
226(3) 5' CG G A W-3' PyImImPy-Y-HpPy-J3-Im -W
227(3) 5' CG C T W-3' PyImPyHp-y-PyIm-~3-Im -W
228(3) 5' CG C A W-3' PyImPyPy-y-HpIm-(3-Im -W
2293) 5' CC T T W-3' PyPyHpHp-y-Py-(3-ImIm -W
2303) 5' CC T A W-3' PyPyHpPy-y-Hp-p-ImIm -W
2313) 5' CC T G W-3' PyPyHpIm-y-Py-~3-ImIm -W
231(32) 5' CC T G W-3' p p ~~
-W Y Y-t'-Im-y-Py-~3-ImIm 232(3) 5' CC T C W-3' PyPyHpPy-y-Im-~3-ImIm -W
2333) 5' CC A T W-3' PyPyPyHp-y-Py-(3-ImIm -W
234(3) 5' CC A A W-3' PyPypypy-y-Hp-R-ImIm -W
235~i) 5' CC A G W-3' PyPyPyIm-y-Py-p-Imlm -W
235(32) 5' CC A G W-3' p 'p -W Y Y-~-Im-y-Py-~3-Imlm 236(3) 5' CC A C W-3' PyPyPyPy-y-Im-~3-ImIm -W
2370 5' CC G T W-3' PyPyImHp-y-Py-p-ImIm -W
2372) 5' CC G T W-3' Py-(3-ImHp-Y-Py-~-Imlm -W
2383) 5' CC G A W-3' PyPyImPy-y-Hp-(3-ImIm -W
238(32) 5' CC G A W-3' Py-~3-ImPy-y-Hp-~3-ImIm -W
G9~3) 5' CG G G W-3' PyImImIm-y-pypy-~3-Im -W
G10(3) 5' CG G C W-3' PyImImPy-Y-ImPy-(3-Im -W
TABLE 19 (cont): 8-ring Hairpin Poiyamides for recognition of 6-by 5'-WCSNNW-3' with (3-substitutions -included.
DNA sequence aromatic amino acid sequence 611(3) 5' -W C G C G W-3' PyImPyIm-y-PyIm-~3-Im 611(32)5' -W C G C G W-3' Pylm-[3-Im-y-Pylm-/3-Im G12R) 5' -W C G C C W-3' PyImPyPy-'y-ImIm-~3-Im 613(3) 5' -W C C G G W-3' PyPyImIm-y-Py-~3-Imlm 613(32)5' -W C C G G W-3' Py-(3-ImIm-y-Py-~3-ImIm G14~3) 5' -W C C G C W-3' PyPyImPy-y-Im-(3-ImIm G14~2)5' -W C C G C W-3' Py-(3-ImPy-y-Im-(3-Imlm 615(3) 5' -W C C C G W-3' PyPy-(3-Im-y-PyImImim If the process described above of designing a preferred polyamide molecule y-XSX6X~Xg comprising eight aromatic aminoacid residues does not produce a selective polyamide that binds to the target identified DNA sequence with subnanomolar affinity and with a selectivity over mismatch sequences of greater than a factor of ten, a polyamide molecule X 1 X2X3X4X5-y-X6X~XgX9X 1 p having five carboxamide binding pairs can be designed that is 2o selective for a seven base pair identified target 5'-WNI~I~~1NNW-3' sequence. The design and synthesis of the five binding pair polyamide is similar to that of the four binding pair polyamide X1X2X3X4-y-XSX6X~Xg described above.
The polyamide design process, shown schematically in Figure 7 provides a method for designing a ten carboxamide residue molecule comprising five carboxamide binding pairs for selective detection and binding of a target seven base pair 5'- -3' sequence in the minor groove of double stranded DNA. The design process identifies an appropriate polyamide ligand for recognition of a predetermined seven base pair, 5'-VVI'11~TNNNVV-3' sequence with subnanomolar affinity and >10-fold specificity versus mismatch sites. Trauger, J.W., Baird, E.
3o E. Dervan, P.B. describes the recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (/996).
In order to prepare a polyamide molecule specific for an identified seven base pair sequence of double stranded DNA, a user starts the 10-ring hairpin design process that implements the minor groove recognition pairing code summarized in Table 2 above. In the . design process a 5'-WNNNNNW-3' sequence was identified. In a preferred embodiment, the identified sequence was located within a gene promoter. The identified sequence was then defined as S'-WabcdeW-3' in a stepwise process wherein a, b, c, d,and e, were sequentially and independently defined as A, G, C, or T. The structure of the polyamide molecule was then s correspondingly defined by sequentially chosing antiparallel carboxamide binding pairs according to the minor groove pairing code summarized in Table 2 above. Thus, if a was G, then X 1 was defined as Im, and X 1 p was defined as Py. If a was C, then X 1 was defined as Py, and X 1 p was defined as Im. If a was T, then X 1 was def ned as Hp, and X I p was defined as Py. If a was A, then X 1 was defined as Py, and X 1 p was defined as Hp.
Similarly, b was defined as A, G, C, or T and corresponding carboxamide binding pairs were defined. According to the same rules, if b was G, then X2 was defined as Im, and X9 was defined as Py. If b was C, then X2 was defined as Py, and X9 was defined as Im. Likewise, if b was T, then X~ was defined as Hp, and X9 was defined as Py. If b was A, then X2 was defined ~ 5 as Py, and X9 was defined as Hp.
The next step was to define c as A, G, C, or T and then define corresponding carboxamide binding pairs. Following the same rules, if c was G, then X3 was defined as Im, and Xg was defined as Py. If c was C, then X3 was defned as Py, and Xg was defined as Im.
Similarly, if c was T, then X3 was defined as Hp, and Xg was defined as Py. If c was A, then X3 was defined as Py, and Xg was defined as Hp. Similarly, d was defined as A, G, C, or T and the corresponding carboxamide binding pair was defined. According to the above rules, if d was G, then X4 was defined as Im, and X~ was defined as Py. If d was C, then X4 was defined as Py, and X~ was defined as Im. If d was T, then X4 was defined as Hp, and X~
was defined as 25 Py. If d was A, then X4 was defined as Py, and X~ was defined as Hp.
Finally, a was defined as - A, G, C, or T and the corresponding carboxamide binding pair was defined.
According to the above rules, if a was G, then XS was defined as Im, and X6 was defined as Py.
If a was C, then XS was defined as Py, and X6 was defined as Im. If a was T, then XS was defined as Hp, and X6 was defined as Py. If a was A, then XS was defined as Py, and X6 was defined as Hp.
With all ten carboxamide residues that participate in the binding pairs now defined, the designed polyamide X1X2X3X4X5-y-X6X~XgX9Xlp suitable for binding to the identified sequence was synthesized using known techniques. Baird, E. E. & Dervan, P. B.
describes~the solid phase synthesis of polyamides containing imidazole and pyrrole amino acids: J. Am.
Chem. Soc. 118, 6141-6146 (1996); also see PCT US 97/003332.
The binding affinity of the synthesized polyamide to the identified sequence was determined using a quantitative DNase footprint titration method for studying protein-DNA
interactions described by Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K., Methods Enzymol. 130, 132-181 {1986). If the affinity of the synthesized polyamide at the target site was not subnanomolar affinity then substituting at least one (3-alanine residue for a pyrrole or 3-1o hydroxypyrrole residue was considered in order to optimize the exact positions of the binding pairs of aromatic amino acids. If the affinity of the polyamide at the target site was subnanomolar affinity then the sequence specificity of the polyamide versus mismatch sequences was determined. If the specificity versus mismatch sites was not >
10-fold specificity then adding a (3-alanine (shown schematically in Figure 8) was considered, in order to optimize the positions of the aromatic amino acids in relationship to the base pairs in the minor groove.
Specificity of the polyamide molecule for the target identified sequence versus mismatch sequence sites of greater than 10-fold was considered a successful result of design process.
The 1024 polyamide molecules comprising five carboxamide binding pairs that were 2o designed using this method are useful for binding to the 1024 target S'-NNMVN-3' core sequences, and are listed in Tables 20-S 1. A corresponding polyamide molecule was designed for each DNA sequence (241-1232) and {G17-G48) using the process outlined above and shown schematically in Figure 7.
If the synthesized polyamide molecule did not bind to the target identified sequence with subnanomolar affinity or if the synthesized polyamide molecule did not exhibit a specificity for the target identified sequence versus mismatch sequence sites of greater than 10-fold, the option of substituting an aliphatic amino acid residue for one of the carboxamide residues was considered. The preferred aliphatic amino acid residue is /3-alanine. At least one aliphatic 3o amino acid residue such as a (3-alanine residue provided some flexibility to the central portion of the polyamide molecule, acting as a "spring" to permit optimization of the hydrogen bonding between the carboxamide binding pairs and the nucleotide bases of the double stranded DNA.
In general, it was not found to be advantageous to replace either member of the terminal carboxamide binding pair, X1/X10, with (3-alanine. Similarly, ~3-alanine was not substituted for members of the binding pair, XS/X6, adjacent to the y hairpin residue. (3-alanine residues were not substituted for N-mcthylimidazole residues. The use of (3-alanine in place of a pyrrole or 3-hydroxypyrrole amino acid residue provides aromatic/aliphatic pairing (Im/~, ~3/Im, Hp/(3, (i/Hp, Py/(3, and ~3/Py) and aliphatic/aliphatic pairing (~i/(3) substitution.
The method for selecting which pyrrole amino acid to substitute with (3-alanine is schematically illustrated in Figure 8. Selective placement of an aliphatic ~-alanine (~i) residue to paired with either a pyrrole (Py), 3-hydroxypyrrole (Hp), or imidazole (Im) aromatic amino acid or another (3-alanine residue is found to compensate for sequence composition effects to improve recognition and binding of the minor groove of DNA by pyrrole-imidazole polyamides of the present invention. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be reduced by replacement of an aromatic amino acid with an aliphatic (3-alanine residue. In a polyamide molecule that comprises five binding pairs it is only beneficial to place (3-alanine in positions X2, X3, X4, X~, Xg, and X9. No more than two ~3-alanine residues may be placed within a single hairpin structure. No more than a single ~3-residue may be placed within each individual polyamide subunit, e.g., if X2 2o is replaced with (3-alanine, X3 or X4 cannot be replaced as well.
These rules and others were implemented in the method schematically illustrated in Figure 8. This process is suitable for the refinement of the design polyamide comprising five binding pairs that has been designed by the method illustrated in Figure 7, but which lacks subnanomolar affinity or greater than 10-fold specificity at the identified target DNA sequence.
As in the basic design method, the designed polyamides are synthesized and the affinity and specificity of binding to the target DNA were determined.
As discussed above, for a given 10-ring polyamide molecule there are six possible outcomes for the process of substituting a ~3-alanine residue for an aromatic amino acid residue.
First, there may be no position at which it is possible to add a (3-alanine residue; in such case, a better binding affinity or selectivity can be sought in the design and synthesis of a polyamide with four or six carboxamide binding pairs, described below. Second, the process may result in a derivative which contains a single (3-alanine substitution (such derivatives are numbered according to the parent numbering scheme such that a single (3-derivative of compound 5 would be called 5[3), which is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and at which point the process is deemed complete.
Third, the process of Figure 8 may result in a polyamide which contains a single j3-alanine substitution which is not sufficient to produce subnanomolar binding affinity and >IO-fold specificity, but where there are no additional positions in which it is possible to substitute a ~3-alanine residue, and in such a case a paired (3-alanine residue should be added as described in Figure 9 and text below. Fourth, the process of Figure 7 may result in a polyamide that contains a single ~3-alanine substitution that is not sufficient to produce subnanomolar binding affinity and >10-fold specificity, but where there is an additional position for ~3-alanine substitution that does produce a polyamide with the criterion level of affinity and selectivity.
Tables 52-83 list polyamide compounds 241(3-12323 and G17~3 -G48~, corresponding to DNA
sequences 241-1232 and G17 - G48, that contain one or two (3-alanine residues.
A fifth possibility is that substitution at a second position by the method illustrated in Figure 9 with a paired ~3-alanine residue is not sufficient to produce a polyamide having the 2o subnanomolar binding affinity and >10-fold specificity, and a polyamide with four or six carboxamide binding pairs, should be designed and synthesized, as described below. Finally, the design process may result in a polyamide that has a paired (3-alanine substitution that is sufficient to produce subnanomolar binding affinity and >10-fold specificity, and therefore the.
design process is deemed complete. Tables 52-83 list polyamide compounds 241 (3-1232(3 and G17~3 -G48~3, corresponding to DNA sequences 241-1232 and G17 - G48, that contain one or two (3-alanine residues. In addition, Tables 52-83 list polyamides corresponding to sequences (241-1232) and (G17-G48) labeled (241(3p-1232(3p) and (G17(3p-G48(3p) that contain paired ~3/~
residues added by the process described in Figure 9.
TABLE 20:10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGWNNW-3' DNA aromatic amino acid sequence sequence 241) 5'-W G GT T T W-3' ImImHpHpHp-y-PyPypypypy S 242) 5'-W G GT T A W-3' ImImHpHpPy-y-HpPypypypy 243} 5'-W G GT T G W-3' ImImHpHpIm-y-PyPyPyPyPy 244) 5'-W G GT T C W-3' ImImHpHpPy-y-ImPyPyPypy 245) 5'-W G GT A T W-3' ImImHpPyHp-y-PyHpPyPyPy 246) 5'-W G GT A A W-3' ImImHpPyPy-y-HpHpPyPyPy 247} 5'-W G GT A G W-3' ImImHpPyIm-y-PyHpPyPyPy 248) 5'-W G GT A C W-3' ImImHpPyPy-y-ImHpPyPyPy 249) 5'-W G GT G T W-3' ImImHpImHp-y-PyPyPypypy 250) 5'-W G GT G A W-3' ImImHpImPy-y-HpPyPyPyPy 251) 5'-W G GT G G W-3' ImImHpImIm-y-pypypypypy 252) 5'-W G GT G C W-3' ImImHpImPy-y-ImPypyPypy 253) 5'-W G GT C T W-3' ImImHpPyHp-y-pyImPyPyPy 254) 5'-W G GT C A W-3' ImImHpPyPy-y-HpImPyPyPy 255) 5'-W G GT C G W-3' ImImHpPyIm-y-PyImPyPyPy 256) 5'-W G GT C C W-3' ImImHpPyPy-y-ImImPyPyPy 257) 5'-W G GA T T W-3' ImImPyHpHp-y-PyPyHpPyPy 258) 5'-W G GA T A W-3' ImImPyHpPy-y-HpPyHpPyPy 259) 5'-W G GA T G W-3' ImImPyHpIm-y-PyPyHpPyPy 260) 5'-W G GA T C W-3' ImImPyHpPy-y-ImPyHpPyPy 261) 5'-W G GA A T W-3' ImImPyPyHp-y-PyHpHpPyPy 262) 5'-W G GA A A W-3' ImImPyPyPy-y-HpHpHpPyPy 263) 5'-W G GA A G W-3' ImZmPyPyIm-y-PyHpHpPyPy 264) 5'-W G GA A C W-3' ImImPyPyPy-y-ImHpHpPyPy 265) 5'-W G GA G T W-3' ImImPyImHp-y-PyPyHpPyPy 266) 5'-W G GA G A W-3' ImImPyimPy-y-HpPyHpPyPy 267) 5'-W G GA G G W-3' ImImPyImIm-y-PyPyHpPyPy 268) 5'-W G GA G C W-3' ImImPyImPy-y-ImPyHpPyPy 269) 5'-W G GA C T W-3' ImImPyPyHp-y-PyImHpPyPy 270) 5'-W G GA C A W-3' ImImPyPyPy-y-HpImHpPyPy 271) 5'-W G GA C G W-3' ImImPyPyIm-y-PyImHpPyPy 272) 5'-W G GA C C W-3' ImImPyPyPy-y-ImImHpPyPy TABLE
21:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGSNNW-3' DNA aromatic amino acid sequence sequence 273) 5' G GG T T W-3' ImImImHpHp-y-PyPyPyPyPy -W
274) 5' G GG T A W-3' ImImImHpPy-y-HppyPyPyPy ~W
275) 5' G GG T G W-3' ImImImHpIm-y-PyPyPyPyPy -W
276) 5' G GG T C W-3' ImImImHpPy-y-ImPyPyPyPy -W
277 ) 5' G GG A T W-3' ImImImPyHp-y-PyHpPyPyPy -W
278) 5' G GG A A W-3' ImImImPyPy-y-HpHpPypyPy -W
279) 5' G GG A G W-3' ImImImPyIm-y-PyHppyPyPy -W
2 8 0 5 ' G GG A C W- 3 ImImImPyPy-y- ImHpPyPypy ) -W ' 281) 5' G GG G T W-3' ImImImImHp-y-PyPyPyPyPy -W
282) 5' G GG G A W-3' ImImImImPy-y-HpPyPyPyPy -W
283) 5' G GG C T W-3' ImImImPyHp-y-PyImPyPyPy -W
284) 5' G GG C A W-3' ImImImPypy-y-HpImPyPyPy -W
285) 5' G GC T T W-3' ImImPyHpHp-y-PyPyImPyPy -W
286) 5' G GC T A W-3' ImImPyHpPy-y-HpPyImPyPy -W
287) 5' G GC T G W-3' ImImPyHpIm-y-PyPyImPyPy -W
288) 5' G GC T C W-3' ImImPyHpPy-y-ImPyImPyPy -W
289) 5' G GC A T W-3' ImImPyPyHp-y-PyHpImPyPy -W
290) 5' G GC A A W-3' ImImPyPyPy-y-HpHpImPyPy -W
291) 5' G GC A G W-3' ImImPyPyIm-y-PyHpImPyPy -W
292) 5' G GC A C W-3' ImImPyPyPy-y-ImHpImPyPy -W
293) 5' G GC G T W-3' ImImpyImHp-y-PyPyImPyPy -W
294) 5' G GC G A W-3' ImImPyImPy-y-HpPyImPyPy -W
295) 5' G GC C T W-3' ImImPyPyHp-y-PyImImPyPy -W
296) 5' G GC C A W-3' ImImPyPyPy-y-HpImImPyPy -W
G17 ) 5' G GG G G W-3 ' ImImImImIm-y-PyPyPyPyPy -W
G18) 5' G GG G C W-3' ImImImImPy-y-ImPypyPypy -W
Gl9) 5' G GG C G W-3' ImImImPyIm-y-PyImPyPyPy -W
G20) 5' G GG C C W-3' ImImImPypy-y-ImImPyPyPy -W
G21) 5' G GC G G W-3' ImImPyImIm-y-PyPyImPyPy -W
G22) 5' G GC G C W-3' ImImPyImPy-y-ImPyImPyPy -W
G23) 5' G GC C G W-3' ImImPyPyIm-y-PyImImPyPy -W
G24) 5'-W G GC C C W-3' ImImPyPyPy-y-ImImImPypy '/'ABLE
22:
10-ring Hairpin Polyamides for recognition of ?-by 5'-WGTWNNW-3' DNA aromatic amino acid sequence sequence 297) 5'-W GT T T T W-3' ImHpHpHpHp-y-pypypypypY
298) 5'-W GT T T A W-3' ImHpHpHpPy-y-HpPyPyPyPy 299) 5'-W GT T T G W-3' ImHpHpHpIm-y-pypypypypY
300) 5'-W GT T T C W-3' ImHpHpHpPy-y-ImPYPyPyPy 301) 5'-W GT T A T W-3' ImHpHpPyHp-y-pyHpPyPYPy 302) 5'-W GT T A A W-3' ImHpHpPyPy-y-HpHpPYPyPy 303) 5'-W GT T A G W-3' ImHpHpPyIm-y-PyHpPyPyPy 304) 5'-W GT T A C W-3' ImHpHpPyPy-y-ImHpPyPYPy 305) 5'-W GT T G T W-3' ImHpHpImHp-y-PyPYPyPYPy 3 0 6 5 ' GT T G A W- 3 ImHpHp ImPy-y-HpPyPyPyPy ) -W ' 307) 5'-W GT T G G W-3' ImHpHpImIm-y-PyPyPypypy 308) 5'-W GT T G C W-3' ImHpHpImPy-y-ImPyPyPyPy 309) 5'-W GT T C T W-3' ImHpHpPyHp-y-PyImPYPYPy 310) 5'-W GT T C A W-3' ImHpHpPyPy-y-HpImPyPyPy 311) 5' GT T C G W-3' ImHpHpPyim-y-PyImPYPYPy -W
312 ) 5 ' GT T C C W- 3 ImHpHpPyPy-y- ImImPyPyPy -W ' 313) 5' GT A T T W-3' ImHpPyHpHp-y-PyPyHpPyPy -W
3 14) 5'-W GT A T A W-3' ImHpPyHpPy-y-HpPyHpPyPy 315) 5' GT A T G W-3' ImHppyHpIm-y-PyPyHpPyPy -W
316) 5' GT A T C W-3' ImHpPyHpPy-y-ImPyHpPyPy -W
317) 5' GT A A T W-3' ImHpPyPyHp-y-PyHpHpPyPy -W
318) 5' GT A A A W-3' ImHpPyPypy-y-HpHpHpPyPy -W
319) 5' GT A A G W-3' ImHpPYPyIm-y-PyHpHpPyPy -W
3 2 0 5 ' GT A A C W- 3 ImHpPyPyPy-y- ImHpHpPyPy ) -W ' 321) 5' GT A G T W-3' I,~ppYl~p_y_pypyHppypY
-W
322) 5' GT A G A W-3' ImHpPyImPy-y-HpPyHpPyPy -W
323) 5'-W GT A G G W-3' ImHpPyImIm-y-PypyHpPyPy 324 ) 5 ' GT A G C W-3 ' ImHpPyImPy-y- ImPyHpPyPy -W
325) 5' GT A C T W-3' ImHpPyPyHp-y-PyImHpPYPy -W
326) 5' GT A C A W-3' ImHpPyPYPy-y-HpImHpPyPy -W
327) 5' GT A C G W-3' ImHpPyPYIm-y-PyImHpPyPy -W
328) 5' GT A C C W-3' ImApPyPyPy-y-ImImHpPyPy -W
TABLE
23:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTSNNW-3' DIVA aromatic amino acid sequence sequence 329) 5' G T G T T W-3' ImHpImHpHp-y-PyPyPyPyPy -W
330) 5' G T G T A W-3' ImHpImHpPy-y-HpPyPyPyPy -W
331) 5' G T G T G W-3' ImHpImHpIm-y-PyPyPyPyPy -W
332) 5'-W G T G T C W-3' ImHpImHpPy-y-ImPyPyPyPy 333) 5'-W G T G A T W-3' ImHpImPyHp-y-PyHpPyPyPy 334) 5'-W G T G A A W-3' ImHpImPyPy-y-HpHpPyPyPy 335) 5'-W G T G A G W-3' ImHpImPyIm-y-PyHpPyPyPy 336) 5' G T G A C W-3' ImHpImPyPy-y-ImHpPyPyPy -W
337) 5'-W G T G G T W-3' ImHpImImHp-y-PyPyPyPyPy 338) 5'-W G T G G A W-3' ImHpImImPy-y-HpPyPyPyPy 339) 5'-W G T G C T W-3' ImHpImPyHp-y-PyImPyPyPy 340) 5'-W G T G C A W-3' ImHpImPyPy-y-HpImPyPyPy 341) 5'-W G T G G G W-3' ImHpImImIm-y-PyPyPyPyPy 342) 5' G T G G C W-3' ImHpImImPy-y-ImPyPyPyPy -W
343) 5'-W G T G C G W-3' ImHpImPyIm-y-PyImPyPyPy 344) 5'-W G T G C C W-3' ImHpImPyPy-y-ImImPyPyPy 345) 5' G T C T T W-3' ImHpPyHpHp-y-PyPyImPyPy -W
346) 5'-W G T C T A W-3' ImHpPyHpPy-y-HpPyImPyPy 347) 5'-W G T C T G W-3' ImHpPyHpIm-y-PyPyImPyPy 348) 5'-W G T C T C W-3' ImHpPyHpPy-y-ImPyImPyPy 349) 5'-W G T C A T W-3' ImHpPyPyHp-y-PyHpImPyPy 350) 5' G T C A A W-3' ImHpPyPyPy-y-HpHpImPyPy -W
351) 5' G T C A G W-3' ImHpPyPyIm-y-PyHpImPyPy -W
352) 5'-W G T C A C W-3' ImHpPyPyPy-y-ImHpImPyPy 353) 5'-W G T C G T W-3' ImHpPyImHp-y-PyPyImPyPy 354) 5' G T C G A W-3' ImHpPyImPy-y-HpPyImPyPy -W
355) 5' G T C C T W-3' ImHpPyPyHp-y-PyImImPyPy -W
356) 5'-W G T C C A W-3' ImHpPyPyPy-y-HpImImPyPy 357) 5'-W G T C G G W-3' ImHpPyImIm-y-PyPyImPyPy 358) 5'-W G T C G C W-3' ImHpPyImPy-y-ImPyImPyPy 359) 5'-W G T C C G W-3' ImHpPyPyIm-y-PyImImPyPy 3 6 0 5 ' G T C C C W- 3 ImApPyPyPy-y- ImImImPyPy ) -W ' TABLE
24:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGAWNNW-3' DNA aromatic amino acid sequence sequence 361) 5' G A TT T W-3' ImPyHpHpHp-y-PyPyPyHppy -W
362) 5' G A TT A W-3' ImPyHpHpPy-y-HpPyPyHpPy -W
363) 5'-W G A TT G W-3' ImPyHpHpIm-y-PyPyPyHpPy 364} 5'-W G A TT C W-3' ImPyHpHpPy-y-ImPyPyHpPy 365) 5' G A TA T W-3' ImPylipPyHp-y-pyHpPyHpPy -W
366) 5' G A TA A W-3' ImPyHpPyPy-y-HpHpPyHpPy -W
367) 5'-W G A TA G W-3' ImPyHpPyIm-y-PyHpPyHpPy 368) 5'-W G A TA C W-3' ImPyHpPyPy-y-ImHpPyHpPy 369) 5' G A TG T W-3' ImPyHpImHp-y-PyPypygppy -W
370) 5' G A TG A W-3' ImPyHpImPy-y-HpPyPyHpPy -W
371) 5' G A TG G W-3' ImPyHpImIm-y-PyPyPyHpPy -W
372) 5'-W G A TG C W-3' ImPyHpImPy-y-ImPyPyHpPy 373 ) 5' G A TC T W-3' ImPyHpPyHp-y-PyImPyHpPy -W
374) 5' G A TC A W-3' ImPyHpPyPy-y-HpImPyHpPy -W
375) 5' G A TC G W-3' ImPyHpPyIm-y-PyImPyHpPy -W
37 6 5 ' G A TC C W- 3 ImPyHpPyPy-y- ImImPyHpPy ) -W ' 377) 5'-W G A AT T W-3' ImPyPyHpHp-y-PyPyHpHpPy 378) 5' G A AT A W-3' ImPyPyHpPy-y-HpPyHpHpPy -W
379) 5'-W G A AT G W-3' ImPyPyHpIm-y-PyPyHpHpPy 3 8 0 5 ' G A AT C W- 3 ImPyPyHpPy-y- ImPyHpHpPy ) -W ' 3 81 5 ' G A AA T W- 3 ImPyPyPyHp -y- PyHpHpHpPy ) -W ' 382) 5'-W G A AA A W-3' ImPyPyPyPy-y-HpHpHpHpPy 3 83 5 ' G A AA G W-3 ' IrriPyPypylm-y-PyHpHpHpPy ) -W
384) 5' G A AA C W-3' ImPyPyPyPy-y-ImllpHpHpPy -W
385) 5' G A AG T W-3' ImPyPyImHp-y-PyPyHpHpPy -W
386) 5'-W G A AG A W-3' ImPyPyImpy-y-HpPyHpHpPy 387) 5'-W G A AG G W-3' ImPyPyImIm-y-PyPyHpHpPy 388) 5' G A AG C W-3' ImPyPyImPy-y-ImPyHpHpPy -W
389) 5'-W G A AC T W-3' ImPyPyPyHp-y-PyImHpHpPy 390) 5' G A AC A W-3' ImPyPyPypy-y-HpImHpHpPy -W
391) 5'-W G A AC G W-3' ImPyPypyIm-y-PyImHpHpPy 392) 5' G A AC C W-3' ImPyPyPyPy-y-ImImHpHpPy -W
TABLE
25:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' DNA aromatic amino acid sequence sequence 393) 5'-W G AG T T W-3' ImPyImHpHp-y-PyPyPyHpPy 394) 5'-W G AG T A W-3' ImPyImHpPy-y-HpPyPyHpPy 395) 5'-W G AG T G W-3' ImPyImHpIm-y-PyPyPyHpPy 396) 5'-W G AG T C W-3' ImPyImHpPy-y-ImPyPyHpPy 397) 5'-W G AG A T W-3' imPyImPyHp-y-PyHpPyHpPy 398) 5'-W G AG A A W-3' ImPyImPyPy-y-HpHpPyHpPy 399) 5'-W G AG A G W-3' ImPyImPyIm-y-PyHpPyHpPy 400) 5'-W G AG A C W-3' ImPyImPyPy-y-ImHpPyHpPy 401) 5'-W G AG G T W-3' ImPyImImHp-y-PyPyPyHpPy 402) 5'-W G AG G A W-3' ImPyImImPy-y-HpPyPyHpPy 403) 5'-W G AG C T W-3' ImPyImPyHp-y-PyImPyHpPy 404) 5' G AG C A W-3' ImPyImPyPy-y-HpImPyHpPy -W
405) 5'-W G AG G G W-3' ImPyImImIm-y-PyPyPyHpPy 406) 5' G AG G C W-3' ImPyImImPy-y-ImPyPyHpPy -W
407) 5'-W G AG C G W-3' ImPyImPyIm-y-PyImPyHpPy 408) 5'-W G AG C C W-3' ImPyImPyPy-y-ImImPyHpPy 409) 5' G AC T T W-3' ImPyPyHpHp-y-PyPyImHpPy -W
4 10) 5'-W G AC T A W-3' ImPyPyHpPy-y-HpPyImHpPy 411) 5'-W G AC T G W-3' ImPyPyHpIm-y-PyPyImHpPy 412) 5'-W G AC T C W-3' ImPyPyHpPy-y-ImPyImHpPy 413) 5' G AC A T W-3' ImPyPyPyHp-y-PyHpImHpPy -W
414) 5'-W G AC A A W-3' ImPyPyPyPy-y-HpHpImHpPy 415) 5'-W G AC A G W-3' ImPyPyPyIm-y-PyHpImHpPy 416) 5'-W G AC A C W-3' ImPyPyPyPy-y-ImHpImHpPy 417) 5'-W G AC G T W-3' ImPyPyImAp-y-PyPyImHpPy 418) 5'-W G AC G A W-3' ImPyPyImPy-y-HpPyImHpPy 419) 5'-W G AC C T W-3' ImPyPyPyHp-y-PyImImHpPy 420) 5' G AC C A W-3' ImPyPyPyPy-y-HpimImHpPy -W
421) 5' G AC G G W-3' ImPyPyImIm-y-PyPyImHpPy -W
422) 5'-W G AC G C W-3' ImPyPyImPy-y-ImPyImHpPy 423) 5'-W G AC C G W-3' ImPyPyPyIm-y-PyImImHpPy 424) 5'-W G AC C C W-3' ImPyPyPyPy-y-ImImImHpPy TABLE
26:
10-ring Hairpin Poiyamides for recognition of 7-by 5'-WGCWNNW-3' DNA aromatic amino acid sequence sequence 425) 5'-W G CT T T W-3' ImPyHpHpHp-y-PyPyPyImpy S 426) 5'-W G CT T A W-3' ImPyHpHpPy-y-HpPyPyImPy 427) 5'-W G CT T G W-3' ImPyHpHpIm-y-PyPyPyImPy 428) 5' -W G CT T C W-3' ImPyHpHpPy-y-ImPyPyImPy 429) 5'-W G CT A T W-3' ImPyHpPyHp-y-PyHpPyImPy 430) 5'-W G CT A A W-3' ImPyHpPyPy-y-HpHpPyImPy 431) 5' -W G CT A G W-3' ImPyHpPyIm-y-PyHpPyImPy 432) 5' -W G CT A C W-3' ImPyHpPyPy-y-ImHpPyImPy 433) 5' -W G CT G T W-3' ImPyHpImHp-y-PyPyPyImpy 434) 5'-W G CT G A W-3' ImPyHpImPy-y-HpPyPyImPy 435) 5'-W G CT G G W-3' ImPyHpImIm-y-PyPyPyImPy 436) 5'-W G CT G C W-3' ImPyHpImpy-y-ImPyPyImPy 437) 5' -W G CT C T W-3' ImPyHpPyHp-y-PyImPyImPy 438) 5' -W G CT C A W-3' ImPyHpPyPy-y-HpImPyImPy 439) 5' -W G CT C G W-3' ImPyHpPyIm-y-PyImPyImPy 440) 5' -W G CT C C W-3' ImPyHpPyPy-y-ImImPyImPy 441) 5' -W G CA T T W-3' ImPyPyHpHp-y-PyPyHpImPy 442) 5'-W G CA T A W-3' ImPyPyHpPy-y-HpPyHpImPy 443 ) 5' -W G CA T G W-3' ImPyPyHpIm-y-PyPyHpImPy 444) 5'-W G CA T C W-3' ImPyPyHpPy-y-ImPyHpImPy 445) 5' -W G CA A T W-3' ImPyPyPyHp-y-PyApHpImPy 446) 5'-W G CA A A W-3' ImPyPyPyPy-y-HpHpHpImPy 447) 5'-W G CA A G W-3' ImpyPyPyIm-y-PyHpHpImPy 4 4 8 5 ' G CA A C W- 3 ImPyPyPypy-y- ImHpHpImPy ) -W ' 449) 5' -W G CA G T W-3' ImPyPyImHp-y-PyPyHpImPy 450) 5' -W G CA G A W-3' ImPyPyImPy-y-HpPyHpImPy 4 51 5 ' G CA G G W- 3 ImPyPyImIm-y-PyPyHpImPy ) -W ' 452) 5' -W G CA G C W-3' ImPyPyImPy-y-ImPyFipImPy 453) 5' -W G CA C T W-3' ImPyPyPyHp-y-PyImHpImPy 454) 5'-W G CA C A W-3' ImPyPyPyPy-y-HpImHpImPy 455) 5' -W G CA C G W-3' ImPyPyPyIm-y-PyImHpImPy 456) 5'-W G CA C C W-3' ImPyPyPyPy-y-ImImHpImPy TABLE
27:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' DNA aromatic amino acid sequence sequence 457) 5'-W G C G T T W-3' ImPyImHpHp-y-PyPyPyImPy 458) 5'-W G C G T A W-3' ImPyImHpPy-y-HpPyPyImPy 459) 5' G C G T G W-3' ImPyImHpIm-y-PyPyPyImPy -W
460) 5'-W G C G T C W-3' ImPyImHpPy-y-ImPyPyImPy 46I) 5'-W G C G A T W-3' ImPyImPyHp-y-PyHpPyImPy 462) 5'-W G C G A A W-3' ImPyImPyPy-y-HpHpPyImPy 463) 5'-W G C G A G W-3' ImPyImPyIm-y-PyHpPyImPy 464) 5'-W G C G A C W-3' ImPyImPyPy-y-ImHpPyImPy 465) 5'-W G C G G T W-3' ImPyImImHp-y-PyPyPyImPy 466) 5'-W G C G G A W-3' ImPyImImPy-y-HpPyPyImPy 467) 5'-W G C G C T W-3' ImPyImPyHp-y-PyImPyImPy 468) 5'-W G C G C A W-3' ImPyImPyPy-y-HpImPyImPy 469) 5'-W G C C T T W-3' ImPyPyHpHp-y-PyPyImImPy 470) 5'-W G C C T A W-3' ImPyPyHpPy-y-HpPyImImPy 471) 5'-W G C C T G W-3' ImPyPyHpIm-y-PyPyImImPy 472) 5'-W G C C T C W-3' ImPyPyHpPy-y-ImPyImImPy 473) 5'-W G C C A T W-3' ImPyPyPyHp-y-PyHpImImPy 474) 5'-W G C C A A W-3' ImPyPyPyPy-y-HpHpImImPy 475) 5'-W G C C A G W-3' ImPyPyPyIm-y-PyHpImImPy 47 6 5' G C C A C W- 3 ImPyPyPyPy-y- ImHpImImPy ) -W ' 477) 5'-W G C C G T W-3' ImPyPyImHp-y-PyPyImImPy 478) 5'-W G C C G A W-3' ImPyPyImPy-y-HpPyImImPy 479) 5' G C C C T W-3' Ir~iPyPyPyHp-y-PyImImImPy -W
480) 5' G C C C A W-3' ImPyPyPyPy-y-HpImImImPy -W
G25) 5' G C G G G W-3' ImPyImImIm-y-PyPyPyImPy -W
G26) 5' G C G G C W-3' ImPyImImPy-y-ImPyPyImPy -W
G27) 5'-W G C G C G W-3' ImPyImPyIm-y-PyImPyImPy G28) 5' G C G C C W-3' ImPyImPyPy-y-ImImPyImPy -W
G29) 5' G C C G G W-3' ImPyPyImIm-y-PyPyImImPy -W
G30) 5'-W G C C G C W-3' ImPyPyImPy-y-ImPyImImPy G31) 5' G C C C G W-3' ImPyPyPyIm-y-PyImImImPy -W
G32) 5' G C C C C W-3' ImPyPyPyPy-y-ImImImImPy -W
TABLE 28:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGWNNW-3' DNA aromatic amino acid sequence sequence 481) 5'-W C G T T T W-3' PyImHpHpHp-y-PyPypypylm 482) 5' C G T T A W-3' PyImHpHppy-y-HpPyPyPyIm =W
483) 5'-W C G T T G W-3' PyImHpHpIm-y-PyPypypylm 484) 5'-W C G T T C W-3' PyImHpHpPy-y-ImPyPyPyIm 485) 5' C G T A T W-3' PyImHpPyHp-y-pyHpPyPyIm -W
486) 5'-W C G T A A W-3' PyImHpPyPy-y-HpHpPyPyIm 487) 5' C G T A G W-3' PyImHpPyIm-y-PyHpPyPyIm -W
488) 5'-W C G T A C W-3' PyImHpPyPy-y-ImHpPyPyIm 489) 5'-W C G T G T W-3' PyImHpImHp-y-PyPypypylm 490) 5' C G T G A W-3' PyImHpImPy-y-HpPyPyPyIm -W
491) 5' C G T G G W-3' PyImHpImIm-y-PyPyPyPyIm -W
492) 5' C G T G C W-3' PyImHpImPy-y-ImPyPyPyIm -W
493} 5' C G T C T W-3' PyImHpPyHp-y-PyImPyPyIm -W
494) 5'-W C G T C A W-3' PyImHpPyPy-y-HpImPyPyIm 495) 5'-W C G T C G W-3' PyImHpPyIm-y-PyImPyPyIm 496) 5' C G T C C W-3' PyImHpPyPy-y-ImImPypyIm -W
497) 5'-W C G A T T W-3' PyImPyHpHp-y-PyPyHpPyIm 498) 5' C G A T A W-3' PyImPyHpPy-y-HpPyHpPyIm -W
499) 5' C G A T G W-3' PyImPyHpIm-y-PyPyHpPyIm -W
500) 5' C G A T C W-3' PyImPyHpPy-y-ImPyHpPyIm -W
501) 5'-W C G A A T W-3' PyImPyPyHp-y-PyHpHpPyIm 502) 5'-W C G A A A W-3' PyImPyPyPy-y-HpHpHpPyIm 503) 5'-W C G A A G W-3' PyImPyPyIm-y-PyHpHpPyIm 504) 5'-W C G A A C W-3' PyImPyPyPy-y-ImHpHpPyIm 505) 5'-W C G A G T W-3' PyImPyImHp-y-PyPyHpPyIm 506) 5'-W C G A G A W-3' PyImPyImPy-y-HpPyHpPyIm 507) 5'-W C G A G G W-3' PyImPyImIm-y-PyPyHpPyIm 508) 5' C G A G C W-3' PyImPyImPy-y-ImPyHpPyIm -W
509) 5' C G A C T W-3' PyImPyPyHp-y-PyImHpPyIm -W
510) 5' C G A C A W-3' PyImPyPyPy-y-HpImHpPyIm -W
511) 5' C G A C G W-3' PyImPyPyIm-y-PyImHpPyIm -W
512) 5' C G A C C W-3' PyImPyPyPy-y-ImImHpPyIm -W
TABLE
29:
10-ring Hairpin Polyanudes for recognition of 7-by 5'-WCGSNNW-3' DNA aromatic amino acid sequence sequence 513) 5'-W C G G T TW-3' PyImImHpHp-y-PyPyPyPyIm 514) 5'-W C G G T AW-3' PyImImHpPy-y-HppyPypylm 515) 5' C G G T GW-3' PyImImHpIm-y-pypypypylm -W
516) 5'-W C G G T CW-3' PyImImHpPy-y-ImPyPyPyIm 517) 5'-W C G G A TW-3' PyImImPyHp-y-PyHpPyPyIm 518) 5' C G G A AW-3' PyImImPyPy-y-HpHpPyPyIm -W
519) 5' C G G A GW-3' PyImImPyIm-y-PyHpPyPyIm -W
520) 5'-W C G G A CW-3' PyImImPyPy-y-ImHpPyPyIm 521) 5' C G G G TW-3' PyImImImHp-y-PyPyPyPyIm -W
522) 5'-W C G G G AW-3' PyImImImPy-y-HpPyPyPyIm 523) 5' C G G C TW-3' PyImImPyHp-y-PyImPyPyIm -W
524) 5'-W C G G C AW-3' PyImImPyPy-y-HpImPyPyIm 525) 5'-W C G C T TW-3' PyImPyHpHp-y-PyPyImPyIm 526) 5' C G C T AW-3' PyImPyHpPy-y-HpPyImPyIm -W
527) 5'-W C G C T GW-3' PyImPyHpIm-y-PyPyImPyIm 528) 5' C G C T CW-3' PyImPyHpPy-y-ImPyImPyIm -W
529) 5' C G C A TW-3' PyImPyPyHp-y-PyHpImPyIm -W
530) 5'-W C G C A AW-3' PyImPypyPy-y-HpHpImPyIm 531) 5' C G C A GW-3' PyImPyPyIm-y-PyHpImPyIm -W
532) 5'-W C G C A CW-3' PyImPyPyPy-y-ImHpImPyIm 533) 5'-W C G C G TW-3' PyImPyImHp-y-PyPyImPyIm 534) 5'-W C G C G AW-3' PyImPyImPy-y-HpPyImPyIm 535) 5'-W C G C C TW-3' PyImPyPyAp-y-PyImImPyIm 536) 5'-W C G C C AW-3' PyImPyPyPy-y-HpImImPyIm G33) 5'-W C G G G GW-3' PyImImImIm-y-PyPyPyPyIm G34) 5'-W C G G G CW-3' PyImImImPy-y-ImPyPyPyIm G35) 5' C G G C GW-3' PyImImPyIm-y-PyImPyPyim -W
G36) 5'-W C G G C CW-3' PyImImPyPy-y-ImImPyPyIm G37) 5'-W C G C G GW-3' PyImPyImIm-y-PyPyImPyIm G38) 5' C G C G CW-3' PyImPyImPy-y-ImPyImPyIm -W
G39) 5' C G C C GW-3' PyImPyPyIm-y-PyImImPyim -W
G40) 5' C G C C CW-3' PyImPyPyPy-y-ImImImPyim -W
TABLE
30:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' DNA aromatic amino acid sequence sequence 537) 5'-W C TT T T W-3' PyHpHpHpHp-y-PyPypypyIm 538) 5'-W C TT T A W-3' PyHpHpHpPy-y-IipPyPyPyIm 539) 5'-W C TT T G W-3' PyHpHpHpIm-y-PyPyPyPyIm 540) 5'-W C TT T C W-3' PyHpHpHpPy-y-ImPyPyPyIm 541) 5'-W C TT A T W-3' PyHpHpPyHp-y-PyHpPyPyIm 542) 5'-W C TT A A W-3' PyHpHpPyPy-y-HpHpPyPyIm 543) 5'-W C TT A G W-3' PyHpHppyIm-y-PyHpPyPyIm 544) 5'-W C TT A C W-3' PyHpHpPyPy-y-ImHpPyPyIm 545) 5'-W C TT G T W-3' PyHpHpImHp-y-PyPyPypylm 546) 5'-W C TT G A W-3' PyHpHpImPy-y-HpPyPyPyIm 547) 5'-W C TT G G W-3' PyHpHpImIm-y-PyPyPypylm 548) 5'-W C TT G C W-3' PyHpHpImPy-y-ImpyPyPyIm 549) 5'-W C TT C T W-3' PyHpHpPyHp-y-PyImpyPyIm 550) 5'-W C TT C A W-3' PyHpHpPyPy-y-HpImPyPyIm 551) 5'-W C TT C G W-3' PyHpHpPyIm-y-pylmpyPyIm 552) 5'-W C TT C C W-3' PyHpHppyPy-y-ImImPyPyIm 553 ) 5' -W C TA T T W-3' PyHpPyHpHp-y-PyPyHpPyIm 554) 5'-W C TA T A W-3' PyHpPyHpPy-y-HpPyHpPyIm 555) 5'-W C TA T G W-3' PyHpPyHpIm-y-PyPyHpPyIm 556) 5'-W C TA T C W-3' PyHpPyHpPy-y-ImPyHppyIm 557) 5'-W C TA A T W-3' PyHpPyPyHp-y-PyHpHpPyIm 558) 5'-W C TA A A W-3' PyHpPyPyPy-y-HpHpHpPyIm 559) 5'-W C TA A G W-3' PyHpPyPyIm-y-PyHpHpPyIm 560) 5'-W C TA A C W-3' PyHpPyPyPy-y-ImHpHpPyIm 561) 5'-W C TA G T W-3' PyHppyImHp-y-PyPyHpPyIm 562) 5'-W C TA G A W-3' PyHpPyImpy-y-HpPyHpPyIm 563) 5'-W C TA G G W-3' PyHpPyImIm-y-PyPyHpPyIm 564) 5' -W C TA G C W-3' PyHpPyImPy-y-ImPyHpPyIm 565) 5'-W C TA C T W-3' PyHpPyPyHp-y-PyImHpPyIm 566) 5' -W C TA C A W-3' PyHpPyPyPy-y-HpImHpPyIm 567) 5'-W C TA C G W-3' PyHpPyPyIm-y-PyImHpPyIm 568) 5' -W C TA C C W-3' PyHpPyPyPy-y-ImImHpPyIm TABLE
31:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTSNNW-3' DIVA aromatic amino acid sequence sequence 569) 5'-W CT G T T W-3' PyHpImHpHp-y-PyPyPyPyIm 570) -5'-W CT G T A W-3' PyIipImHpPy-y-HpPyPyPyIm 571) 5'-W CT G T G W-3' PyHpImHpIm-y-PyPyPyPyIm 572) 5'-W CT G T C W-3' PyHpImHpPy-y-ImPyPyPyIm 573) 5'-W CT G A T W-3' PyHpImPyHp-y-PyHpPyPyIm 574) 5'-W CT G A A W-3' PyHpImPyPy-y-HpHpPyPyIm 575) 5' -W CT G A G W-3' PyHpImPyIm-y-PyHpPyPyIm 576) 5'-W CT G A C W-3' PyHpImPyPy-y-ImHpPyPyIm 577) 5'-W CT G G T W-3' PyHpImImHp-y-PyPyPyPyIm 578) 5'-W CT G G A W-3' PyHpImImPy-y-HpPyPyPyIm 579) 5'-W CT G C T W-3' PyHpImPyHp-y-PyImPyPyIm 580) 5'-W CT G C A W-3' PyHpImPyPy-y-HpImPyPyIm 581) 5'-W CT ~GG G W-3' PyHpImImIm-y-PyPyPyPyIm 582) 5'-W CT G G C W-3' PyHpImImPy-y-ImPyPyPyIm 583) 5'-W CT G C G W-3' PyHpImPyIm-y-PyImPyPyIm 584) 5'-W CT G C C W-3' PyHpImPyPy-y-ImImPyPyIm 585) 5' -W CT C T T W-3' PyHpPyHpHp-y-PyPyImPyIm 586) 5'-W CT C T A W-3' PyHpPyHpPy-y-HpPyImPyIm 587) 5'-W CT C T G W-3' PyHpPyHpIm-y-PyPyImPyIm 588) 5' -W CT C T C W-3' PyHpPyHpPy-y-ImPyImPyIm 589) 5'-W CT C A T W-3' PyHpPyPyHp-y-PyHpImPyIm 590) 5'-W CT C A A W-3' PyHpPyPyPy-y-HpHpImPyIm 591) 5' -W CT C A G W-3' PyHpPyPyIm-y-PyHpImPyIm 592) 5'-W CT C A C W-3' PyHpPyPyPy-y-ImHpImPyIm 593) 5'-W CT C G T W-3' PyHpPyImHp-y-PyPyImPyIm 594) 5' -W CT C G A W-3' PyHpPyImPy-y-HpPyImPyIm 595) 5'-W CT C C T W-3' PyHpPyPyHp-y-PyImImPyIm 596) 5'-W CT C C A W-3' PyHpPyPyPy-y-HpImImPyIm 597) 5'-W CT C G G W-3' PyHpPyImIm-y-PyPyImPyIm 598) 5'-W CT C G C W-3' PyHpPyImPy-y-ImPyImPyIm 599) 5' -W CT C C G W-3' PyHpPyPyIm-y-PyImImPyIm 600) 5'-W CT C C C W-3' PyHpPyPyPy-y-ImImImPyIm TABLE
32:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCAWNNW-3' DNA aromatic amino acid sequence sequence 601) 5'-W C A T T TW-3' PypyHpHpHp-y-PyPyPyHpIm 602) '5'-W C A T T AW-3' PyPyHpHpPy-y-HpPyPyHpIm 603) 5'-W C A T T GW-3' PypyHpHpIm-y-PyPyPyHpIm 604) 5'-W C A T T CW-3' PyPyHpHppy-y-ImPyPyHpIm 605) 5' C A T A TW-3' PyPyHpPyHp-y-PyHpPyHpIm -W
606) 5'-W C A T A AW-3' pypyHpPyPy-y-HpHpPyHpIm 607) 5'-W C A T A GW-3' PyPyHpPyIm-y-PyHpPyHpIm 608) 5' C A T A CW-3' PyPyHpPyPy-y-ImHppyHpIm -W
609) 5' C A T G TW-3' PyPyHpImHp-y-PyPyPyHpIm -W
610) 5'-W C A T G AW-3' PyPyHpImPy-y-HpPypyHpIm 611) 5' C A T G GW-3' PyPyHpImIm-y-PypypyHpIm -W
612) 5' C A T G CW-3' PyPyHpImpy-y-ImPyPyHpIm -W
613) 5'-W C A T C TW-3' pyPyHpPyHp-y-PyImPyHpIm 614) 5' C A T C AW-3' PyPyHpPyPy-y-HpImPyHpIm -W
615) 5' C A T C GW-3' PypyHpPyIm-y-PyImPyHpIm -W
616) 5' C A T C CW-3' PyPyHpPyPy-y-ImImPyHpIm -W
617) 5' C A A T TW-3' PyPyPyHplip-y-pyPyHpHpIm -W
618) 5' C A A T AW-3' PyPyPyHpPy-y-HpPyHpHpIm -W
619) 5' C A A T GW-3' PyPyPyHpIm-y-PypyHpHpIm -W
620) 5'-W C A A T CW-3' PyPypyHpPy-y-ImPyHpHpIm 621) 5'-W C A A A TW-3' PypypypyHp-y-PyHpHpHpIm 622) 5'-W C A A A AW-3' PyPypypypy-y-HpHpHpHpIm 623) 5'-W C A A A GW-3' PyPyPypylm-y-PyHpHpHpIm 624) 5' C A A A CW-3' pyPyPypypy-y-I~pgpHpIm -W
625) 5'-W C A A G TW-3' PyPyPyImHp-y-pyPyHpHpIm 626) 5'-W C A A G AW-3' PypypylmPy-y-HpPyHpHpIm 627) 5'-W C A A G GW-3' PyPyPyImIm-y-PyPyHpHpIm 628) 5'-W C A A G CW-3' PyPypyImPy-y-ImPyHpHpIm 629) 5' C A A C TW-3' PyPypypygp-y-pyl~pHpIm -W
630) 5' C A A C AW-3' pyPypypypy-y-HpImHpHpIm -W
631) 5' C A A C GW-3' PyPypypyim-y-PyImHpHpIm -W
632) 5'-W C A A C CW-3' PyPypypypy-y-ImImHpHpIm TABLE 10-ring 33: Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' DNA aromatic amino acid sequence sequence 633) 5' -W CA G T T W-3' PyPyImHpHp-y-PyPyPyHpIm 634) ~5' CA G T A W-3' PyPyImHpPy-y-HpPyPyHpIm -W
635) 5' -W CA G T G W-3' PyPyImHpIm-y-PyPyPyHpIm 636) 5'-W CA G T C W-3' PyPyImHpPy-y-ImPyPyHpIm 637) 5'-W CA G A T W-3' PyPyImPyHp-y-PyHpPyHpIm 638) 5'-W CA G A A W-3' PyPyImPyPy-y-HpHpPyHpIm 639) 5' -W CA G A G W-3' PyPyImPyIm-y-PyHpPyHpIm 640) 5' -W CA G A C W-3' PyPyImPyPy-y-ImHpPyHpIm 641) 5' -W CA G G T W-3' PyPyImImHp-y-PyPyPyHpIm 642) 5'-W CA G G A W-3' PyPyImImPy-y-HpPyPyHpIm 643) 5'-W CA G C T W-3' PyPyImPyHp-y-PyImPyHpIm 644) 5' -W CA G C A W-3' PyPyImPyPy-y-HpImPyHpIm 645) 5'-W CA G G G W-3' PyPyImImIm-y-PyPyPyHpIm 646) 5' -W CA G G C W-3' PyPyImImPy-y-ImPyPyHpIm 647) 5'-W CA G C G W-3' PyPyImPyIm-y-PyImPyHpIm 648) 5'-W CA G C C W-3' PyPyImPyPy-y-ImImPyHpIm 649) 5' -W CA C T T W-3' PyPyPyHpFip-y-PyPyImHpIm 650) 5' -W CA C T A W-3' PyPyPyHpPy-y-HpPyImHpIm 651) 5' -W CA C T G W-3' PyPyPyHpIm-y-PyPyImHpIm 652) 5'-W CA C T C W-3' PyPyPyHpPy-y-ImPyimHpim 653) 5'-W CA C A T W-3' PyPyPyPyHp-y-PyHpImHpIm 654) 5' -W CA C A A W-3' PyPyPyPyPy-y-HpHpImHpIm 655) 5'-W CA C A G W-3' ~PyPyPyPyIm-y-PyHpImHpIm 656) 5'-W CA C A C W-3' PyPyPyPyPy-y-ImHpImHpIm 657 5' -W CA C G T W-3' PyPyPyImHp-y-PyPyImHpIm ) 658) 5' -W CA C G A W-3' PyPyPyImPy-y-HpPyImHpIm 659) 5' -W CA C C T W-3' PyPyPyPyHp-y-PyImImHpIm 660) 5' -W CA C C A W-3' PyPyPyPyPy-y-HpImImHpIm 661) 5' -W CA C G G W-3' PyPyPyImIm-y-PyPyImHpIm 662) 5'-W CA C G C W-3' PyPyPyImPy-y-ImPyImHpIm 663) 5'-W CA C C G W-3' PyPyPyPyIm-y-PyImImHpIm 664) 5' -W CA C C C W-3' PyPyPyPyPy-y-ImImImHpIm 'TABLE
34:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCWNNW-3' DNA aromatic anuno acid sequence sequence 665) 5'-W C C T T TW-3' PyPyHpHpHp-y-PyPypylmim 666) ~5'-W C C T T AW-3' PyPyHpHpPy-y-HpPyPyImIm 667) 5'-W C C T T GW-3' PyPyHpHpIm-y-PypypylmIm 668) 5' C C T T CW-3' PyPyHpHpPy-y-ImPyPyImIm -W
669) 5'-W C C T A TW-3' PyPyHpPyHp-y-PyHpPyImIm 670) 5'-W C C T A AW-3' PyPyHpPyPy-y-HpHpPyImIm 671) 5'-W C C T A GW-3' PyPyHpPyIm-y-PyHpPyImIm 672) 5'-W C C T A CW-3' PypyHpPyPy-y-ImHpPyImIm 673) 5'-W C C T G TW-3' PyPyHpImHp-y-PyPypyImlm 674) 5'-W C C T G AW-3' PyPyHpImPy-y-HpPyPyImIm 675) 5'-W C C T G GW-3' PyPyHpImIm-y-PyPypyImIm 676) 5' C C T G CW-3' PyPyHpImPy-y-ImPyPyImIm -W
677) 5'-W C C T C TW-3' PyPyHpPyHp-y-PyImPyImIm 678) 5'-W C C T C AW-3' PyPyHpPyPy-y-HpImPyImIm 679) 5'-W C C T C GW-3' PyPyHpPyIm-y-PyImPyImIm 680) 5'-W C C T C CW-3' PyPyHpPyPy-y-ImImPyImIm 681) 5'-W C C A T TW-3' PyPypyHpHp-y-PyPyHpImIm 682) 5' C C A T AW-3' PyPyPyHpPy-y-HpPyHpImIm -W
683) 5'-W C C A T GW-3' PyPyPyHpIm-y-PyPyHpImIm 684) 5'-W C C A T CW-3' PyPyPyHpPy-y-ImPyHpImIm 685) 5'-W C C A A TW-3' PyPyPyPyHp-y-PyHpHpImIm 2S 686) 5'-W C C A A AW-3' PyPyPyPyPy-y-HpHpHpImIm 687) 5'-W C C A A GW-3' PyPypypylm-y-pyHpHpImIm 688) 5'-W C C A A CW-3' PyPyPyPyPy-y-ImHpHpImIm 689) 5'-W C C A G TW-3' PyPyPyImHp-y-PyPyHpImIm 690) 5'-W C C A G AW-3' PyPyPyImPy-y-HpPyHpImIm 691) 5'-W C C A G GW-3' PyPyPyImIm-y-PyPyHpImIm 692) 5' C C A G CW-3' PyPyPyImPy-y-ImPyHpImIm -W
693) 5'-W C C A C TW-3' PyPyPyPyHp-y-PyImHpImIm 694) 5'-W C C A C AW-3' PyPyPyPyPy-y-HpImHpImIm 695) 5'-W C C A C GW-3' pyPypypylm-y-pyImHpImIm 696) 5' C C A C CW-3' PyPyPyPypy-y-ImImHpImIm -W
WO 98!37067 PCT/US98/01714 TABLE
35:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' DNA aromatic amino acid sequence sequence 697) 5'-W C CG T T W-3' PyPyImHpHp-y-PyPypyImIm 698) ~5' C CG T A W-3' PyPyImHpPy-y-HpPyPyImIm -W
699) 5' C CG T G W-3' PyPyImHpIm-y-PyPyPyImIm -W
700) 5' C CG T C W-3' PyPyImHppy-y-ImPyPyImIm -W
701) 5' C CG A T W-3' PyPyImPyHp-y-PyHpPyImIm -W
702) 5' C CG A A W-3' PyPyImPyPy-y-HpHpPyImIm -W
703) 5'-W C CG A G W-3' PyPyImPyIm-y-PyHpPyImIm 704) 5' C CG A C W-3' PyPyImPyPy-y-ImHpPyImIm -W
705) 5' C CG G T W-3' PyPyImImHp-y-PyPyPyImIm -W
706) 5' C CG G A W-3' PyPyImImPy-y-HpPyPyImIm -W
707) 5' C CG C T W-3' PyPyImPyHp-y-PyImPyImIm -W
708) 5' C CG C A W-3' PyPyImPyPy-y-HpImPyImIm -W
709) 5' C CC T T W-3' PyPyPyHpHp-y-PyPyImImIm -W
710) 5' C CC T A W-3' PyPyPyHpPy-y-HpPyImImIm -W
711) 5' C CC T G W-3' PyPyPyHpIm-y-PyPyImImIm -W
712) 5' C CC T C W-3' PyPyPyHpPy-y-ImPyImImIm -W
713) 5' C CC A T W-3' PypyPyPyHp-y-PyHpImImIm -W
714) 5' C CC A A W-3' PyPyPyPyPy-y-HpHpImImIm -W
715) 5' C CC A G W-3' PyPyPyPyIm-y-PyHpImImIm -W
716) 5' C CC A C W-3' PyPyPyPyPy-y-ImHpImImIm -W
717 ) 5' C CC G T W-3' PyPyPyImHp-y-PyPyImImIm -W
718 ) 5' C CC G A W-3 ' PyPyPyImPy-y-HpPyImImIm -W
719) 5' C CC C T W-3' PyPyPyPyHp-y-PyImImImIm -W
720) 5' C CC C A W-3' PyPyPyPypy-y-HpImImImIm -W
G41) 5' C CG G G W-3' PyPyImImIm-y-PyPyPyImIm -W
G42) 5'-W C CG G C W-3' PyPyImImPy-y-ImPyPyImIm G43) 5' C CG C G W-3' PyPyImPyIm-y-PyImPyImIm -W
G44) 5' C CG C C W-3' PyPyImPyPy-y-ImImPyImIm -W
G45) 5' C CC G G W-3' PyPyPyImIm-y-PyPyImImIm -W
G46) 5' C CC G C W-3' PyPyPyImPy-y-ImPyImImIm -W
G47) 5'-W C CC C G W-3' PyPyPyPyIm-y-PyImImImIm G48) 5'-W C CC C C W-3' PyPyPyPyPy-y-ImImImImIm TABLE
36:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGWNNW-3' DNA aromatic amino acid sequence sequence 721) 5' -WA G T T T W-3' PyImHpHpHp-y-PyPyPypyHp 722) ~5' -WA G T T A W-3' PyImHpHpPy-y-HpPyPyPyHp 723) 5' -WA G T T G W-3' PyImHpHpIm-y-PyPypypyHp 724) 5' -WA G T T C W-3' PyImHpHpPy-y-ImPyPyPyHp 725) 5' -WA G T A T W-3' PyImHpPyHp-y-PyHpPyPyHp 726) 5' -WA G T A A W-3' PyImHpPyPy-y-HpHpPyPyHp 727) 5' -WA G T A G W-3' PyImHpPyIm-y-PyHpPyPyHp 728) 5' -WA G T A C W-3' PyImHpPyPy-y-ImHppypyI-Ip 729) 5' -WA G T G T W-3' PyImHpImHp-y-PyPyPyPyHp 730) 5' -WA G T G A W-3' PyImHpImPy-y-HpPyPyPyHp 731) 5' -WA G T G G W-3' PyImHpImIm-y-Pypypypygp 732) 5' -WA G T G C W-3' PyImHpImPy-y-ImPyPyPyHp 733) 5' -WA G T C T W-3' PyImHpPyHp-y-PyImPyPyHp 734) 5' -WA G T C A W-3' PyImHpPyPy-y-HpImPyPyHp 735) 5' -WA G T C G W-3' PyImHpPyIm-y-PyImPyPyHp 736) 5' -WA G T C C W-3' PyImHpPyPy-y-ImImPyPyHp 737) 5' -WA G A T T W-3' PyImPyHpHp-y-PyPyHpPyHp 73 8 5' -WA G A T A W-3 PyImPyHpPy-y-HpPyHpPyHp ) ' 739) 5' -WA G A T G W-3' PyImPyHpIm-y-PyPyHpPyHp 740) 5' -WA G A T C W-3' PyImPyHpPy-y-ImPyHpPyllp 741) 5' -WA G A A T W-3' PyImPyPyHp-y-PyHpHpPyHp 742) 5' -WA G A A A W-3' PyImPyPyPy-y-HpHpHpPyHp 743) 5' -WA G A A G W-3' PyImPyPyIm-y-PyHpHpPyHp 744) 5' -WA G A A C W-3' PyImPyPyPy-y-ImHpHpPyHp 745) 5' -WA G A G T W-3' PyImPyImHp-y-PyPyHpPyHp 746) 5' -WA G A G A W-3' PyImPyImPy-y-HpPyHpPyHp 747) 5' -WA G A G G W-3' PyImPyImIm-y-PyPyHpPyHp 748) 5' -WA G A G C W-3' PyImPyImPy-y-ImPyHpPyHp 749) 5' -WA G A C T W-3' PyImPyPyHp-y-PyImHpPyHp 750) 5' -WA G A C A W-3' PyImPyPyPy-y-HpImHpPyHp 751) 5' -WA G A C G W-3' PyImPyPyIm-y-PyImHpPyHp 752) 5' -WA G A C C W-3' PyImPyPyPy-y-ImImHpPyHp 'TABLE pin 37: Polyamides 10-zing for Hair recognition of 7-by 5'-WAGSNNW
3' DNA aromatic amino acid sequence sequence 753) 5'-W A G G T T W-3' PyImImHpHp-y-Pypypypygp 754) ~5' A G G T A W-3' PyImImHpPy-y-HpPyPyPyHp -W
755) 5' A G G T G W-3' PyImImHpIm-y-PypypypyHp -W
756) 5' -WA G G T C W-3' PyImImHpPy-y-ImPyPyPyHp 757) 5' -WA G G A T W-3' PyImImPyHp-y-PyHpPyPyHp 758) 5' -WA G G A A W-3' PyImImPyPy-y-HpHpPyPyHp 759) 5' -WA G G A G W-3' PyImImPyIm-y-PyHpPyPyHp 760) 5' -WA G G A C W-3' PyImImPyPy-y-ImHpPyPyHp 761) 5' -WA G G G T W-3' PyImImImHp-y-PyPyPyPyHp 762) 5' -WA G G G A W-3' PyImImImPy-y-HpPyPyPyHp 763) 5' -WA G G C T W-3' PyImImPyFip-y-PyImPyPyHp 764) 5' -WA G G C A W-3' PyImImPyPy-y-HpImPyPyHp 765) 5' -WA G C T T W-3' PyImPyApHp-y-PypyImPyHp 766) 5' -WA G C T A W-3' PyImPyHpPy-y-HpPyImPyHp 767) 5' -WA G C T G W-3' PyImPyHpIm-y-PyPyImPyHp 7 6 8 5' -WA G C T C W-3 PyImpyHpPy-y-ImPyImPyHp ) ' 769) 5' -WA G C A T W-3' PyImPyPyHp-y-PyHpImPyHp 770) 5' -WA G C A A W-3' PyImPyPyPy-y-HpHpImPyHp 771) 5' -WA G C A G W-3' PyImPyPyIm-y-PyHpImPyHp 772) 5' -WA G C A C W-3' PyImPyPyPy-y-ImHpImPyHp 773) 5' -WA G C G T W-3' PyImPyImHp-y-PypyImPyHp 774) 5' -WA G C G A W-3' PyImPyImPy-y-HpPyImPyHp 775) 5' -WA G C C T W-3' PyImPyPyHp-y-PyImImPyHp 776) 5' -WA G C C A W-3' PyImPyPyPy-y-HpImImPyHp 777) 5' -WA G G G G W-3' PyImImImIm-y-Pypypypygp 778) 5' -WA G G G C W-3' PyImImImPy-y-ImPyPyPyHp 779) 5' -WA G G C G W-3' PyImImPyIm-y-PyImPyPyHp 780) 5' -WA G G C C W-3' PyImImPyPy-y-ImImPyPyHp 781) 5' -WA G C G G W-3' PyImPyImIm-y-PyPyImPyHp 782) 5' -WA G C G C W-3' PyImPyImPy-y-ImPyIrnPyHp 783) 5' -WA G C C G W-3' PyImPyPyIm-y-PyImImPyHp 784) 5' -WA G C C C W-3' PyImPyPyPy-y-ImImImPyHp r . , TABLE
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGWNNW-3' DNA aromatic amino acid sequence sequence 721) 5' -WA G T T T W-3' PyImHpHpHp-y-PyPyPypyHp 722) ~5' -WA G T T A W-3' PyImHpHpPy-y-HpPyPyPyHp 723) 5' -WA G T T G W-3' PyImHpHpIm-y-PyPypypyHp 724) 5' -WA G T T C W-3' PyImHpHpPy-y-ImPyPyPyHp 725) 5' -WA G T A T W-3' PyImHpPyHp-y-PyHpPyPyHp 726) 5' -WA G T A A W-3' PyImHpPyPy-y-HpHpPyPyHp 727) 5' -WA G T A G W-3' PyImHpPyIm-y-PyHpPyPyHp 728) 5' -WA G T A C W-3' PyImHpPyPy-y-ImHppypyI-Ip 729) 5' -WA G T G T W-3' PyImHpImHp-y-PyPyPyPyHp 730) 5' -WA G T G A W-3' PyImHpImPy-y-HpPyPyPyHp 731) 5' -WA G T G G W-3' PyImHpImIm-y-Pypypypygp 732) 5' -WA G T G C W-3' PyImHpImPy-y-ImPyPyPyHp 733) 5' -WA G T C T W-3' PyImHpPyHp-y-PyImPyPyHp 734) 5' -WA G T C A W-3' PyImHpPyPy-y-HpImPyPyHp 735) 5' -WA G T C G W-3' PyImHpPyIm-y-PyImPyPyHp 736) 5' -WA G T C C W-3' PyImHpPyPy-y-ImImPyPyHp 737) 5' -WA G A T T W-3' PyImPyHpHp-y-PyPyHpPyHp 73 8 5' -WA G A T A W-3 PyImPyHpPy-y-HpPyHpPyHp ) ' 739) 5' -WA G A T G W-3' PyImPyHpIm-y-PyPyHpPyHp 740) 5' -WA G A T C W-3' PyImPyHpPy-y-ImPyHpPyllp 741) 5' -WA G A A T W-3' PyImPyPyHp-y-PyHpHpPyHp 742) 5' -WA G A A A W-3' PyImPyPyPy-y-HpHpHpPyHp 743) 5' -WA G A A G W-3' PyImPyPyIm-y-PyHpHpPyHp 744) 5' -WA G A A C W-3' PyImPyPyPy-y-ImHpHpPyHp 745) 5' -WA G A G T W-3' PyImPyImHp-y-PyPyHpPyHp 746) 5' -WA G A G A W-3' PyImPyImPy-y-HpPyHpPyHp 747) 5' -WA G A G G W-3' PyImPyImIm-y-PyPyHpPyHp 748) 5' -WA G A G C W-3' PyImPyImPy-y-ImPyHpPyHp 749) 5' -WA G A C T W-3' PyImPyPyHp-y-PyImHpPyHp 750) 5' -WA G A C A W-3' PyImPyPyPy-y-HpImHpPyHp 751) 5' -WA G A C G W-3' PyImPyPyIm-y-PyImHpPyHp 752) 5' -WA G A C C W-3' PyImPyPyPy-y-ImImHpPyHp 'TABLE pin 37: Polyamides 10-zing for Hair recognition of 7-by 5'-WAGSNNW
3' DNA aromatic amino acid sequence sequence 753) 5'-W A G G T T W-3' PyImImHpHp-y-Pypypypygp 754) ~5' A G G T A W-3' PyImImHpPy-y-HpPyPyPyHp -W
755) 5' A G G T G W-3' PyImImHpIm-y-PypypypyHp -W
756) 5' -WA G G T C W-3' PyImImHpPy-y-ImPyPyPyHp 757) 5' -WA G G A T W-3' PyImImPyHp-y-PyHpPyPyHp 758) 5' -WA G G A A W-3' PyImImPyPy-y-HpHpPyPyHp 759) 5' -WA G G A G W-3' PyImImPyIm-y-PyHpPyPyHp 760) 5' -WA G G A C W-3' PyImImPyPy-y-ImHpPyPyHp 761) 5' -WA G G G T W-3' PyImImImHp-y-PyPyPyPyHp 762) 5' -WA G G G A W-3' PyImImImPy-y-HpPyPyPyHp 763) 5' -WA G G C T W-3' PyImImPyFip-y-PyImPyPyHp 764) 5' -WA G G C A W-3' PyImImPyPy-y-HpImPyPyHp 765) 5' -WA G C T T W-3' PyImPyApHp-y-PypyImPyHp 766) 5' -WA G C T A W-3' PyImPyHpPy-y-HpPyImPyHp 767) 5' -WA G C T G W-3' PyImPyHpIm-y-PyPyImPyHp 7 6 8 5' -WA G C T C W-3 PyImpyHpPy-y-ImPyImPyHp ) ' 769) 5' -WA G C A T W-3' PyImPyPyHp-y-PyHpImPyHp 770) 5' -WA G C A A W-3' PyImPyPyPy-y-HpHpImPyHp 771) 5' -WA G C A G W-3' PyImPyPyIm-y-PyHpImPyHp 772) 5' -WA G C A C W-3' PyImPyPyPy-y-ImHpImPyHp 773) 5' -WA G C G T W-3' PyImPyImHp-y-PypyImPyHp 774) 5' -WA G C G A W-3' PyImPyImPy-y-HpPyImPyHp 775) 5' -WA G C C T W-3' PyImPyPyHp-y-PyImImPyHp 776) 5' -WA G C C A W-3' PyImPyPyPy-y-HpImImPyHp 777) 5' -WA G G G G W-3' PyImImImIm-y-Pypypypygp 778) 5' -WA G G G C W-3' PyImImImPy-y-ImPyPyPyHp 779) 5' -WA G G C G W-3' PyImImPyIm-y-PyImPyPyHp 780) 5' -WA G G C C W-3' PyImImPyPy-y-ImImPyPyHp 781) 5' -WA G C G G W-3' PyImPyImIm-y-PyPyImPyHp 782) 5' -WA G C G C W-3' PyImPyImPy-y-ImPyIrnPyHp 783) 5' -WA G C C G W-3' PyImPyPyIm-y-PyImImPyHp 784) 5' -WA G C C C W-3' PyImPyPyPy-y-ImImImPyHp r . , TABLE
38:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WATWNNW-3' -DNA aromatic amino acid sequence sequence 785) 5' A T T T TW-3' PyHpHpHpHp-y-pypypypygp -W
786) '5'-W A T T T AW-3' PyHpHpHpPy-y-HppypypyHp 787) 5'-W A T T T GW-3' PyHpHpHpIm-y-pypypypygp 788) 5' A T T T CW-3' PyHpHpHpPy-y-ImPyPyPyHp -W
789) 5' A T T A TW-3' PyHpHpPyHp-y-PyHpPyPyHp -W
790) 5' A T T A AW-3' PyHpHpPyPy-y-HpHpPyPyHp -W
791) 5' A T T A GW-3' PyHpHpPyIm-y-PyHpPyPyHp -W
792) 5' A T T A CW-3' PyHpHpPypy-y-I~ppyp~,Hp -W
793) 5'-W A T T G TW-3' PyHpHpImHp-y-PyPyPyPyHp 794) 5' A T T G AW-3' PyHpHpImPy-y-HpPyPyPyHp -W
795) 5'-W A T T G GW-3' PyHpHpImIm-y-pypypypyHp 796) 5'-W A T T G CW-3' PyHpHpImPy-y-ImPyPyPyHp 797) 5' A T T C TW-3' PyHpHpPyHp-y-PyImPyPyHp -W
798) 5'-W A T T C AW-3' PyHpHpPyPy-y-HpImpyPyHp 799) 5' A T T C GW-3' PyHpHpPyIm-y-PyImPyPyHp -W
8 00 5' A T T C CW-3 ' PyHpHpPyPy-y- ImImPyPyFip ) -W
801) 5' A T A T TW-3' PyHpPyHpHp-y-PyPyHpPyHp -W
802) 5'-W A T A T AW-3' PyHpPyHpPY-Y-HpPYHpPYHP
803) 5'-W A T A T GW-3' PyHpPyHpIm-y-PyPyHpPyHp 804) 5' A T A T CW-3' PyHpPyHpPy-y-ImPyHpPyHp -W
805) 5' A T A A TW-3' PyHpPyPyHp-y-PyHpHpPyHp -W
806) 5' A T A A AW-3' PyHpPyPyPy-y-HpHpHpPyHp -W
807 ) 5' A T A A GW-3' PyHpPyPyIm-y-PyHpHpPyHp -W
808) 5'-W A T A A CW-3' PyHpPypyPy-y-ImHpHpPYHp 809) 5'-W A T A G TW-3' PyHpPyImHp-y-PyPyHpPyHp 810) 5' A T A G AW-3' PyHpPyImPy-y-HpPyHpPyHp -W
811) 5' A T A G GW-3' PyHpPyImIm-y-PypyHpPyHp -W
812) 5' A T A G CW-3' PyHpPyImPy-y-ImPyHpPyHp -W
813) 5'-W A T A C TW-3' PyHpPyPyHp-y-PyImHpPyHp 814) 5'-W A T A C AW-3' PyHpPyPyPy-y-HpImHpPyHp 815) 5' A T A C GW-3' PyHpPyPyIm-y-pyImHpPyHp -W
816) 5' A T A C CW-3' PyHpPyPyPy-y-ImImHpPyHp -W
TABLE
10-ring Hairpin Polyamides for recognition of 7-by 5'-WATWNNW-3' -DNA aromatic amino acid sequence sequence 785) 5' A T T T TW-3' PyHpHpHpHp-y-pypypypygp -W
786) '5'-W A T T T AW-3' PyHpHpHpPy-y-HppypypyHp 787) 5'-W A T T T GW-3' PyHpHpHpIm-y-pypypypygp 788) 5' A T T T CW-3' PyHpHpHpPy-y-ImPyPyPyHp -W
789) 5' A T T A TW-3' PyHpHpPyHp-y-PyHpPyPyHp -W
790) 5' A T T A AW-3' PyHpHpPyPy-y-HpHpPyPyHp -W
791) 5' A T T A GW-3' PyHpHpPyIm-y-PyHpPyPyHp -W
792) 5' A T T A CW-3' PyHpHpPypy-y-I~ppyp~,Hp -W
793) 5'-W A T T G TW-3' PyHpHpImHp-y-PyPyPyPyHp 794) 5' A T T G AW-3' PyHpHpImPy-y-HpPyPyPyHp -W
795) 5'-W A T T G GW-3' PyHpHpImIm-y-pypypypyHp 796) 5'-W A T T G CW-3' PyHpHpImPy-y-ImPyPyPyHp 797) 5' A T T C TW-3' PyHpHpPyHp-y-PyImPyPyHp -W
798) 5'-W A T T C AW-3' PyHpHpPyPy-y-HpImpyPyHp 799) 5' A T T C GW-3' PyHpHpPyIm-y-PyImPyPyHp -W
8 00 5' A T T C CW-3 ' PyHpHpPyPy-y- ImImPyPyFip ) -W
801) 5' A T A T TW-3' PyHpPyHpHp-y-PyPyHpPyHp -W
802) 5'-W A T A T AW-3' PyHpPyHpPY-Y-HpPYHpPYHP
803) 5'-W A T A T GW-3' PyHpPyHpIm-y-PyPyHpPyHp 804) 5' A T A T CW-3' PyHpPyHpPy-y-ImPyHpPyHp -W
805) 5' A T A A TW-3' PyHpPyPyHp-y-PyHpHpPyHp -W
806) 5' A T A A AW-3' PyHpPyPyPy-y-HpHpHpPyHp -W
807 ) 5' A T A A GW-3' PyHpPyPyIm-y-PyHpHpPyHp -W
808) 5'-W A T A A CW-3' PyHpPypyPy-y-ImHpHpPYHp 809) 5'-W A T A G TW-3' PyHpPyImHp-y-PyPyHpPyHp 810) 5' A T A G AW-3' PyHpPyImPy-y-HpPyHpPyHp -W
811) 5' A T A G GW-3' PyHpPyImIm-y-PypyHpPyHp -W
812) 5' A T A G CW-3' PyHpPyImPy-y-ImPyHpPyHp -W
813) 5'-W A T A C TW-3' PyHpPyPyHp-y-PyImHpPyHp 814) 5'-W A T A C AW-3' PyHpPyPyPy-y-HpImHpPyHp 815) 5' A T A C GW-3' PyHpPyPyIm-y-pyImHpPyHp -W
816) 5' A T A C CW-3' PyHpPyPyPy-y-ImImHpPyHp -W
TABLE
39:
i0-ring Hairpin Polyamides for recognition of 7-by 5'-WATSNNW-3' DNA aromatic amino acid sequence sequence 817 ) 5' -WA T G T TW-3 ' PyHpImHpHp-y-PyPypyPyHp 818) '5' -WA T G T AW-3' PyHpImHppy-y-HpPyPyPyHp 819) 5' -WA T G T GW-3' PyHpImHpIm-y-PypypypyHp 820) 5' -WA T G T CW-3' PyHpImHpPy-y-ImPyPyPyHp 821) 5' -WA T G A TW-3' PyHpImPyHp-y-PyHpPyPyHp 822) 5' -WA T G A AW-3' PyHpImPyPy-y-HpHpPyPyHp 823) 5' -WA T G A GW-3' PyHpImPyIm-y-PyHpPyPyHp 824) 5' -WA T G A CW-3' PyHpImPyPy-y-ImHpPyPyHp 825) 5' -WA T G G TW-3' PyHpImImHp-y-Pypypypygp 826) 5' -WA T G G AW-3' PyHpImImPy-y-HpPyPyPyHp 827) 5' -WA T G C TW-3' PyHpImPyHp-y-PyImPyPyHp 828) 5' -WA T G C AW-3' PyHpImPyPy-y-HpImPyPyHp 829) 5' -WA T G G GW-3' PyHpImImIm-y-PyPyPyPyHp 830) 5' -WA T G G CW-3' PyHpImImPy-y-ImPyPyPyHp 831) 5' -WA T G C GW-3' PyHpImPyIm-y-PyImPyPyHp 832) 5' -WA T G C CW-3' PyHpImPyPy-y-ImImPyPyHp 833) 5' -WA T C T TW-3' PyHpPyHpHp-y-PyPyImPyHp 834) 5' -WA T C T AW-3' PyHpPyHpPy-y-HpPyImPyHp 835) 5' -WA T C T GW-3' PyHpPyHpIm-y-PyPyImPyHp 836) 5' -WA T C T CW-3' PyHpPyHpPy-y-ImPyImPyHp 837) 5' -WA T C A TW-3' PyHpPyPyHp-y-PyHpImPyHp 838) 5' -WA T C A AW-3' PyHpPyPyPy-y-HpHpImPyHp 839) 5' -WA T C A GW-3' ~ PyHpPyPyIm-y-PyHpImPyHp 840) 5' -WA T C A CW-3' PyHpPyPyPy-y-ImHpImPyHp 841) 5' -WA T C G TW-3' PyHpPyImHp-y-PyPyImPyHp 842) 5' -WA T C G AW-3' PyHpPyImPy-y-HpPyImPyHp 843) 5' -WA T C C TW-3' PyHpPyPyHp-y-PyImImPyHp 844) 5' -WA T C C AW-3' PyHpPyPyPy-y-HpImImPyHp 845) 5' -WA T C G GW-3' PyHpPyImIm-y-PyPyImPyHp 846) 5' -WA T C G CW-3' PyHpPyImPy-y-ImPyImPyHp 847) 5' -WA T C C GW-3' PyHpPyPyIm-y-PyImImPyHp 848) 5' -WA T C C CW-3' PyHpPyPyPy-y-ImImImPyHp TABLE
i0-ring Hairpin Polyamides for recognition of 7-by 5'-WATSNNW-3' DNA aromatic amino acid sequence sequence 817 ) 5' -WA T G T TW-3 ' PyHpImHpHp-y-PyPypyPyHp 818) '5' -WA T G T AW-3' PyHpImHppy-y-HpPyPyPyHp 819) 5' -WA T G T GW-3' PyHpImHpIm-y-PypypypyHp 820) 5' -WA T G T CW-3' PyHpImHpPy-y-ImPyPyPyHp 821) 5' -WA T G A TW-3' PyHpImPyHp-y-PyHpPyPyHp 822) 5' -WA T G A AW-3' PyHpImPyPy-y-HpHpPyPyHp 823) 5' -WA T G A GW-3' PyHpImPyIm-y-PyHpPyPyHp 824) 5' -WA T G A CW-3' PyHpImPyPy-y-ImHpPyPyHp 825) 5' -WA T G G TW-3' PyHpImImHp-y-Pypypypygp 826) 5' -WA T G G AW-3' PyHpImImPy-y-HpPyPyPyHp 827) 5' -WA T G C TW-3' PyHpImPyHp-y-PyImPyPyHp 828) 5' -WA T G C AW-3' PyHpImPyPy-y-HpImPyPyHp 829) 5' -WA T G G GW-3' PyHpImImIm-y-PyPyPyPyHp 830) 5' -WA T G G CW-3' PyHpImImPy-y-ImPyPyPyHp 831) 5' -WA T G C GW-3' PyHpImPyIm-y-PyImPyPyHp 832) 5' -WA T G C CW-3' PyHpImPyPy-y-ImImPyPyHp 833) 5' -WA T C T TW-3' PyHpPyHpHp-y-PyPyImPyHp 834) 5' -WA T C T AW-3' PyHpPyHpPy-y-HpPyImPyHp 835) 5' -WA T C T GW-3' PyHpPyHpIm-y-PyPyImPyHp 836) 5' -WA T C T CW-3' PyHpPyHpPy-y-ImPyImPyHp 837) 5' -WA T C A TW-3' PyHpPyPyHp-y-PyHpImPyHp 838) 5' -WA T C A AW-3' PyHpPyPyPy-y-HpHpImPyHp 839) 5' -WA T C A GW-3' ~ PyHpPyPyIm-y-PyHpImPyHp 840) 5' -WA T C A CW-3' PyHpPyPyPy-y-ImHpImPyHp 841) 5' -WA T C G TW-3' PyHpPyImHp-y-PyPyImPyHp 842) 5' -WA T C G AW-3' PyHpPyImPy-y-HpPyImPyHp 843) 5' -WA T C C TW-3' PyHpPyPyHp-y-PyImImPyHp 844) 5' -WA T C C AW-3' PyHpPyPyPy-y-HpImImPyHp 845) 5' -WA T C G GW-3' PyHpPyImIm-y-PyPyImPyHp 846) 5' -WA T C G CW-3' PyHpPyImPy-y-ImPyImPyHp 847) 5' -WA T C C GW-3' PyHpPyPyIm-y-PyImImPyHp 848) 5' -WA T C C CW-3' PyHpPyPyPy-y-ImImImPyHp TABLE
40:
10-ring Hairpin Yolyamides for recognition of 7-by 5'-WAAWNNW-3' DNA aromatic amino acid sequence sequence ' 849) 5' -WA A T TT W-3' PyPyHpHpHp-y-PypypyHpHp S 850) 'S' -WA A T TA W-3' PyPyHpHpPy-y-HpPyPyHpHp 851) 5' -WA A T TG W-3' PyPyHpI-iplm-y-PYPypyHpHp 852) 5' -WA A T TC W-3' PyPyHpHpPy-y-ImPyPyHpHp 853) 5' -WA A T AT W-3' PyPyHpPyHp-y-PyHpPyHpHp 854) 5' -WA A T AA W-3' PyPyHpPyPy-y-HpHpPyHpHp 855) 5' -WA A T AG W-3' PyPyHpPyIm-y-PyHpPyHpHp 856) 5' -WA A T AC W-3' PyPyHpPyPy-y-I~pPyHpHp 857) 5' -WA A T GT W-3' PYPYHPImHp-y-PyPyPyHpHp 858) 5' -WA A T GA W-3' PyPyHpImPy-y-HpPyPyHpHp 859) 5' -WA A T GG W-3' PyPyHpImIm-y-PypypyHpHp ?5 860) 5' -WA A T GC W-3' PyPyHpImPy-y-ImPyPyHpHp 861) 5' -WA A ~TCT W-3' PyPyHpPyHp-y-PyImPyHpHp 862) 5' -WA A T CA W-3' PyPyHpPyPy-y-HpImPyHpHp 863) 5' -WA A T CG W-3' PyPyHpPyIm-y-PyImPyHpHp 864) 5' -WA A T CC W-3' PyPyHpPyPy-y-ImImPyHpHp 865) 5' -WA A A TT W-3' PyPyPyHpHp-y-PypyHpHpHp 866) 5' -WA A A TA W-3' PyPypygppy-y-HpPyHpHpHp 867) 5' -WA A A TG W-3' Pypypygplm-y-PyPyHpHpHp 868) 5' -WA A A TC W-3' PyPyPyHpPy-y-ImPyHpHpHp 869) 5' -WA A A AT W-3' PyPyPyPyHp-y-PyHpHpHpHp 870) 5' -WA A A AA W-3' PyPyPypyPy-y-HpHpHpHpHp 871) 5' -WA A A AG W-3' Pypypypylm-y-PyHpHpHpHp 872) 5' -WA A A AC W-3' Pypypypypy-y-I~pHpHpHp 873) 5' -WA A A GT W-3' PyPyPyImHp-y-PyPyHpHpHp 874 ) 5' -WA A A GA W-3 ' PyPyPyImPy-y-HpPyHpHpHp 875) 5' -WA A A GG W-3' PyPyPyImIm-y-PyPyHpHpHp 876) 5' -WA A A GC W-3' PyPyPyImPy-y-ImPyHpHpHp 877) 5' -WA A A CT W-3' Pypypypygp-y-pyl~pHpHp 878) 5' -WA A A CA W-3' PyPyPyPypy-y-HpI~pHpHp 879) 5' -WA A A CG W-3' PyPyPyPyIm-y-PyImHpHpHp 880) 5' -WA A A CC W-3' PyPyPyPyPy-y-ImImHpHpHp TABLE
10-ring Hairpin Yolyamides for recognition of 7-by 5'-WAAWNNW-3' DNA aromatic amino acid sequence sequence ' 849) 5' -WA A T TT W-3' PyPyHpHpHp-y-PypypyHpHp S 850) 'S' -WA A T TA W-3' PyPyHpHpPy-y-HpPyPyHpHp 851) 5' -WA A T TG W-3' PyPyHpI-iplm-y-PYPypyHpHp 852) 5' -WA A T TC W-3' PyPyHpHpPy-y-ImPyPyHpHp 853) 5' -WA A T AT W-3' PyPyHpPyHp-y-PyHpPyHpHp 854) 5' -WA A T AA W-3' PyPyHpPyPy-y-HpHpPyHpHp 855) 5' -WA A T AG W-3' PyPyHpPyIm-y-PyHpPyHpHp 856) 5' -WA A T AC W-3' PyPyHpPyPy-y-I~pPyHpHp 857) 5' -WA A T GT W-3' PYPYHPImHp-y-PyPyPyHpHp 858) 5' -WA A T GA W-3' PyPyHpImPy-y-HpPyPyHpHp 859) 5' -WA A T GG W-3' PyPyHpImIm-y-PypypyHpHp ?5 860) 5' -WA A T GC W-3' PyPyHpImPy-y-ImPyPyHpHp 861) 5' -WA A ~TCT W-3' PyPyHpPyHp-y-PyImPyHpHp 862) 5' -WA A T CA W-3' PyPyHpPyPy-y-HpImPyHpHp 863) 5' -WA A T CG W-3' PyPyHpPyIm-y-PyImPyHpHp 864) 5' -WA A T CC W-3' PyPyHpPyPy-y-ImImPyHpHp 865) 5' -WA A A TT W-3' PyPyPyHpHp-y-PypyHpHpHp 866) 5' -WA A A TA W-3' PyPypygppy-y-HpPyHpHpHp 867) 5' -WA A A TG W-3' Pypypygplm-y-PyPyHpHpHp 868) 5' -WA A A TC W-3' PyPyPyHpPy-y-ImPyHpHpHp 869) 5' -WA A A AT W-3' PyPyPyPyHp-y-PyHpHpHpHp 870) 5' -WA A A AA W-3' PyPyPypyPy-y-HpHpHpHpHp 871) 5' -WA A A AG W-3' Pypypypylm-y-PyHpHpHpHp 872) 5' -WA A A AC W-3' Pypypypypy-y-I~pHpHpHp 873) 5' -WA A A GT W-3' PyPyPyImHp-y-PyPyHpHpHp 874 ) 5' -WA A A GA W-3 ' PyPyPyImPy-y-HpPyHpHpHp 875) 5' -WA A A GG W-3' PyPyPyImIm-y-PyPyHpHpHp 876) 5' -WA A A GC W-3' PyPyPyImPy-y-ImPyHpHpHp 877) 5' -WA A A CT W-3' Pypypypygp-y-pyl~pHpHp 878) 5' -WA A A CA W-3' PyPyPyPypy-y-HpI~pHpHp 879) 5' -WA A A CG W-3' PyPyPyPyIm-y-PyImHpHpHp 880) 5' -WA A A CC W-3' PyPyPyPyPy-y-ImImHpHpHp TABLE
41:
10-ring Haitpin Polyamides for recognition of 7-by 5'-WAASNNW-3' DNA aromatic amino acid sequence sequence 881) 5' -WA A G T T W-3' PyPyImHpHp-y-PyPyPyHpHp 882) ~5' -WA A G T A W-3' PyPyImHpPy-y-HpPyPyHpHp 883) 5' -WA A G T G W-3' PyPyImHpIm-y-PyPyPyHpHp 884) 5' -WA A G T C W-3' PyPyImHpPy-y-ImPyPyHpHp 885) 5' -WA A G A T W-3' PyPyImPyHp-y-PyHpPyHpHp 886) 5' -WA A G A A W-3' PyPyImPyPy-y-HpHpPyHpHp 887) 5' -WA A G A G W-3' PyPyImPyIm-y-PyHpPyHpHp 888) 5' -WA A G A C W-3' PyPyImPyPy-y-ImHpPyHpHp 889) 5' -WA A G G T W-3' PyPyImImHp-y-PyPyPyHpHp 890) 5' -WA A G G A W-3' PyPyImImPy-y-HpPyPyHpHp 891} 5' -WA A G C T W-3' PyPyImPyHp-y-PyImPyHpHp 892) 5' -WA A G C A W-3' PyPyImPyPy-y-HpImPyHpHp 893) 5' -WA A G G G W-3' PyPyImImIm-y-PyPyPyHpHp 894) 5' -WA A G G C W-3' PyPyImImPy-y-ImPyPyHpHp 895) 5' -WA A G C G W-3' PyPyImPyIm-y-PyImPyHpHp 896) 5' -WA A G C C W-3' PyPyImPyPy-y-ImImPyHpHp 897) 5' -WA A C T T W-3' PyPyPyHpHp-y-PyPyImHpHp 898) 5' -WA A C T A W-3' PyPyPyHpPy-y-HpPyImHpHp 899) 5' -WA A C T G W-3' PyPyPyHpIm-y-PyPyImHpHp 900) 5' -WA A C T C W-3' PyPyPyHpPy-y-ImPyImHpHp 901) 5' -WA A C A T W-3' PyPyPyPyHp-y-PyHpImHpHp 902} 5' -WA A C A A W-3' PyPyPyPyPy-y-HpHpImHpHp 903) 5' -WA A C A G W-3' PyPyPyPyIm-y-PyHpImHpHp 904) 5' -WA A C A C W-3' PyPyPyPyPy-y-ImHpImHpHp 905) 5' -WA A C G T W-3' PyPyPyImHp-y-PyPyImHpHp 906) 5' -WA A C G A W-3' PyPyPyImPy-y-HpPyImHpHp 907) 5' -WA A C C T W-3' PyPyPyPyHp-y-PyImImHpHp 908} 5' -WA A C C A W-3' PyPyPyPyPy-y-HpImImFipHp 909) 5' -WA A C G G W-3' PyPyPyImIm-y-PyPyImHpHp 910) 5' -WA A C G C W-3' PyPyPyImPy-y-ImPyImHpHp 911) 5' -WA A C C G W-3' PyPyPyPyIm-y-PyImImHpHp 912) 5' -WA A C C C W-3' PyPyPyPyPy-y-ImImImHpHp TABLE
10-ring Haitpin Polyamides for recognition of 7-by 5'-WAASNNW-3' DNA aromatic amino acid sequence sequence 881) 5' -WA A G T T W-3' PyPyImHpHp-y-PyPyPyHpHp 882) ~5' -WA A G T A W-3' PyPyImHpPy-y-HpPyPyHpHp 883) 5' -WA A G T G W-3' PyPyImHpIm-y-PyPyPyHpHp 884) 5' -WA A G T C W-3' PyPyImHpPy-y-ImPyPyHpHp 885) 5' -WA A G A T W-3' PyPyImPyHp-y-PyHpPyHpHp 886) 5' -WA A G A A W-3' PyPyImPyPy-y-HpHpPyHpHp 887) 5' -WA A G A G W-3' PyPyImPyIm-y-PyHpPyHpHp 888) 5' -WA A G A C W-3' PyPyImPyPy-y-ImHpPyHpHp 889) 5' -WA A G G T W-3' PyPyImImHp-y-PyPyPyHpHp 890) 5' -WA A G G A W-3' PyPyImImPy-y-HpPyPyHpHp 891} 5' -WA A G C T W-3' PyPyImPyHp-y-PyImPyHpHp 892) 5' -WA A G C A W-3' PyPyImPyPy-y-HpImPyHpHp 893) 5' -WA A G G G W-3' PyPyImImIm-y-PyPyPyHpHp 894) 5' -WA A G G C W-3' PyPyImImPy-y-ImPyPyHpHp 895) 5' -WA A G C G W-3' PyPyImPyIm-y-PyImPyHpHp 896) 5' -WA A G C C W-3' PyPyImPyPy-y-ImImPyHpHp 897) 5' -WA A C T T W-3' PyPyPyHpHp-y-PyPyImHpHp 898) 5' -WA A C T A W-3' PyPyPyHpPy-y-HpPyImHpHp 899) 5' -WA A C T G W-3' PyPyPyHpIm-y-PyPyImHpHp 900) 5' -WA A C T C W-3' PyPyPyHpPy-y-ImPyImHpHp 901) 5' -WA A C A T W-3' PyPyPyPyHp-y-PyHpImHpHp 902} 5' -WA A C A A W-3' PyPyPyPyPy-y-HpHpImHpHp 903) 5' -WA A C A G W-3' PyPyPyPyIm-y-PyHpImHpHp 904) 5' -WA A C A C W-3' PyPyPyPyPy-y-ImHpImHpHp 905) 5' -WA A C G T W-3' PyPyPyImHp-y-PyPyImHpHp 906) 5' -WA A C G A W-3' PyPyPyImPy-y-HpPyImHpHp 907) 5' -WA A C C T W-3' PyPyPyPyHp-y-PyImImHpHp 908} 5' -WA A C C A W-3' PyPyPyPyPy-y-HpImImFipHp 909) 5' -WA A C G G W-3' PyPyPyImIm-y-PyPyImHpHp 910) 5' -WA A C G C W-3' PyPyPyImPy-y-ImPyImHpHp 911) 5' -WA A C C G W-3' PyPyPyPyIm-y-PyImImHpHp 912) 5' -WA A C C C W-3' PyPyPyPyPy-y-ImImImHpHp TABLE
42:
10-ring Hairpin Polyamides for recognition of ?-by 5'-WACWNNW-3' DNA aromatic amino acid sequence sequence 913 ) 5' -WA C T T T W-3' PyPyHpHpHp-y-PyPyPyImHp 914 ) '5' -WA C T T A W-3 PyPyHpHpPy-Y-HpPyPyImHp ' 915) 5' -WA C T T G W-3' PYPYHpgpIm-Y-PYPYPyImHp 916) 5' -WA C T T C W-3' PyPyHpHpPy-y-ImPyPyImHp 917) 5' -WA C T A T W-3' PyPyHpPyHp-Y-PyHpPyImHp 918) 5' -WA C T A A W-3' PyPyHpPyPy-y-HpHpPyImHp 919) 5' -WA C T A G W-3' PyPyHpPyIm-y-PyHpPyImHp 92 0 5' -WA C T A C W- 3 PyPyHpPyPy-Y- ImHppyImHp ) ' 921) 5' -WA C T G T W-3' pypygpl~p-Y-p~,pypyl~p 922) 5' -WA C T G A W-3' PyPyHpImPy-y-HpPyPyImHp 923) 5' -WA C T G G W-3' PypyHpImIm-y-PyPyPyImHp 924} 5' -WA C T G C W-3' PyPyHpImPy-y-ImPyPyImHp 925) 5' -WA C T C T W-3' PyPyHpPyHp-y-PyImPyImHp 926) 5' -WA C T C A W-3' PyPyHpPyPy-Y-HpImPyImHp 927 ) 5' -WA C T C G W-3' PyPyHpPyim-y-PyImPyImHp 928) 5' -WA C T C C W-3' PypyHppypy-y-ImImPyImHp 929) 5' -WA C A T T W-3' PyPyPyHpHp-y-PyPyHpImHp 930) 5' -WA C A T A W-3' PypyPyHpPy-y-HpPyHpImHp 931) 5' -WA C A T G W-3' PyPyPyHpIm-y-PyPyHpImHp 932) 5' -WA C A T C W-3' PyPyPyHpPy-y-ImPyHpImHp 933) 5' -WA C A A T W-3' PypypypyHp-y-PyHpHpImHp 934) 5' -WA C A A A W-3' PyPyPyPyPy-y-HpHpHpImHp 935) 5' -WA C A A G W-3' PyPyPyPyIm-y-PyHpHpImHp 93 6 5' -WA C A A C W-3 PyPyPyPyPy-y- ImHpHpImHp ) ' 937) 5' -WA C A G T W-3' PyPypyImHp-y-PyPYHpImHp 938} 5' -WA C A G A W-3' PyPyPyImPy-y-HpPyHpImHp 939) 5' -WA C A G G W-3' PyPyPyImIm-y-PyPyHpImHp 940) 5' -WA C A G C W-3' PyPypyImPy-y-ImPyHpImHp 941) 5' -WA C A C T W-3' PyPyPyPyHp-Y-PyImI3pImHp 942 ) 5' -WA C A C A W-3 PyPyPyPyPy-y-HpImHpImHp ' 943 ) 5' -WA C A C G W-3 PyPypypylm-y-pyImHpImHp ' 944) 5' -WA C A C C W-3' pypypypypy-Y-ImImHpImHp 'TABLE 10-ring 43: Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' DNA aromatic amino acid sequence sequence 945) 5' A C G TT W-3' PyPyImHpHp-y-pypypylmHp -W
946) ~5'-W A C G TA W-3' PyPyImHpPy-y-HpPyPyImHp 947) 5'-W A C G TG W-3' PyPyImHpIm-y-PyPyPyImHp 948) 5' A C G TC W-3' PyPyImHpPy-y-ImPyPyImHp -W
949) 5'-W A C G AT W-3' PyPyImPyHp-y-pyHpPyImHp 950) 5'-W A C G AA W-3' PyPyImPyPy-y-HpHpPyImHp 951) 5' A C G AG W-3' PyPyImPyIm-y-PyHpPyImHp -W
952) 5' A C G AC W-3' PyPyImPyPy-y-ImHpPyImHp -W
953) 5'-W A C G GT W-3' PyPyImImHp-y-PyPyPyImHp 954) 5' A C G GA W-3' PyPyImImPy-y-HpPyPyImHp -W
955) 5' A C G CT W-3' PyPyImPyHp-y-PyImPyImHp -W
956) 5' A C G CA W-3' PyPyImPyPy-y-HpImPyImHp -W
957) 5'-W A C ~CTT W-3' PyPyPyHpHp-y-PyPyImImHp 958) 5'-W A C C TA W-3' PyPyPyHpPy-y-HpPyImImHp 959) 5' A C C TG W-3' PyPyPyHpIm-y-PyPyImImHp -W
960) 5' A C C TC W-3' PyPyPyHpPy-y-ImPyImImHp -W
961) 5' A C C AT W-3' PyPyPyPyHp-y-PyHpImImHp -W
962) 5'-W A C C AA W-3' PyPyPyPyPy-y-HpHpImImHp 963) 5'-W A C C AG W-3' PyPyPyPyIm-y-PyHpImImHp 964) 5' A C C AC W-3' PyPyPyPyPy-y-ImHpImImHp -W
965) 5' A C C GT W-3' PyPyPyImHp-y-PypyImImHp -W
966) 5' A C C GA W-3' PyPyPyImPy-y-HpPyImImHp -W
967) 5' A C C CT W-3' PyPyPyPyHp-y-PyImImImHp -W
968) 5' A C C CA W-3' PyPyPyPyPy-y-HpImImImHp -W
969) 5'-W A C G GG W-3' PyPyImImIm-y-PyPyPyImHp 970) 5'-W A C G GC W-3' PyPyImImPy-y-ImPyPyImHp 971) 5' A C G CG W-3' PyPyImPyIm-y-PyImPyImHp -W
972) 5' A C G CC W-3' PyPyImPyPy-y-ImImPyImHp -W
973) 5'-W A C C GG W-3' PyPyPyImIm-y-PyPyImImHp 974) 5'-W A C C GC W-3' PyPyPyImPy-y-ImPyImImHp 975) 5'-W A C C CG W-3' PyPyPyPyIm-y-PyImImImHp 976) 5'-W A C C CC W-3' PyPypypypy-y-ImImImImHp TABLE 44:
10-ring Hairpin Poiyamides for recognition of 7-by 5'-WTGWNNW-3' DNA aromatic amino acid sequence sequence 977 ) 5' -WT G T TT W-3 ' HpImHpHpHp-y-PyPYPYPyPy 978) ~5' -WT G T TA W-3' HpImHpHpPy-y-HpPyPyPYPy 979) 5' -WT G T TG W-3' HpImHpHpIm-y-PYPyPyPypy 980) 5' -WT G T TC W-3' HpImHpHpPy-y-ImPyPyPyPy 981) 5' -WT G T AT W-3' HpImHpPyHp-y-PYHpPYPyPy 982) 5' -WT G T AA W-3' HpImHppyPy-y-HpHpPyPYPy 983) 5' -WT G T AG W-3' HpImHpPyIm-y-PyHpPyPYPy 984) 5' -WT G T AC W-3' HpImHpPyPy-y-ImHpPYPYpy 985) 5' -WT G T GT W-3' HpImHpImHp-y-PYpyPYpypY
986) 5' -WT G T GA W-3' HpImHpImPy-y-HpPYPyPyPy 987) 5' -WT G T GG W-3' HpImHpImIm-y-PyPYPyPYPy IS 988) 5' -WT G T GC W-3' HpImHpImPy-y-ImPyPYPyPy 989) 5' -WT G T CT W-3' HpImHpPyHp-y-PYImPyPyPy 990) 5' -WT G T CA W-3' HpImHpPyPy-y-HpImPyPyPy 991) 5' -WT G T CG W-3' HpImHpPyIm-y-PyImPyPyPy 992) 5' -WT G T CC W-3' HpImHpPYPy-y-ImImPyPYPy 993) 5' -WT G A TT W-3' HpImPyHpHp-y-pypyHpPyPy 994) 5' W HpImPyHpPy-y-HpPyHpPyPy T
G
A
T
A
W-3' 995) 5' -WT G A TG W-3' HpImPyl3plm-y-PyPyHpPypy 996) 5' -WT G A TC W-3' HpImPyHpPy-y-ImPyHpPyPy 997) 5' -WT G A AT W-3' HpImPYPyHp-y-PyHpHpPyPy 998) 5' -WT G A AA W-3' HpImPYPyPy-y-HpHpHpPyPy 999) 5' -WT G A AG W-3' HpImPyPyIm-y-PyHpHpPyPy 1000) 5' -WT G A AC W-3' HpImPyPyPy-y-ImHpHpPYPy 1001) 5' -WT G A GT W-3' Hpln,pyl~p-y_pypYHppypy 1002) 5' -WT G A GA W-3' HpImPyImPy-y-HpPyHpPyPy 1003 5' -WT G A GG W-3 ' HpImPYImIm-y-PyPyHpPyPy ) 1004) 5' -WT G A GC W-3' HpImPyImPy-y-ImPyHpPyPy 1005) 5' -WT G A CT W-3' HpImPyPyHp-y-PYImHpPyPy 1006) 5' -WT G A CA W-3' HpImPYPYPy-y-HpImHpPyPy 1007) 5' -WT G A CG W-3' HpImPyPyIm-y-PyImHpPypy 1008) 5' -WT G A CC W-3' HpImPyPyPy-y-ImImHpPyPy TABLE
45:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGSNNW-3' DNA aromatic amino acid sequence sequence 1009) 5' -W T GG T T W-3' HpImImHpHp-y-PyPyPyPyPy 1010) 'S'-W T GG T A W-3' HpImImHpPy-y-HpPyPyPyPy 1011) 5' -W T GG T G W-3' HpImImHpIm-y-PyPyPyPyPy 1012) 5' -W T GG T C W-3' HpImImHpPy-y-ImPyPyPyPy 1013) 5' -W T GG A T W-3' HpImImPyHp-y-PyHpPyPyPy 1014) 5' -W T GG A A W-3' HpImImPyPy-y-HpHpPyPyPy 1015) 5' -W T GG A G W-3' HpImImPyIm-y-PyHpPyPyPy 1016) 5' -W T GG A C W-3' HpImImPyPy-y-ImHpPyPyPy 1017) 5' -W T GG G T W-3' HpImImImHp-y-PyPyPyPyPy 1018) 5' -W T GG G A W-3' HpImImImPy-~/-HpPyPyPyPy 1019) 5' -W T GG C T W-3' HpImImPyHp-y-PyImPyPyPy 1020) 5' -W T GG C A W-3' HpImImPyPy-y-HpImPyPyPy 1021) 5' -W T GC T T W-3' HpImPyHpHp-y-PyPyImPyPy 1022) 5' -W T GC T A W-3' HpImPyHpPy-y-HpPyImPyPy 1023 5' -W T GC T G W-3 ' HpImPyHpIm-y-PyPyImPyPy ) 1024) 5' -W T GC T C W-3' HpImPyHpPy-y-ImPyImPyPy 1025) 5' -W T GC A T W-3' HpImPyPyHp-y-PyHpImPyPy 1026) 5' -W T GC A A W-3' HpImPyPyPy-y-HpHpImPyPy 1027) 5' -W T GC A G W-3' HpImPyPyIrn-y-PyHpImPyPy 1028) 5' -W T GC A C W-3' HpImPyPyPy-y-ImHpImPyPy 1029) 5' -W T GC G T W-3' HpImPyImHp-y-PyPyImPyPy 1030) 5' -W T GC G A W-3' HpImPyImPy-y-HpPyImPyPy 1031) 5' -W T GC C T W-3' HpImPyPyHp-y-PyImImPyPy 1032) 5' -W T GC C A W-3' HpImPyPyPy-y-HpImImPyPy 1033) 5' -W T GG G G W-3' HpImImImIm-y-PyPyPyPyPy 1034) 5' -W T GG G C W-3' HpImImImPy-y-ImPyPyPyPy 1035) 5' -W T GG C G W-3' HpImImPyIm-y-PyImPyPyPy 1036) 5' -W T GG C C W-3' HpImImPyPy-y-ImImPyPyPy 1037 5' -W T GC G G W-3 ' HpImPyImIm-y-PyPyImPyPy ) 1038) 5' -W T GC G C W-3' HpImPyImPy-y-ImPyImPyPy 1039) 5' -W T GC C G W-3' HpImPyPyIm-y-PyImImPyPy 104 0 5' -W T GC C C W-3 ' HpImPyPyPy-y-ImImImPyPy ) WO 98/3?067 PCT/US98/01714 _71_ TABLE
46:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTWNNW-3' DNA aromatic amino acid sequence sequence 1041) 5' -WT T T T T W-3' HpHpHpHpHp-y-PyPyPypypy 1042) '5'-W T T T T A W-3' HpHpHpHpPy-y-HpPyPyPypy 1043) 5' -WT T T T G W-3' HpHpHpHpIm-y-PyPyPyPyPy 1044) 5' -WT T T T C W-3' HpHpHpHpPy-y-ImPyPyPyPy 1045) 5' -WT T T A T W-3' HpHpHpPyHp-y-PyHpPyPyPy 1046) 5' -WT T T A A W-3' HpHpHpPyPy-y-HpHpPyPyPy 1047) 5' -WT T T A G W-3' HpHpHpPyIm-y-PyHpPyPyPy 1048) 5' -WT T T A C W-3' HpHpHpPyPy-y-ImHpPyPyPy 1049) 5' -WT T T G T W-3' HpHpHpImHp-y-Pypypypypy 1050) 5' -WT T T G A W-3' HpHpHpImPy-y-HpPyPyPyPy 1051) 5' -WT T T G G W-3' HpHpHpImIm-y-PyPypypypy 1052) 5' -WT T T G C W-3' HpHpHpImPy-y-ImPyPyPyPy 1053) 5' -WT T T C T W-3' HpHpHpPyHp-y-PyImPyPyPy 1054) 5' -WT T T C A W-3' HpHpHpPyPy-y-HpImPyPyPy 1055) 5' -WT T T C G W-3' HpHpHpPyIm-y-PyImPyPyPy 1056) 5' -WT T T C C W-3' HpHpHpPyPy-y-ImTmPyPyPy 1057) 5' -WT T A T T W-3' HpHpPyHpHp-y-PypyHpPyPy 1058) 5' -WT T A T A W-3' HpHpPyHpPy-y-HpPyHpPyPy 1059) 5' -WT T A T G W-3' HpHpPyHpIm-y-PyPyHpPyPy 1060) 5' -WT T A T C W-3' HpHpPyHpPy-y-ImPyHpPyPy 1061) 5' -WT T A A T W-3' HpHpPyPyHp-y-pyHpHpPyPy 1062) 5' -WT T A A A W-3' HpHpPyPyPy-y-HpHpHpPyPy 1063) 5' -WT T A A G W-3' HpHpPyPyIm-y-PyHpHpPyPy 1064) 5' -WT T A A C W-3' HpHpPyPyPy-y-ImHpHpPyPy 1065) 5' -WT T A G T W-3' HpHpPyImHp-y-PyPyHpPyPy 1066) 5' -WT T A G A W-3' HpHpPyImPy-y-HpPyHpPyPy 1067) 5' -WT T A G G W-3' HpHpPyImIm-y-PyPyHpPyPy 1068) 5' -WT T A G C W-3' HpHpPyImPy-y-ImPyHpPyPy 1069) 5' -WT T A C T W-3' HpHpPyPyHp-y-PyImHpPyPy 1070) 5' -WT T A C A W-3' HpHpPyPyPy-y-HpImHpPyPy 1071} 5' -WT T A C G W-3' HpApPyPyIm-y-PyImHpPyPy 1072) 5' -WT T A C C W-3' HpApPyPyPy-y-ImImHpPyPy TABLE
47:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' DNA aromatic amino acid sequence sequence 1073) 5'-W T T G TT W-3' HpHpImHpHp-y-PyPyPyPYPy 1074) -5'-WT T G TA W-3' HpHpImHpPy-y-HpPyPyPYPy 1075) 5' T T G TG W-3' HpHpImHpIm-y-Pypypypypy -W
1076) 5'-W T T G TC W-3' HpHpImHpPy-y-ImPyPyPyPy 1077) 5'-W T T G AT W-3' HpHpImPYHp-y-pygppyPyPy 1078) 5'-W T T G AA W-3' HpHpImPyPy-y-HpHpPYPyPy 1079) 5' T T G AG W-3' HpHpImPyIm-y-PYHpPyPyPy -W
1080) 5' T T G AC W-3' HpHpImPyPy-y-ImHpPYPYPy -W
1081) 5' T T G GT W-3' HpHpImImHp-y-pypypypypy -W
1082) 5' T T G GA W-3' HpHpImImPy-y-HpPyPyPyPy -W
1083) 5'-W T T G CT W-3' HpHpImPYHp-y-PyImPyPyPy 1084) 5'-W T T G CA W-3' HpHpImPyPy-y-HpImPyPyPy 1085) 5' T T G GG W-3' HpHpImImIm-y-pypypypypy -W
1086) 5' T T G GC W-3' HpHpImImPy-y-ImPyPyPYPy -W
1087) 5'-W T T G CG W-3' HpHpImPYIm-y-PyImPyPyPy 1088) 5' T T G CC W-3' HpHpImPyPy-y-ImImPyPYPy -W
1089) 5'-W T T C TT W-3' HpHpPyHpHp-y-PypyImPYPy 1090) 5' T T C TA W-3' HpHpPYHpPy-y-HpPYImPyPy -W
1091) 5' T T C TG W-3' HpHpPyHpIm-y-PypyImPyPy -W
1092) 5'-W T T C TC W-3' HpHpPyHpPy-y-ImPyImPyPy 1093) 5'-W T T C AT W-3' HpHpPyPyHp-y-PyHpImPYPy 1094) 5'-W T T C AA W-3' HpHpPyPyPy-y-HpHpImPyPy 1095) 5' T T C AG W-3' ' HpHpPyPyIm-y-PYHpImPypy -W
1096) 5'-W T T C AC W-3' HpHpPYPYPy-y-ImHpImPYPY
1097) 5'-W T T C GT W-3' HpgppYl~p_y_pypylmpypy 1098) 5' T T C GA W-3' HpHpPyImPy-y-HpPyImPyPy -W
1099) 5' T T C CT W-3' HpHpPyPyHp-y-PyImImPyPy -W
1100) 5' T T C CA W-3' HpHpPyPyPy-y-HpImImPYPy -W
1101) 5' T T C GG W-3' HpHpPyImIm-y-PyPyImPyPy -W
1102) 5'-W T T C GC W-3' HpHpPyImPy-y-ImPyImPyPy 1103) 5'-W T T C CG W-3' HpHpPyPyIm-y-PyImImPyPy 1104) 5'-W T T C CC W-3' HpHpPyPyPy-y-ImImImPyPy . , TABLE
48:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTAWNNW-3' DNA aromatic amino acid sequence sequence 1105) 5' -WT A T T T W-3' HpPyHpHpHp-y-PyPyPyHpPy S 1106) ~5'-WT A T T A W-3' HpPyHpHpPy-y-HpPyPyHpPy 1107) 5' -WT A T T G W-3' HpPyHpHpIm-y-PypyPyHpPy 1108) 5' -WT A T T C W-3' HpPyHpHpPy-y-ImPyPyHpPy 1109) 5' -WT A T A T W-3' HpPyHpPyHp-y-PyHpPyHpPy 1110) 5' -WT A T A A W-3' HpPyHpPyPy-y-HpHpPyHpPy 1111) 5' -WT A T A G W-3' HpPyHpPyIm-y-PyHpPyHpPy 1112) 5' -WT A T A C W-3' HpPyHpPyPy-y-ImHpPyHpPy 1113) 5' -WT A T G T W-3' HpPyHpImHp-y-PyPyPyHpPy 1114) 5' -WT A T G A W-3' HpPyHpImPy-y-HpPyPyHpPy 1115) 5' -WT A T G G W-3' HpPyHpImIm-y-PyPyPyHpPy 1116) 5' -WT A T G C W-3' HpPyHpImPy-y-ImPyPyHppy 1117) 5' -WT A T C T W-3' HpPyHpPyHp-y-PyImPyHpPy 1118) 5' -WT A T C A W-3' HpPyHpPyPy-y-HpImPyHpPy 1119) 5' -WT A T C G W-3' HpPyHpPyIm-y-PyImPyHpPy 1120) 5' -WT A T C C W-3' HpPyHpPyPy-y-ImImPyHpPy 1121) 5' -WT A A T T W-3' HpPyPyHpHp-y-PyPyHpHpPy 1122) 5' -WT A A T A W-3' HpPyPyHpPy-y-HpPyHpHpPy 1123) 5' -WT A A T G W-3' HpPyPyHpIm-y-PyPyHpHpPy 1124) 5' -WT A A T C W-3' HpPyPyHpPy-y-ImPyHpHpPy 1125) 5' -WT A A A T W-3' HpPyPyPyHp-y-PyHpHpHpPy 1126) 5' -WT A A A A W-3' HpPyPyPyPy-y-HpHpHpHpPy 1127) 5' -WT A A A G W-3' HpPyPyPyIm-y-PyHpHpHpPy 1128) 5' -WT A A A C W-3' HpPyPyPyPy-y-ImHpHpHpPy 1129) 5' -WT A A G T W-3' HpPyPyImHp-y-PyPyHpHpPy 1130) 5' -WT A A G A W-3' HpPyPyImPy-y-HpPyHpHpPy 1131) 5' -WT A A G G W-3' HpPyPyImIm-y-PyPyHpHpPy 1132) 5' -WT A A G C W-3' HpPyPyImPy-y-ImPyHpHpPy 1133) 5' -WT A A C T W-3' HpPyPyPyHp-y-PyImHpHpPy 1134) 5' -WT A A C A W-3' HpPyPyPyPy-y-HpImHpHpPy 1135) 5' -WT A A C G W-3' HpPyPyPyIm-y-PyImHpHpPy 1136) 5' -WT A A C C W-3' HpPyPyPyPy-y-ImImHpHpPy TABLE
49:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTASNNW-3' DNA aromatic amino acid sequence sequence 1137 ) 5' -WT A G T T W-3 HpPyImHpHp-y-PyPypyHpPy ' S 1138) ~5'-WT A G T A W-3' HpPyImHpPy-y-HpPyPyHpPy 1139) 5' -WT A G T G W-3' HpPyImHpIm-y-PyPyPyHpPy 1140) 5' -WT A G T C W-3' HpPyImHpPy-y-ImPypyHpPy 1141) 5' -WT A G A T W-3' HpPyImPyHp-y-PyHpPyHpPy 1142) 5' -WT A G A A W-3' HpPyImPyPy-y-HpHpPyHpPy 1143) 5' -WT A G A G W-3' HpPyImPyIm-y-PyHpPyHpPy 1144) 5' -WT A G A C W-3' HpPyImPyPy-y-ImHpPyI-IpPy 1145) 5' -WT A G G T W-3' HpPyImImHp-y-PyPyPyHpPy 1146) 5' -WT A G G A W-3' HpPyImImPy-y-HpPyPyHpPy 1147) 5' -WT A G C T W-3' HpPyImPyHp-y-PyImPyI-IpPy 1148) 5' -WT A G C A W-3' HpPyImPyPy-y-HpImPyHpPy 1149) 5' -WT A G G G W-3' HpPyImImIm-y-PyPyPyHpPy 1150) 5' -WT A G G C W-3' HpPyImImPy-y-ImPyPyHpPy 1151) 5' -WT A G C G W-3' HpPyImPyIm-y-PyImPyHpPy 1152) 5' -WT A G C C W-3' HpPyImPyPy-y-ImImPyHpPy 1153) 5' -WT A C T T W-3' HpPyPyHpHp-y-PyPyImHppy 1154) 5' -WT A C T A W-3' HpPyPyHpPy-y-HpPyImHpPy 1155) 5' -WT A C T G W-3' HpPyPyHpIm-y-PyPyImHpPy 1156 ) 5' -WT A C T C W-3 HppyPyHpPy-y-ImPyImHpPy ' 1157) 5' -WT A C A T W-3' HpPyPyPyHp-y-PyHpImHpPy 1158) 5' -WT A C A A W-3' HpPyPyPyPy-y-HpHpImHpPy 1159) 5' -WT A C A G W-3' HpPyPyPyIm-y-PyHpImHpPy 1160) 5' -WT A C A C W-3' HpPyPyPyPy-y-ImHpImHpPy 1161) 5' -WT A C G T W-3' HppyPyImHp-y-PyPyImHpPy 1162) 5' -WT A C G A W-3' HpPyPyImPy-y-HpPyImHpPy 1163) 5' -WT A C C T W-3' HpPyPyPyHp-y-PyImImHpPy 1164 ) 5' -WT A C C A W-3 HpPyPyPyPy-y-HpImImHpPy ' 1165) 5' -WT A C G G W-3' HpPyPyImIm-y-PyPyImHpPy 1166 ) 5' -WT A C G C W-3 HpPyPyImPy-y-ImPyImHpPy ' 1167) 5' -WT A C C G W-3' HpPyPyPyIm-y-PyImImHpPy 1168) 5' -WT A C C C W-3' HpPyPyPyPy-y-ImImImHpPy l Al3LH
50:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCWNNW-3' DNA aromatic amino acid sequence sequence 1169) 5'-W T C TT T W-3' HpPyHpHpHp-y-PypypylmPy 1170) ~5'-W T C TT A W-3' HpPyHpHpPy-y-HpPyPyImPy 1171) 5'-W T C TT G W-3' HpPyHpHpIm-y-Pypypylmpy 1172) 5'-W T C TT C W-3' HpPyHpHpPy-y-ImPyPyImPy 1173) 5'-W T C TA T W-3' HPPYHPPYHP-Y-PYHPPYImPy 1174) 5'-W T C TA A W-3' HpPyHpPyPy-y-HpHpPyImPy 1175) 5'-W T C TA G W-3' HpPyHpPyIm-y-PyHpPyImPy 1176) 5'-W T C TA C W-3' HpPyHpPypy-y-ImHppyImPy 1177) 5'-W T C TG T W-3' HppyHpl~p_Y-pypypylmPy 1178) 5'-W T C TG A W-3' HpPyHpImPy-y-HpPyPyImPy 1179) 5'-W T C TG G W-3' HpPyHpImIm-y-PyPyPyImPy 1180) 5'-W T C TG C W-3' HpPyHpImPy-y-ImPyPyImPy 1181) 5'-W T C TC T W-3' HpPyHpPyHp-y-PyImPyImPy 1182) 5'-W T C TC A W-3' HpPyHpPypy-y-HpImPyImPy 1183) 5'-W T C TC G W-3' HpPyHpPyIm-y-PyImPyImPy 1184) 5'-W T C TC C W-3' HpPyHpPyPy-y-ImImPyImPy 1185) 5'-W T C AT T W-3' HpPyPyHpHp-y-PyPyHpImPy 1186) 5'-W T C AT A W-3' HpPyPyHpPy-y-HpPyHpImPy 1187) 5'-W T C AT G W-3' HpPyPyHpIm-y-PyPyHpImPy 1188) 5'-W T C AT C W-3' HpPyPyHpPy-y-ImPyHpImPy 1189) 5'-W T C AA T W-3' HpPyPyPyHp-y-PyHpHpImPy 1190) 5'-W T C AA A W-3' HpPyPyPyPy-y-HpHpHpImPy 1191) 5'-W T C AA G W-3' ~ HpPyPyPyIm-y-PyHpHpImPy 1192) 5'-W T C AA C W-3' HpPyPyPyPy-y-ImHpHpImPy 1193) 5'-W T C AG T W-3' HpPyPyImHp-y-PyPyHpImPy 1194) 5'-W T C AG A W-3' HpPyPyImPy-y-HpPyHpImPy 1195) 5'-W T C AG G W-3' HpPyPyImIm-y-PyPyHpImPy 1196) 5'-W T C AG C W-3' HpPyPyImPy-y-ImPyHpImPy 1197) 5'-W T C AC T W-3' HpPyPyPyHp-y-PyImHpImPy 1198) 5'-W T C AC A W-3' HpPyPyPyPy-y-HpImHpImPy 1199) 5'-W T C AC G W-3' HpPyPyPyIm-y-PyImHpImPy 1200) 5'-W T C AC C W-3' HpPyPyPyPy-y-ImImHpImPy WO 98/37067 PCTlUS98/01714 TABLE
51:
l0~ring Hairpin Polyamides for recognition of 7-by 5'-WTCSNNW-3' DNA aromatic amino acid sequence sequence 1201) 5' -W T CG T T W-3' HpPyImHpHp-y-PyPyPyImPy 1202) ~5'-W T CG T A W-3' HpPyImHpPy-y-HpPyPyImPy 1203) 5' -W T CG T G W-3' HpPyImHpIm-y-PyPyPyImPy 1204) 5' -W T CG T C W-3' HpPyImHpPy-y-ImPyPyImPy 1205) 5' -W T CG A T W-3' HpPyImPyHp-y-PyHpPyImPy 1206) 5' -W T CG A A W-3' HpPyImPyPy-y-HpHpPyImPy 1207) 5' -W T CG A G W-3' HpPyImPyIm-y-PyHpPyImPy 1208) 5' -W T CG A C W-3' HpPyImPyPy-y-ImHpPyImPy 1209) 5' -W T CG G T W-3' HpPyImImHp-y-PyPyPyImPy 1210) 5' -W T CG G A W-3' HpPyImImPy-y-HpPyPyImPy 1211) 5' -W T CG C T W-3' HpPyImPyHp-y-PyImPyImPy 1212) 5' -W T CG C A W-3' HpPyImPyPy-y-HpImPyImPy 1213) 5' -W T CC T T W-3' HpPyPyHpHp-y-PyPyImImPy 1214) 5' -W T CC T A W-3' HpPyPyHpPy-y-HpPyImImPy 1215) 5' -W T CC T G W-3' HpPyPyHpIm-y-PyPyImImPy 1216 5' -W T CC T C W-3 ' HpPyPyHpPy-y- ImPyImImPy ) 1217 5' -W T CC A T W-3 ' HpPyPyPyHp-y-PyHpImImPy ) 1218) 5' -W T CC A A W-3' HpPyPyPyPy-y-HpHpImImPy 1219) 5' -W T CC A G W-3' HpPyPyPyIm-y-PyHpImImPy 1220) 5' -W T CC A C W-3' HpPyPyPyPy-y-ImHpImImPy 1221) 5' -W T CC G T W-3' HpPyPyImHp-y-PyPyImImPy 1222 5' -W T CC G A W-3' HpPyPyImPy-y-HpPyImImPy ) 1223 5' -W T CC C T W-3 ' HpPyPyPyHp-y-PyImImImPy ) 1224) 5' -W T CC C A W-3' HpPyPyPyPy-y-HpImImImPy 1225) 5' -W T CG G G W-3' HpPyImImIm-y-PyPyPyImPy 1226) 5' -W T CG G C W-3' HpPyImImPy-y-ImPyPyImPy 1227) 5' -W T CG C G W-3' HpPyImPyIm-y-PyImPyImPy 1228) 5' -W T CG C C W-3' HpPyImPyPy-y-ImImPyImPy 1229) 5' -W T CC G G W-3' HpPyPyImIm-y-PyPyImImPy 1230) 5' -W T CC G C W-3' HpPyPyImPy-y-ImPyImImPy 1231) 5' -W T CC C G W-3' HpPyPyPyIm-y-PyImImImPy 1232 5' -W T CC C C W-3 ' HpPyPyPyPy-y-ImImImImPy ) _77_ TABLE 52 :
10-ring Hairpin Yolyamides for recognition of 7-by 5'-WGGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 243(3) 5' G G T TG W-3' ImIm-~-HpIm-y-PYpypypypY
-W
243~3p) '5' G G T TG W-3' ImIm-[3-HpIm-y-PYPy-~3-pypy -W
247(3) 5' G G T AG W-3' Imlm-J3-PyIm-y-PyHpPyPyPy -W
247~p) 5' G G T AG W-3' ImIm-~-PyIm-y-PYHp-(3-PyPy -W
249(3) 5' G G T GT W-3' ImIm-(3-ImHp-y-Pypypypypy -W
249(3p) 5' G G T GT W-3' ImIm-~3-ImHp-y-Pypy-~3-pypY
-W
2503) 5' G G T GA W-3' ImIm-~i-ImPy-y-HpPyPyPyPy -W
250(3p) 5' G G T GA W-3' ImIm-(3-ImPy-y-HpPy-~i-PypY
-W
2513) 5' G G T GG W-3' ImIm-(3-ImIm-y-pypypypypy -W
251(3p) 5' G G T GG W-3' Imlm-(3-Imlm-y-PyPy-(3-PyPy -W
252(3) 5' G G T GC W-3' Imlm-/3-ImPy-y-ImPyPyPyPy -W
252(3p) 5' G G T GC W-3' Imam-(3-ImPy-y-ImPy-(3-Pypy -W
255(3) 5' G G T CG W-3' ImIm-~-Pylm-y-pyImPyPyPy -W
255~ip) 5' G G T CG W-3' ImIm-(3-PYIm-y-PyIm-a-PyPy -W
2593) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPyHpPyPy -W
259~3p) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPy-(3-PyPy -W
263(3) 5' G G A AG W-3' ImIm-p-PyIm-y-PyHpHpPyPy -W
263(3p) 5' G G A AG W-3' ImIm-(3-PyIm-y-PyHp-~3-PyPy -W
2653) 5' G G A GT W-3' ImIm-(3-ImHp-y-PypyHppypy -W
265(3p) 5' G G A GT W-3' Imlm-(3-ImHp-y-PyPy-p-PyPy -W
266(3) 5' G G A GA W-3' ImIm-(3-ImPy-y-HpPyHpPyPy -W
266~3p) 5' G G A GA W-3' Imlm-~3-ImPy-y-HpPy-(3-PyPy -W
267(3) 5' G G A GG W-3' ImIm-(3-ImIm-y-PyPyHpPyPy -W
267(3p) 5' G G A GG W-3' ImIm-/3-ImIm-y-Pypy-~-pypy -W
2683) 5' G G A GC W-3' Imlm-~3-ImPy-y-ImpyHpPyPy -W
268~3p) 5' G G A GC W-3' ImIm-(3-ImPy-y-ImPy-~3-PyPy -W
271(3) 5' G G A CG W-3' ImIm-~3-PyIm-y-PyImHpPyPy -W
271(3p) 5' G G A CG W-3' Imlm-(3-PyIm-y-PyIm-j3-PyPy -W
WO 98I370b7 PCT/US98/01714 _78_ TABLE
53: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 273(3) 5' G G G TT W-3' ImImIm-p-Hp-y-PyPyPyPyPy -W
273~3p) ~ G G G TT W-3' ImImIm-(3-Hp-y-Py-(3-PyPyPy 5' -W
274(3) 5' G G G TA W-3' ImImIm-(3-Py-y-HpPyPyPyPy -W
274~3p) 5' G G G TA W-3' ImImIm-~3-Py-y-Hp-(3-PyPyPy -W
275(3) 5' G G G TG W-3' ImImIm-~3-Im-y-PyPyPyPyPy -W
275~3p) 5' G G G TG W-3' ImImIm-~3-Im-y-Py-(3-PyPyPy -W
276(3) 5' G G G TC W-3' ImImIm-(3-Py-y-ImPyPyPyPy -W
276(3p) 5' G G G TC W-3' ImImIm-(3-Py-y-Im-(3-PyPyPy -W
277(3) 5'-W G G G AT W-3' ImImIm-(3-Hp-y-PyHpPyPyPy 277~3p) 5' G G G AT W-3' ImImIm-(3-Hp-y-Py-~3-PyPyPy -W
2783) 5' G G G AA W-3' ImImIm-(3-Py-y-HpHpPyPyPy -W
278(3p) 5' G G G AA W-3' ImImIm-~-Py-y-Hp-/3-PyPyPy -W
279(3) 5' G G G AG W-3' ImImIm-(3-Im-y-PyHpPyPyPy -W
279~3p) 5' G G G AG W-3' ImImIm-~-Im-y-Py-[3-PyPyPy -W
280(3) 5' G G G AC W-3' ImImIm-(3-Py-y-ImHpPyPyPy -W
280(3p) 5' G G G AC W-3' ImImIm-(3-Py-y-Im-~3-PyPyPy -W
283(3) 5' G G G CT W-3' ImImIm-p-Hp-y-PyImPyPyPy -W
284(3) 5' G G G CA W-3' ImImIm-(3-Py-y-HpImPyPyPy -W
285(3) 5' G G C TT W-3' ImImPylipHp-y-Py-p-ImPyPy -W
285(3p) 5' G G C TT W-3' ImImPy-(3-Hp-y-Py-(3-ImPyPy -W
286(3) 5' G G C TA W-3' ImImPyHpPy-y-Hp-~i-ImPyPy -W
286~3p) 5' G G C TA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy -W
287~i) 5' G G C TG W-3' ImIm-~3-HpIm-y-Py-(3-ImPyPy -W
288(3) 5' G G C TC W-3' ImImPyHpPy-y-Im-(3-ImPyPy -W
288~ip) 5' G G C TC W-3' ImImPy-(3-Py-y-Im-(3-ImPyPy -W
289(3) 5' G G C AT W-3' ImImPyPyHp-y-Py-p-ImPyPy -W
289(3p) 5' G G C AT W-3' ImImPy-/3-Hp-y-Py-(3-ImPyPy -W
290(3) 5' G G C AA W-3' ImImPyPyPy-y-Hp-~-ImPyPy -W
290~ip) 5' G G C AA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy -W
_79_ TABLE 53 (cont.): ecogmrion of 7-by 5'-WGGSNNW-3' 10-ring Hairpin with ~3 substitutions Polyamides for r .
DNA aromatic amino acid sequence sequence 291(3) 5'-W GG C A G W-3' ImIm-(3-PyIm-y-py-(3-ImPyPy 292(3) 5' GG C A C W-3' TmImPyPyPy-y-Im-(3-ImPyPy -W
292(3p) ~ GG C A C W-3' ImImPy-(3-Py-y-Im-~i-ImPyPy 5' -W
293(3) 5' GG C G T W-3' Imam-(3-ImHp-y-Py-(3-ImPyPy -W
294(3) 5' GG C G A W-3' ImIm-(3-ImPy-y-Hp-(3-ImPyPy -W
295x) 5'-W GG C C T W-3' ImImPyPyHp-y-pylmlm-(3-Py 2963) 5' GG C C A W-3' ImImPyPypy-y-HpImIm-p-Py -W
619(3) 5' GG G C G W-3' ImImIm-(3-Im-y-PyImPyPyPy -W
G20(3) 5' GG G C C W-3' ImImIm-(3-Py-y-ImImPypyPy -W
G21(3) 5' GG C G G W-3' Imlm-/3-Imlm-y-Py-(3-ImPyPy -W
G22(3) 5' GG C G C W-3' ImIm-(3-Impy-y-Im-~3-ImPyPy -W
G23~3) 5' GG C C G W-3' Imlm-(3-Pylm-y-PyImIm-(3-Py -W
G24(3) 5' GG C C C W-3' ImImPyPyPy-y-ImImIm-(3-Py -W
TABLE :
54 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 299(3) 5' G T T T G W-3' ImHp-(3-HpIm-y-PyPyPyPyPy -W
299~3p) 5' G T T T G W-3' ImHp-J3-HpIm-y-PyPy-(3-PyPy -W
303(3) ' G T T A G W-3' ImHp-(3-PyIm-y-PyHpPyPyPy 5' -W
303~3p) 5' G T T A G W-3' ImHp-(3-PyIm-y-PyHp-(3-PyPy -W
305(3) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPyPyPyPy -W
305(3p) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy -W
306(3) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPyPyPyPy -W
306(3p) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy -W
3073) 5' G T T G G W-3' ImHp-(3-ImIm-y-PyPyPyPyPy -W
307~p) 5' G T T G G W-3' ImHp-J3-ImIm-y-PyPy-~3-PyPy -W
3083) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPyPyPyPy -W
308~3p) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPy-p-PyPy -W
3113) 5' G T T C G W-3' ImHp-~3-PyIm-y-PyImPyPyPy -W
311(3p) 5' G T T C G W-3' ImHp-(3-Pylm-y-Pylm-~i-PyPy -W
3153) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPyHpPyPy -W
315(3p) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPy-(3-PyPy -W
3193) 5' G T A A G W-3' ImHp-(3-Pylm-y-PyHpHpPyPy -W
319(3p) 5' G T A A G W-3' ImHp-~3-PyIm-y-PyHp-(3-PyPy -W
321~i) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPyApPyPy -W
321(3p) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy -W
322(3) 5' G T A G A W-3' ImHp-~i-ImPy-y-HpPyHpPyPy -W
322(3p) 5' G T A G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy -W
323(3) 5' G T A G G W-3' ImHp-~3-Imlm-y-PyPyHpPyPy -W
323(3p) 5' G T A G G W-3' ImHp-~3-ImIm-y-PyPy-(3-PyPy -W
324(3) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPyHpPyPy -W
324~p) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPy--PyPy -W
327(3) 5' G T A C G W-3' ImHp-(3-PyIm-y-PyImHpPyPy -W
327(3p) 5' G T A C G W-3' ImHp-(3-PyIm-y-Pylm-(3-PyPy -W
'TABLE
55: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTSNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 3293) 5' G T G T T W-3' Im-(3-ImHpHp-y-PyPyPYPYPy -W
329(3P) '5'-WG T G T T W-3' Im-(3-ImHpHp-y-Pypypy-p-py 3303) 5' G T G T A W-3' Im-J3-ImHpPy-y-Hppypypypy -W
330(3p 5' G T G T A W-3' Im-(3-ImHpPy-Y-HpPYPy-~3-py -W
3313) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPyPYPyPy -W
331(3p) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPYPy-~3-Py -W
332J3) 5' G T G T C W-3' Im-a-ImHpPy-y-ImPyPyPYPy -W
332(3p) 5' G T G T C W-3' Im-~-ImHpPy-y-ImPYPy-/3-Py -W
333(3) 5' G T G A T W-3' Im-(3-ImPyHp-Y-PYHpPyPyPy -W
333~ip) 5' G T G A T W-3' Im-~3-ImPYHp-y-PyHpPy-(3-Py -W
334(3) 5' G T G A A W-3' Im-~3-ImPyPy-y-HpHpPYPYPy -W
334(3p) 5' G T G A A W-3' Im-(3-ImPyPy-y-HpHpPy-p-Py -W
335~i) 5' G T G A G W-3' Im-(3-ImPyIm-y-PyHpPYPYPy -W
335pp) 5' G T G A G W-3' Im-p-ImPyIm-Y-PyHpPy-(3-Py -W
3363) 5' G T G A C W-3' Im-p-ImPyPy-y-ImHpPYPYPy -W
336(3p) 5' G T G A C W-3' Im-(3-ImPyPy-y-ImHppy-p-Py -W
337(3) 5' G T G G T W-3' Im-(3-ImImHp-y-PyPypypypy -W
337(3p) 5' G T G G T W-3' Im-~3-ImImHp-y-PYPyPy-(3-Py -W
338(3) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPYPYPYPy -W
338~3p) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPyPy-(3-Py -W
339(3) 5' G T G C T W-3' Im-~-ImPyHp-y-PYImPyPyPy -W
339~p) 5' G T G C T W-3' Im-~3-ImPYHp-y-PyImPy-p-Py -W
3403) 5' G T G C A W-3' ~ Im-p-ImPyPy-y-HpImPyPyPy -W
340(3p) 5' G T G C A W-3' Im-p-ImPyPy-Y-HpImPy-~3-Py -W
3413) 5' G T G G G W-3' Im-p-ImImIm-y-PyPyPyPyPy -W
341(3p) 5' G T G G G W-3' Im-~3-ImImIm-y-PypyPy-(3-PY
-W
342(3) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPYPyPy -W
342(3p) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPy-(3-Py -W
343(3) 5' G T G C G W-3' Im-(3-ImPyIm-y-PyImPyPypy -W
TABLE 55 Polyamides (cont.): for 10-ring recognition Hairpin of 7-by 5'-WGTS1VNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 343(3p) 5' G T GC G W-3' Im-(3-ImPyIm-y-PyImPy-(3-Py -W
344(3) 5' G T GC C W-3' Im-(3-ImPyPy-y-ImImPyPyPy -W
344(3p) '5' G T GC C W-3' Im-p-ImPyPy-y-ImImPy-(3-Py -W
345(3) 5' G T CT T W-3' ImHpPyI~IpHp-y-Py-~3-ImPyPy -W
345~3p) 5' G T CT T W-3' ImHpPy-~3-Hp-y-Py-(3-ImPyPy -W
346(3) 5' G T CT A W-3' ImHpPyHpPy-y-Hp-(3-ImPyPy -W
346(3p) 5' G T CT A W-3' ImHpPy-~3-Py-y-Hp-(3-ImPyPy -W
3473} 5' G T CT G W-3' ImHp-(3-HpIm-y-Py-p-ImPyPy -W
3483) 5' G T CT C W-3' ImHpPyHpPy-y-Im-(3-ImPyPy -W
348(3p) 5' G T CT C W-3' ImHpPy-(3-Py-y-Im-~3-ImPyPy -W
349(3) 5' G T CA T W-3' ImHpPypyHp-y-Py-~-ImPyPy -W
349(3p) 5' G T CA T W-3 T ImHpPyPyHp-y-Py--ImPyPy -W
350(3) 5' G T CA A W-3' ImHpPyPyPy-y-Hp-~3-ImPyPy -W
350~3p) 5' G T CA A W-3' ImHpPy-(3-Py-y-Hp-~i-ImPyPy -W
351(3} 5' G T CA G W-3' ImHp-~3-PyIm-y-Py-(3-ImPyPy -W
3523) 5' G T CA C W-3' ImHpPyPyPy-y-Im-~3-ImPyPy -W
352(3p) 5' G T CA C W-3' ImHpPy-(3-Py-y-Im-(3-ImPypy -W
3533) 5' G T CG T W-3' ImHp-(3-ImHp-y-Py-(3-ImPyPy -W
354(3) 5' G T CG A W-3' ImHp-~-Impy-y-Hp--ImPypy -W
3553) 5' G T CC T W-3' ImHpPypyHp-y-PyImIm-(3-Py -W
355~3p) 5' G T CC T W-3' Im-(3-PyPyHp-y-PyImIm-[3-Py -W
3563) 5' G T CC A W-3' ImHppyPyPy-y-HpImIm-p-Py -W
356~3p) 5' G T CC A W-3' Im-~3-PyPyPy-y-HpImIm-(3-Py -W
357(3) 5' G T CG G W-3' ImHp-(3-ImIm-y-Py-p-ImPyPy -W
358(3) 5' G T CG C W-3' ImHp-(i-ImPy-y-Im-(3-ImPyPy -W
359(3) 5' G T CC G W-3' ImHp-/3-Pylm-y-PyImIm-(i-Py -W
360(3) 5' G T CC C W-3' ImHpPyPyPy-y-ImImIm-~3-Py -W
360~ip) 5' G T CC C W-3' Im-p-PyPyPy-y-ImImIm-p-Py -W
_g3_ TABLE 56: l0-ring Hairpin Polyamides for recognition of 7-by 5'-WGAWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 363(3) 5' G A T T G W-3' ImPy-~-HpIm-y-Pypypygppy -W
363~3p) 5' G A T T G W-3' ImPy-(3-HpIm-y-Pypy-(3-Hppy -W
3673) ' G A T A G W-3' ImPy-(3-PyIm-y-pyHpPYHpPy S' -W
367pp) 5' G A T A G W-3' ImPy-p-PyIm-y-PYHp-(3-HpPy -W
369(3) 5' G A T G T W-3' ImPy-~3-ImHp-y-PyPYPYHpPy -W
369(3p) 5' G A T G T W-3' ImPy-~3-ImHp-y-pypy-(3-HpPy -W
370(3) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPYPYHpPy -W
370~p) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPy-~3-HpPy -W
371~i) 5' G A T G G W-3' ImPy-p-ImIm-y-PyPypyHpPy -W
371(3p) 5' G A T G G W-3' ImPy-(3-ImIm-y-Pypy-~-HpPy -W
372(3) 5' G A T G C W-3' -W ImPy- (3 - ImPy-y- ImPYPyHpPy 372(3p) 5' G A T G C W-3' ImPy-p-ImPy-y-ImPy-~3-HpPy -W
375(3) 5' G A T C G W-3' ImPy-(3-Pylm-y-PyImPYHpPy -W
375~3p) 5' G A T C G W-3' ImPy-(3-PyIm-y-pylm-(3-HpPy -W
379(3) 5' G A A T G W-3' ImPy-~-HpIm-y-PYPYHpHpPy -W
379(3p) 5' G A A T G W-3' ImPy-p-HpIm-y-PyPy-(3-HpPy -W
383(3) 5' G A A A G W-3' ImPy-~3-PyIm-y-PYHpHpHpPy -W
383(3p) 5' G A A A G W-3' ImPy-~3-PYIm-y-pyHp-(3-HpPy -W
385(3) 5' G A A G T W-3' ImPy-~3-ImHp-y-PyPYHpHpPy -W
385(3p) 5' G A A G T W-3' ImPy-(3-ImHp-y-Pypy-~3-HppY
-W
386(3) 5' G A A G A W-3' -W ImPy-(3-ImPy-y-HpPyHpHpPy 386(3p) 5' G A A G A W-3' ImPy-~3-ImPy-y-HpPy-(3-HpPy -W
387(3) 5' G A A G G W-3' ImPy-(3-Imlm-y-PyPYHpHpPy -W
387(3p) 5'-WG A A G G W-3' ImPy-(3-ImIm-y-PyPy-(3-HpPy 3883) 5' G A A G C W-3' ImP
-W y-~3-ImPy-y-ImPyHpHpPy 388(3p) 5' G A A G C W-3' ImPy-~3-ImPy-y-ImPy-/3-HpPy -W
391~i) 5'-WG A A C G W-3' ImPy-~-PyIm-y-PyImHpHpPy 391(3p) 5' G A A C G W-3' ImPy-(3-Pylm-y-PyIm-~-HpPy -W
TABLE
57: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 393) 5' G A G TT W-3' Im--ImHpHp-y-PyPyPyHpPy -W
394(3p) 5'-W G A G TA W-3' Im--ImHpPy-y-Hppypy--py 395(3) ~ G A G TG W-3' Im--ImHpIm-y-PyPyPyHpPy 5' -W
395~3p) 5'-W G A G TG W-3' Im--ImHpIm-y-PyPyPy--Py 396) 5'-W G A G TC W-3' Im--ImHpPy-y-ImPyPyHpPy 396p) 5' G A G TC W-3' Im--ImHpPy-y-ImPyPy--Py -W
397) 5' G A G AT W-3' Im--ImPyHp-y-PyHpPyHpPy -W
397~p) 5' G A G AT W-3' Im-~i-ImpyHp-y-PyHpPy--Py -W
398) 5' G A G AA W-3' Im--ImPyPy-y-HpHpPyHpPy -W
398p) 5'-W G A G AA W-3' Im--ImPyPy-y-HpHpPy--Py 399(3) 5' G A G AG W-3' Im--ImPyIm-y-PyI-ippyHpPy -W
399~3p) 5' G A G AG W-3' Im-(3-ImPyIm-y-PyHpPy--Py -W
400(3) 5' G A G AC W-3' Im--ImpyPy-y-ImHpPyHpPy -W
400(3p) 5'-W G A G AC W-3' Im-~-ImpyPy-y-ImHppy-p-Py 401(3) 5' G A G GT W-3' Im--ImImHp-y-PypyPyHpPy -W
401p) 5'-W G A G GT W-3' Im--ImImHp-y-PyPypy--py 402) 5' G A G GA W-3' Im--ImImPy-y-HppyPyHpPy -W
402p) 5'-W G A G GA W-3' Im--ImImPy-y-HpPyPy--Py 403 ) 5'-W G A G CT W-3' Im--ImPyHp-y-PyImPyHpPy 403(3p) 5' G A G CT W-3' Im--ImPyHp-y-PyImPy--Py -W
404) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPyHpPy 404~3p) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPy--Py 405(3) 5' G A G GG W-3' Im--ImImIm-y-PyPyPyHpPy -W
405p) 5'-W G A G GG W-3' 'Im--ImImIm-y-PyPyPy--Py 406(3) 5' G A G GC W-3' Im-(3-ImImPy-y-ImPyPyHpPy -W
406~ip) 5' G A G GC W-3' Im--ImImPy-y-ImPyPy--Py -W
407(3) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPyHpPy 407(3p) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPy--Py 408) 5' G A G CC W-3' Im-(3-ImPyPy-y-ImImPyHpPy -W
408(3p) 5' G A G CC W-3' Im--ImPyPy-y-ImImPy-(3-Py -W
1 AliLlr S / (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' with (3 substitutions.
D NA aromatic amino acid sequence sequence 4093) 5'-W G AC T T W-3' ImPyPyHpHp-y-py-(3-I~pPy 409(3p) 5' G AC T T W-3' ImPyPy-~3-Hp-y-Py-(3-ImHpPy -W
4103) 'S' G AC T A W-3' ImPyPyHpPy-y-Hp-(3-ImHpPy -W
410(3p) 5' G AC T A W-3' ImPyPy-(3-Py-y-Hp-(3-ImHpPy -W
411(3) 5' G AC T G W-3' ImPy-~i-HpIm-y-Py-(3-ImHpPy -W
412(3) 5'-W G AC T C W-3' ImPYPyHpPy-y-Im-(3-ImHpPy 412pp) 5'-W G AC T C W-3' ImPYPy-~-py-y-Im-~-ImHpPy 413(3) 5' G AC A T W-3' ImPYPyPyHp-y-py-(3-I~ppy -W
413~3p) 5' G AC A T W-3' ImPyPy-~3-Hp-y-Py-(~_ImHppy -W
414(3) 5' G AC A A W-3' Impypypypy_y-Hp-~-I~ppy -W
414(3p) 5' G AC A A W-3' ImPyPy-(3-Py-y-Hp-(3-I~ppY
-W
415(3) 5' G AC A G W-3' ImPy-~3-Pylm-y-Py-(3-ImHpPy -W
416(3) 5' G AC A C W-3' ImPypypypy-y-Im-/3-ImHpPy -W
416(3p) 5' G AC A C W-3' ImPyPy-(3-Py-y-Im-(3-ImHpPy -W
417(3) 5' G AC G T W-3' ImPy-(3-ImHp-y-Py-(3-ImHpPy -W
4183) 5' G AC G A W-3' ImPy-~3-ImPy-y-Hp-~3-ImHppy -W
419(3) 5' G AC C T W-3' Im-~-PyPyHp-y-PyImIm-(3-Py -W
419(3p) 5' G AC C T W-3' ImPYPYPyHp-y-PyImIm-(3-Py -W
4200 5' G AC C A W-3' Im-p-Pypypy-y-HpImIm-(3-Py -W
420(3p) 5' G AC C A W-3' ImPYPyPypy-y-HpImIm-~3-Py -W
421(3) 5' G AC G G W-3' ImPy-~3-Imlm-y-Py-~3-ImHpPy -W
422(3) 5' G AC G C W-3' ImPy-y-ImPy-y-Im-(3-ImHpPy -W
423(3) 5' G AC C G W-3' ImPy-(3-Pylm-y-PyImIm-~3-Py -W
424(3) 5' G AC C C W-3' ImPyPyPyPy-y-ImImIm-(3-Py -W
424(3p) 5' G AC C C W-3' Im-(3-PyPyPy-y-ImImIm-~i-Py -W
TABLE 58:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 425(3) 5' G CT T T W-3' ImPyHpHpHp-y-PyPy-(3-ImPy -W
425(3p) ' G CT T T W-3' ImPy-~3-HpHp-y-PyPy-(3-ImPy 5' -W
426x) 5' G CT T A W-3' ImPyHpHpPy-y-HpPy-(3-ImPy -W
426(3p) 5' G CT T A W-3' ImPy-J3-HpPy-y-HpPy-(3-ImPy -W
427(3) 5' G CT T G W-3' ImPy-~3-Hp lm-y-PyPy-(3-Impy -W
428(3) 5' G CT T C W-3' ImPyHpHpPy-y-ImPy-~3-ImPy -W
428(3p) 5' G CT T C W-3' Impy-(3-HpPy-y-ImPy-(3-Impy -W
429(3) 5' G CT A T W-3' ImPyHpPyHp-y-PyHp-(3-ImPy -W
429(3p) 5' G CT A T W-3' ImPy-(3-PyHp-y-PyHp-(3-ImPy -W
4303) 5' G CT A A W-3' ImPyHpPyPy-y-HpHp-(3-ImPy -W
430(3p) 5' G CT A A W-3' ImPy-(3-PyPy-y-HpHp-(3-ImPy -W
431(3) 5' G CT A G W-3' ImPy-~i-Pylm-y-PyHp-(3-ImPy -W
432(3) 5' G CT A C W-3' ImPyHpPyPy-y-ImHp-~i-ImPy -W
432(3p) 5' G CT A C W-3' ImPy-(3-PyPy-y-ImHp-(3-ImPy -W
433(3) 5' G CT G T W-3' ImPy-(3-ImHp-y-Pypy-(3-ImPy -W
434(3) 5' G CT G A W-3' ImPy-(3-ImPy-y-HpPy-a-ImPy -W
435~i) 5' G CT G G W-3' ImPy-(3-ImIm-y-PyPy-~i-ImPy -W
436(3) 5' G CT G C W-3' ImPy-(3-ImPy-y-ImPy-(3-ImPy -W
437(3) 5' G CT C T W-3' ImPyHpPyHp-y-Pylm-(3-ImPy -W
437(3p) 5' G CT C T W-3' ImPy-(3-PyHp-y-PyIm-(3-ImPy -W
438~i) 5' G CT C A W-3' ImPylipPyPy-y-Hplm-(3-ImPy -W
438(3p) 5' G CT C A W-3' ImPy-(3-PyPy-y-Hplm-~i-ImPy -W
439(3) 5'-W G CT C G W-3' Impy-(3-PyIm-y-PyIm-~i-ImPy 4403) 5' G CT C C W-3' ImPyHpPyPy-y-ImIm-ji-ImPy -W
440(3p) 5' G CT C C W-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy -W
441(3) 5' G CA T T W-3' ImPyPyHpHp-y-PyPy-~i-ImPy -W
441~p) 5' G CA T T W-3' ImPy-(3-HpHp-y-PyPy-/3-ImPy -W
442(3} 5' G CA T A W-3' ImPyPyHpPy-y-HpPy-~3-ImPy -W
442(3p) 5' G CA T A W-3' ImPy-~3-HpPy-y-HpPy-(3-ImPy -W
443(3) 5' G CA T G W-3' ImPy-(3-Hplm-y-PyPy-(3-ImPy -W
-87_ TABLE 58 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 444(3) 5' G C A T CW-3' ImPyPyHpPy-y-ImPy-~3-ImPy -W
444~3p) 5' G C A T CW-3' ImPy-(3-HpPy-y-ImPy-(3-Impy -W
445(3) ' G C A A TW-3' ImPyPyPyHp-y-PyHp-(3-ImPy 5' -W
445(3p) 5' G C A A TW-3' ImPy-(3-PyHp-y-PyHp-R-ImPy -W
446(3) 5' G C A A AW-3' ImPyPyPyPy-y-HpHp-(3-ImPy -W
446~3p) 5' G C A A AW-3' ImPy-(3-pypy-y-HpHp-a-ImPy -W
447(3) 5' G C A A GW-3' ImPy-(3-Pylm-y-PyHp-(3-ImPy -W
4483) 5' G C A A CW-3' ImPyPypypy-y-ImHp-(3-ImPy -W
448(3p) 5'-W G C A A CW-3' ImPy-(3-PyPy-y-ImHp-~i-ImPy 449(3) 5'-W G C A G TW-3' ImPy-~3-ImHp-y-PyPy-(3-ImPy 450(3) 5' G C A G AW-3' ImPy-~-ImPy-y-Hppy-(3-Impy -W
4513) 5' G C A G GW-3' ImPy-(3-ImIm-y-PyPy-(3-ImPy -W
4523) 5' G C A G CW-3' ImPy-J3-ImPy-y-ImPy-~i-ImPy -W
4533) 5' G C A C TW-3' ImPyPyPyHp-y-Pylm-(3-ImPy -W
453~3p) 5' G C A C TW-3' ImPy-(3-PyHp-y-Pylm-p-ImPy -W
4540 5' G C A C AW-3' ImPyPyPyPy-y-HpIm-~3-ImPy -W
454(3p) 5' G C A C AW-3' ImPy-~3-PyPy-y-Hplm-(3-ImPy -W
455(3) 5' G C A C GW-3' ImPy-(3-PyIm-y-PyIm-(3-ImPy -W
4563) 5' G C A C CW-3' ImpyPyPypy-y-Imam-(3-ImPy -W
456(3p) 5' G C A C CW-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy -W
_88_ TABLE 59:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 457) 5' G C GT T W-3' Im--ImHpHp-y-PyPy--ImPy -W
458(3) ~ G C GT A W-3' Im--ImHpPy-y-HpPy--ImPy 5' -W
4593) 5' G C GT G W-3' Im--ImHpIm-y-PyPy--ImPy -W
460(3) 5' G C GT C W-3' Im--ImHpPy-y-ImPy--ImPy -W
461) 5' G C GA T W-3' Im--ImPyHp-y-PyHp--ImPy -W
462(3) 5' G C GA A W-3' Im--ImPyPy-y-HpHp--ImPy -W
463) 5' G C GA G W-3' Im--ImPyIm-y-PyHp--ImPy -W
4643) 5' G C GA C W-3' Im--ImPyPy-y-ImHp--ImPy -W
465(3) 5' G C GG T W-3' Im--ImImHp-y-PyPy--ImPy -W
466(3) 5' G C GG A W-3' Im-(3-ImImPy-y-HpPy--ImPy -W
467(3) 5' G C GG T W-3' Im--ImPyHp-y-PyIm--ImPy -W
468(3) 5' G C GC A W-3' Im--ImPyPy-y-HpIm--ImPy -W
469) 5'-W G C CT T W-3' ImPyPyHpHp-y-Py-~-ImImPy 469~3p) 5'-W G C CT T W-3' ImPyPy--Hp-y-Py--ImImPy 470) 5' G C CT A W-3' ImPyPyHpPy-y-Hp--ImImPy -W
470p) 5' G C CT A W-3' ImPyPy--Py-y-Hp--ImImPy -W
4710 5' G C CT G W-3' ImPy--Hplm-y-Py--ImImPy -W
472(3) 5' G C CT C W-3' ImPyPyHpPy-y-Im--ImImPy -W
472(3p) 5' G C CT C W-3' ImPyPy--Py-y-Im--ImImPy -W
473(3) 5' G C CA T W-3' ImPyPyPyHp-y-Py--ImImPy -W
473p) 5'-W G C CA T W-3' ImPyPy--Hp-y-Py--ImImPy 474~i) 5' G C CA A W-3' ImPyPyPyPy-y-Hp--ImImPy -W
474pp) 5'-W G C CA A W-3' ImPyPy--Py-y-Hp--ImImPy 4753) 5' G C CA G W-3' ImPy--Pylm-y-Py--ImImPy -W
476(3) 5' G C CA C W-3' ImPyPyPyPy-y-Im--ImImPy -W
476(3p) 5' G C CA C W-3' ImPyPy--Py-y-Im--ImImPy -W
4773) 5' G C CG T W-3' ImPy--ImHp-y-Py--ImImPy -W
478(3) 5' G C CG A W-3' ImPy--ImPy-y-Hp--ImImPy -W
TABLE 59 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' with ~i substihrtions.
DNA aromatic amino acid sequence sequence G25(3) 5' GC G G W-3' Im-(3-ImImIm-y-PyPy-~3-ImPy -W G
G26(3) 5' GC G C W-3' Im-(3-ImImPy-y-ImPy-p-ImPy -W G
G27~3) ~5' GC C G W-3' Im-(3-ImPyIm-y-Pylm-(3-ImPy -W G
G28(3) 5' GC C C W-3' Im-~3-ImPyPy-y-ImIm-~i-ImPy -W G
G29(3) 5'-W GC G G W-3' ImPy-~3-Imlm-y-Py-(3-ImImPy C
G30(3) 5' GC G C W-3' ImPy-(3-ImPy-y-Im-~3-ImImPy -W C
G31(3) 5' GC C G W-3' ImPy-(3-Pylm-y-PyImImImPy -W C
TABLE 60: 10-ring Hairpin Polyamides for recognition of 7-by S'-WCGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 4810 5' C G T T T W-3' PyImHpHpHp-y-PyPy-(3-PyIm -W
481(3p) '5' C G T T T W-3' PyIm-(3-HpHp-y-PyPy-(3-PyIm -W
4823) 5' C G T T A W-3' PyImHpHpPy-y-HpPy-(3-PyIm -W
482~3P) 5' C G T T A W-3' Pylm-/3-Hppy-y-Hppy-~3-pylm -W
4833) 5' C G T T G W-3' PyIm-~3-HpIm-y-Pypy-p-Pylm -W
484(3) 5' C G T T C W-3' PyImHpHppy-y-ImPy-/3-PyIm -W
484(3p} 5'-WC G T T C W-3' Pylm-(3-HpPy-y-ImPy-(3-PyIm 4853) 5' C G T A T W-3' PyImHpPyHp-y-PyHp-[3-PyIm -W
485(3p) 5' C G T A T W-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm -W
486(3) 5' C G T A A W-3' PyImHpPyPy-y-HpHp-(3-pylm -W
486(3p) 5' C G T A A W-3' PyIm-~3-Pypy-Y-HpHp-(3-pylm -W
4873) 5' C G T A G W-3' PyIm-J3-Pylm-y-PyHp-(3-Pylm -W
488J3) 5' C G T A C W-3' PyImHpPyPy-y-ImHp-~3-Pylm -W
488(3p) 5' C G T A C W-3' PyIm-(3-PyPy-y-ImHp-(3-PyIm -W
489(3} 5' C G T G T W-3' PyIm-~-ImHp-Y-Pypy-~3-pylm -W
490(3) 5' C G T G A W-3' Pylm-(3-Impy-y-HpPy-(3-PyIm -W
491(3) 5' C G T G G W-3' PyIm-~-ImIm-y-pyPy-(3-pyIm -W
492(3) 5' C G T G C W-3' PyIm-[3-ImPy-y-Impy-~3-PyIm -W
493x) 5' C G T C T W-3' PyImHpPyHp-y-PyIm-p-PyIm -W
493(3p) 5' C G T C T W-3' Pylm-(3-PyHp-y-PyIm-(3-PyIm -W
4943) 5' C G T C A W-3' PyImHpPyPy-y-HpIm-~3-PyIm -W
494(3p) 5' C G T C A W-3' PyIm-J3-PyPy-y-HpIm-(3-PyIm -W
495(3) 5' C G T C G W-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm -W
496(3) 5' C G T C C W-3' PyImHpPyPy-y-Imlm-~i-PyIm -W
496(3p) 5' C G T C C W-3' PyIm-~3-PyPy-y-ImIm-~3-PyIm -W
4973) 5' C G A T T W-3' PyImPyHpHp-y-Pypy-(3-pyIm -W
497(3p) 5' C G A T T W-3' PyIm-~3-HpHp-y-PyPy-(3-pyIm -W
498(3) 5' C G A T A W-3' PyImPyHpPy-y-HpPy-p-PyIm -W
498(3p) 5' C G A T A W-3' Pylm-~i-HpPy-y-HpPy-(3-PyIm -W
TABLE 60 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 499(3) 5' C G A T GW-3' Pylm-(3-Hplm-y-Pypy-(3-pylm -W
500(3) 5' C G A T CW-3' PyImPyHpPy-y-ImPy-(3-pylm -W
500(3p) ~ C G A T CW-3' PyIm-(3-HpPy-y-ImPy-~_pyln~
5' -W
501~i) 5' C G A A TW-3' PyImPyPyHp-y-PyHp-(3-PyIm -W
501(3p) 5' C G A A TW-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm -W
5023) 5' C G A A AW-3' PyImPyPyPy-y-HpHp-~3-Pylm -W
502~3p) 5' C G A A AW-3' PyIm-(3-Pypy-y-HpHp-~-PyIm -W
5030 5' C G A A GW-3' PyIm-(3-PyIm-y-PyHp-~3-Pylm -W
504 ) 5' C G A A CW-3' -W PyImPyPyPy-y-ImHp-(3-PyIm 504(3p) 5' C G A A CW-3' Pyim-(3-PyPy-y-ImHp-~3-pylm -W
505(3) 5' C G A G TW-3' -W Pylm-(3-ImHp-y-PyPy-(3-PyIm 5063) 5' C G A G AW-3' PyIm-p-ImPy-y-HpPy-p-pyIm -W
507(3) 5' C G A G GW-3' PyIm-(3-Imlm-y-Pypy-(3-pylm -W
50B(3} 5' C G A G CW-3' PyIm-~i-ImPy-y-ImPy-(3-PyIm -W
5093) 5' C G A C TW-3' PyImPyPyHp-y-PyIm-(3-PyIm -W
509~p) 5'-W C G A C TW-3' PyIm-(3-PyHp-y-pylm-(3-PyIm 5100 5' C G A C AW-3' PyImPyPyPy-y-Hplm-~3-Pylm -W
510(3p} 5' C G A C AW-3' PyIm-~3-PyPy-y-HpIm-(3-PyIm -W
511~i) 5' C G A C GW-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm -W
5123) 5' C G A C CW-3' PyImPyPyPy-y-ImIm-~3-PyIm -W
5I2~3p) 5' C G A C CW-3' PyIm-~3-PyPy-y-ImIm-(3-PyIm -W
TABLE 61:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 513(3) 5' C G GT T W-3' PyImIm-(3-Hp-y-PyPy-(3-PyIm -W
514(3) -5' C G GT A W-3' PyImIm-~i-Py-y-HpPy-(3-Pylm -W
515(3) 5' C G GT G W-3' PyImIm-(3-Im-y-PyPy-(3-Pylm -W
516(3) 5' C G GT C W-3' PyImIm-(3-Py-y-ImPy-(3-Pylm -W
517(3) 5' C G GA T W-3' PyImIm-(3-Hp-y-PyHp-~3-Pylm -W
518(3) 5' C G GA A W-3' PyImIm-(3-Py-y-HpHp-(3-PyIm -W
5193) 5' C G GA G W-3' PyImIm-(3-Im-y-PyHp-(3-PyIm -W
520(3) 5' C G GA C W-3' PyImIm-~3-Py-y-ImHp-~3-PyIm -W
521~i) 5' C G GG T W-3' PyImImImHp-y-PyPy-(3-PyIm -W
522(3) 5' C G GG A W-3' PyImImImPy-y-HpPy-~3-PyIm -W
523(3) 5' C G GC T W-3' PyImIm-~-Hp-y-PyIm-~3-PyIm -W
524(3) 5' C G GC A W-3' PyImIm-~3-Py-y-HpIm-(3-PyIm -W
5250 5' C G CT T W-3' PyImPyHpHp-y-Py-~3-ImPyIm -W
525(3p) 5' C G CT T W-3' PyImPy-(3-Hp-y-Py-(3-ImPyIm -W
526(3) 5' C G CT A W-3' PyImPyHpPy-y-Hp-~3-ImPyIm -W
526(3p) 5' C G CT A W-3' PyImPy-(3-Py-y-Hp-p-ImPyIm -W
5273) 5' C G CT G W-3' Pylm-(3-Hplm-y-Py-p-ImPyIm -W
528(3) 5' C G CT C W-3' PyImPyHpPy-y-Im-(3-ImPyIm -W
528(3p) 5' C G CT C W-3' PyImPy-(3-Py-y-Im-(3-ImPyIm -W
529(3) 5' C G CA T W-3' PyImPyPyHp-y-Py-(3-ImPyIm -W
529(3p) 5' C G CA T W-3' PyImPy-(3-Hp-y-Py-~3-ImPyIm -W
530(3) 5' C G CA A W-3' PyImPyPyPy-y-Hp-(3-ImPyIm -W
530(3p) 5' C G CA A W-3' PyImPy-~3-Py-y-Hp-~3-ImPyIm -W
531(3) 5' C G CA G W-3' PyIm-(3-Pylm-y-Py-[3-ImPyIm -W
532(3) 5'-W C G CA C W-3' PyImPyPyPy-y-Im-p-ImPyIm 532(3p) 5' C G CA C W-3' PyImPy-~3-Py-y-Im-p-ImPyIm -W
533(3) 5' C G CG T W-3' Pylm-p-ImHp-y-Py-p-ImPyIm -W
5343) 5' C G CG A W-3' Pylm-~3-ImPy-y-Hp-(3-ImPyIm -W
TABLE 61 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGSNNW-3' with p substitutions .
DNA aromatic amino acid sequence sequence 5353) 5' C G C C TW-3' PyImPyPyHp-y-PyImIm-p-Im -W
536(3) ~5' C G C C AW-3' PyImPyPyPy-y-HpImIm-(3-Im -W
G33(3) 5' C G G G GW-3' PyImImImIm-y-PyPy-(3-PyIm -W
G34(3) 5' C G G G CW-3' PyImImImPy-y-ImPy-(3-PyIm -W
G35~3) 5' C G G C GW-3' PyImIm-~-Im-y-Pylm-(3-PyIm -W
G36(3) 5' C G G C CW-3' PyImIm-~3-Py-y-ImIm-(3-PyIm -W
G37(3) 5'-W C G C G GW-3' Pylm-(3-ImIm-y-Py-(3-ImPyIm G38(3) 5' C G C G CW-3' PyIm-~3-ImPy-y-Im-(3-ImPyIm -W
G39(3) 5' C G C C GW-3' PyIm-(3-PyIm-y-PyImIm-~i-Im -W
G40(3) 5' C G C C CW-3' PyImPyPyPy-y-ImImIm-(3-Im -W
WO 98/37067. PCT/US98/01714 TABLE 62:
I 0-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 537(3) 5' C T TT T W-3' PyHpHpHpHp-y-PyPy-(3-Pylm -W
537(3p) 'S' C T TT T W-3' PyHp-(3-HpHp-y-PyPy-(3-PyIm -w 538~i) 5' C T TT A W-3' PyHpHpHpPy-y-HpPy-(3-PyIm -W
538(3p) 5' C T TT A W-3' PyHp-(3-HpPy-y-HpPy-~3-Pylm -W
539(3) 5' C T TT G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyIm -W
540~i) 5' C T TT C W-3' PyHpHpHpPy-y-ImPy-(3-PyIm -W
540(3p) 5' C T TT C W-3' PyAp-(3-HpPy-y-ImPy-~3-PyIm -W
541R) 5' C T TA T W-3' PyHpHpPyHp-y-PyHp-(3-PyIm -W
541(3p) 5' C T TA T W-3' PyHp-(3-PyHp-y-PyHp-(3-PyIm -W
5420 5' C T TA A W-3' PyHpHpPyPy-y-HpHp-(3-PyIm -W
542(3p) 5' C T TA A W-3' PyHp-p-PyPy-y-HpHp-(3-PyIm -W
543~i) 5' C T TA G W-3' PyHp-~i-PyIm-y-PyHp-~-PyIm -W
544(3) 5' C T TA C W-3' PyHpHpPyPy-y-ImHp-(3-Pylm -W ~
544(3p) 5' C T TA C W-3' PyHp-(3-PyPy-y-ImHp-~3-Pylm -W
545(3) 5' C T TG T W-3' PyHp-(3-ImI-Ip-y-PyPy-(3-PyIm -W
5463) 5' C T TG A W-3' PyHp-(3-ImPy-y-HpPy-~-PyIm -W
547(3) 5' C T TG G W-3' PyHp-(3-Imlm-y-PyPy-(3-Pylm -W
548(3) 5' C T TG C W-3' PyHp-(3-ImPy-y-ImPy-(3-PyIm -W
549(3) 5' C T TC T W-3' PyHpHpPyHp-y-PyIm-~3-Pylm -W
549(3p) 5' C T TC T W-3' PyHp-~3-PyHp-y-PyIm-~3-PyIm -W
550(3) 5' C T TC A W-3' PyHpHpPyPy-y-HpIm-[3-PyIm -W
550~3p) 5' C T TC A W-3' PyHp-[3-PyPy-y-HpIm-(3-PyIm -W
5513) 5' C T TC G W-3' PyHp-~i-Pylm-y-PyIm-~3-Pylm -W
5523) 5' C T TC C W-3' PyHpHpPyPy-y-ImIm-(3-PyIm -W
552(3p) 5' C T TC C W-3' PyHp-(3-PyPy-y-Imlm-(3-PyIm -W
553(3) 5' C T AT T W-3' PyHpPyHpHp-y-PyPy-~i-PyIm -W
553(3p) 5' C T AT T W-3' PyHp-~i-HpHp-y-PyPy-~i-PyIm -W
554(3) 5' C T AT A W-3' PyHpPyHpPy-y-HpPy-(3-PyIm -W
(cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 554(3p) 5' C TA T A W-3' PyHp-(3-HpPy-y-HpPy-~i-Pylm -W
555(3) ~ C TA T G W-3' PyHp-(i-Hplm-y-PyPy-p-pyIm 5' -W
5563) 5' C TA T C W-3' PyHpPyHpPy-Y-ImPy-~3-PyIm -W
556(3p) 5' C TA T C W-3' PyHp-(3-HpPy-y-ImPy-(3-PyIm -W
557(3) 5' C TA A T W-3' PyHpPyPyHp-Y-PyHp-(3-PyIm -W
557~3p) 5' C TA A T W-3' PyHp-(3-PyHp-y-PyHp-(3-Pylm -W
5580 5' C TA A A W-3' PyHpPyPyPy-Y-HpHp-/3-PyIm -W
558~ip) 5' C TA A A W-3' PyHp-(3-PyPy-y-HpHp-(3-PyIm -W
559(3) 5' C TA A G W-3' PyHp-~-PyIm-y-PyHp-(3-PyIm -W
5603) 5' C TA A C W-3' PyHpPyPyPy-y-ImHp-(3-PYIm -W
560(3p) 5' C TA A C W-3' PyHp-(3-PyPy-y-ImHp-(3-Pylm -W
5613) 5' C TA G T W-3' PyHp-(3-ImHp-y-PYPy-(3-pylm -W
562~i) 5' C TA G A W-3 T PyHp-(3-ImPy-y-HpPy-(3-PyIm -W
563(3) 5' C TA G G W-3' PyHp-(3-ImIm-y-PyPy-(3-PyIm -W
564~i) 5' C TA G C W-3' PyHp-~3-ImPy-y-ImPy-~3-PyIm -W
565(3) 5' C TA C T W-3' PyHpPyPyHp-y-PyIm-(3-PyIm -W
565~3p) 5' C TA C T W-3' PyHp-(3-PyHp-Y-PyIm-(3-PyIm -W
5663) 5' C TA C A W-3' PyHppyPyPy-Y-HpIm-(3-PyIm -W
566(3p) 5' C TA C A W-3' PyHp-~i-PyPy-y-Hplm-(3-PyIm -W
567(3) 5' C TA C G W-3' PyHp-(3-PyIm-y-PyIm-(3-PyIm -W
5683) 5'-W C TA C C W-3' PyHpPyPyPy-y-ImIm-(3-PyIm 568pp) 5' C TA C C W-3' PyHp-yPYPY-y-Imlm-(3-Pylm -W
TABLE
63: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTSNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 5693) 5' C T GT T W-3' Py-(3-ImHpHp-y-PyPy-(3-PyIm -W
570(3) 'S' C T GT A W-3' Py-(3-ImHpPy-y-HpPy-~i-PyIm -W
571(3) 5' C T GT G W-3' Py-~i-ImHpIm-y-PyPy-(3-Pylm -W
572(3) 5' C T GT C W-3' Py-(3-ImHpPy-y-ImPy-(3-Pylm -W
5733) 5' C T GA T W-3' Py-(3-ImPyHp-y-PyHp-(3-PyIm -W
574(3) 5' C T GA A W-3' Py-(3-ImPyPy-y-HpHp-(3-PyIm -W
5753) 5' C T GA G W-3' Py-(3-ImPyIm-y-PyHp-(3-PyIm -W
576(3) 5' C T GA C W-3' Py-(3-ImPyPy-y-ImHp-(3-PyIm -W
577(3) 5' C T GG T W-3' Py-~3-ImImHp-y-PyPy-(3-PyIm -W
578(3) 5' C T GG A W-3' Py-(3-ImImPy-y-HpPy-(3-PyIm -W
579(3) 5' C T GC T W-3' Py-(3-ImPyHp-y-PyIm-~-PyIm -W
5803) 5' C T GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-PyIm -W
581(3) 5' C T GG G W-3' Py-~3-ImImIm-y-PyPy-(3-Pylm -W
5823) 5' C T GG C W-3' Py-(3-ImImPy-y-ImPy-p-PyIm -W
583(3) 5' C T GC G W-3' Py-(3-ImPyIm-y-PyIm-p-PyIm -W
584(3) 5' C T GC C W-3' Py-(3-ImPyPy-y-ImIm-~-PyIm -W
5853) 5' C T CT T W-3' PyHpPyHpHp-y-Py-(3-ImPyIm -W
585~3p) 5' C T CT T W-3' PyHpPy-/3-Hp-y-Py-(3-ImPyIm -W
586(3) 5' C T CT A W-3' PyHpPyHpPy-y-Hp-p-ImPyIm -W
586(3p) 5' C T CT A W-3' PyHpPy-(3-Py-y-Hp-(3-ImPyIm -W
587(3) 5' C T CT G W-3' PyHp-p-HpIm-y-Py-(3-ImPyIm -W
5883) 5' C T CT C W-3' PyHpPyHpPy-y-Im-a-ImPyim -W
588(3p} 5' C T CT C W-3' PyHpPy-(3-Py-y-Im-(3-ImPyIm -W
589(3) 5' C T CA T W-3' PyHpPyPyAp-y-Py-~3-ImPyIm -W
589(3p) 5' C T CA T W-3' PyHpPy-(3-Hp-y-Py-~3-ImPyIm -W
590(3) 5' C T CA A W-3' PyHpPyPyPy-y-Hp-(3-ImPyIm -W
590(3p) 5' C T CA A W-3' PyHpPy-~3-Py-y-Hp-~-ImPyIm -W
591(3) 5' C T CA G W-3' PyHp-(3-PyIm-y-Py-(3-ImPyIm -W
_97_ TABLE 63 (cont): in 10-ring Hairp Polyamides for recognition of 7-by 5'-WCTSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 592(3) 5' C TC A C W-3' PyHpPyPyPy-y-Im-~3-ImPyIm -W
592(3p) 5' C TC A C W-3' PyHpPy-(3-Py-y-Im-~i-ImPyIm - -W
593R) 'S'-WC TC G T W-3' PYHP-~-I~P-y-PY-~-ImPYIm 594(3) 5' C TC G A W-3' PyHp-(3-ImPy-y-Hp-~3-ImPYIm -W
595~i) 5' C TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Im -W
595(3p) 5' C TC C T W-3' Py-~3-PypyHp-y-PyImIm-~-Im -W
596(3) 5' C TC C A W-3' PyHpPyPyPy-y-HpImIm-(3-Im -W
596(3p) 5' C TC C A W-3' Py-~3-Pypypy-y-HpImIm-~3-Im -W
5973) 5' C TC G G W-3' PyHp-p-ImIm-y-Py-(3-ImPyIm -W
598(3) 5' C TC G C W-3' P H
-W Y p-~3-ImPy-y-Im-(3-ImPyIm 599(3) 5' C TC C G W-3' PyHp-~i-Pylm-y-pylmIm-~3-Im -W
600R) 5'-W C TC C C W-3' PyHpPyPYPy-y-ImImIm-(3-Im 600(3p) 5' C TC C C W-3' Py-(3-PyPyPy-y-ImImIm-~-Im -W
TABLE 64:
10-ring Hairpin Polyamides for recognition of 7-by S'-WCAWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 6013) 5' C AT T T W-3' PyPyHpHpHp-y-PyPy-/3-HpIm -W
601(3p) '5' C AT T T W-3' PyPy-R-HpHp-y-PyPy-(3-HpIm -W
6023) 5' C AT T A W-3' PyPyHpHpPy-y-HpPy-(3-HpIm -W
602(3p) 5' C AT T A W-3 ' PyPy-(3-HpPy-y-HpPy-~i-Hplm -W
603(3) 5' C AT T G W-3' PyPy-~3-HpIm-y-PyPy-~i-Hplm -W
6040 5' C AT T C W-3' PyPyHpHpPy-y-ImPy-(3-HpIm -W
604~3p) 5' C AT T C W-3' PyPy-R-HpPy-y-ImPy-(3-Hplm -W
6053) 5' C AT A T W-3' PyPyHpPyHp-y-PyHp-~i-HpIm -W
605~3p) 5' C AT A T W-3' PyPy-(3-PyHp-y-PyHp-J3-Hplm -W
6063) 5' C AT A A W-3' PyPyHpPyPy-y-HpHp-(3-HpIm -W
606(3p) 5' C AT A A W-3' PyPy-(3-PyPy-y-HpHp-(3-Hplm -W
607(3) 5' C AT A G W-3' PyPy-(3-Pylm-y-PyHp-(3-Hplm -W
608~i) 5' C AT A C W-3' PyPyHpPyPy-y-ImHp-(3-HpIm -W
608(3p) 5' C AT A C W-3' PyPy-(3-PyPy-y-ImHp-(3-HpIm -W
609(3) 5' C AT G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpIm -W
610(3) 5' C AT G A W-3' PyPy-(3-ImPy-y-HpPy-~i-HpIm -W
611(3) 5' C AT G G W-3' PyPy-(3-ImIm-y-PyPy-(3-HpIm -W
612(3) 5' C AT G C W-3' PyPy-(3-ImPy-y-ImPy-(3-HpIm -W
613(3) 5' C AT C T W-3' PyPyHpPyHp-y-PyIm-[3-HpIm -W
613~p) 5' C AT C T W-3' PyPy-p-PyHp-y-PyIm-(3-HpIm -W
6143) 5' C AT C A W-3 ' PyPyHpPyPy-y-HpIm-~3-HpIm -W
614~3p) 5' C AT C A W-3' PyPy-j3-PyPy-y-HpIm-(3-HpIm -W
615(3) 5' C AT C G W-3' PyPy-(3-PyIm-y-PyIm-~i-HpIm -W
6163) 5' C AT C C W-3' PyPyHpPyPy-y-ImIm-(3-HpIm -W
616~3p) 5' C AT C C W-3' PyPy-~i-PyPy-y-ImIm-~-HpIm -W
6I7~3) 5' C AA T T W-3' PyPyPyHpHp-y-PyPy-(3-HpIm -W
617~p) 5' C AA T T W-3' PyPy-(3-HpHp-y-PyPy-~i-HpIm -W
6180 5' C AA T A W-3' PyPyPyHpPy-y-HpPy-p-HpIm -W
618(3p) 5' C AA T A W-3' PyPy-~-HpPy-y-HpPy-(3-HpIm -W
_9c~_ . TABLE 64 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCAWNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 619(3) 5' C A A T G W-3' Pypy--Hplm-y-pypy_-Hplm -W
620) 5' C A A T C W-3' PyPyPyHpPy-~-ImPy--HpIm -W
620~ip) ~ C A A T C W-3' Pypy--HpPy-y-ImPy-(3-Hplm 5' -W
6Z1) 5'-W C A A A T W-3' PyPyPyPyHp-r-PyHp--HpIm 621(3p) 5' C A A A T W-3' PyPy-(3-PyHp-y-PyHp-(3-HpIm -W
622(3) 5'-W C A A A A W-3' PyPyPyPyPy-y-HpHp--Hplm 622p) 5' C A A A A W-3' PyPy--Pypy-y-Hpgp-(3-HpIm -W
623) 5' C A A A G W-3' PyPy--Pylm-y-PyHp--HpIm -W
6243) 5' C A A A C W-3' PyPyPyPyPy-'y-ImHp--Hplm -W
624p) 5' C A A A C W-3' PyPy--pypy-~-ImHp_-Hplm -W
625) 5' C A A G T W-3' PyPy--ImHp-y-PyPy--HpIm -W
626) 5' C A A G A W-3' PyPy--ImPy-y-HpPy--HpIm -W
IS 627(3) 5' C A A G G W-3' PyPy--ImIm-y-PyPy--Hplm -W
6283) 5' C A A G C W-3' PyPy--ImPy-y-ImPy--HpIm -W
6293) 5'-W C A A C T W-3' PyPyPyPyHp-y-PyIm--HpIm 629p) 5'-W C A A C T W-3' PyPy--PyHp-y-PyIm--HpIm 630(3) 5' C A A C A W-3' PyPyPyPyPy-y-HpIm--HpIm -W
630p) 5'-W C A A C A W-3' PyPy--PyPy-y-HpIm--HpIm 631) 5'-W C A A C G W-3' PyPy--PyIm-y-PyIm--HpIm 632(3) 5' C A A C C W-3' PyPyPyPyPy-y-Imlm--HpIm -W
632p) 5'-W C A A C C W-3' PyPy--PyPy-y-ImIm--HpIm TABLE 65:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 633~i) 5' C A G TT W-3' Py-(3-ImHpHp-y-PyPy-(3-HpIm -W
6343) ' C A G TA W-3' Py-(3-ImHppy-y-Hppy-/3-Hpim 5' -W
635~i) 5' C A G TG W-3' Py-~3-ImHpIm-y-PyPy-(3-Hplm -W
636(3) 5' C A G TC W-3' Py-(3-ImHpPy-y-ImPy-(3-HpIm -W
637(3) 5' C A G AT W-3' Py-(3-ImPyHp-y-PyHp-(3-HpIm -W
638(3) 5' C A G AA W-3' Py-(3-ImPyPy-y-HpHp-(3-Hplm -W
6393) 5' C A G AG W-3' Py-~i-ImPyIm-y-PyHp-~3-HpIm -W
640(3) 5' C A G AC W-3' Py-(3-ImPyPy-y-ImHp-(3-HpIm -W
641(3) 5' C A G GT W-3' Py-(3-ImImHp-y-PyPy-(3-HpIm -W
6423) 5' C A G GA W-3' Py-(3-ImImPy-y-HpPy-~3-HpIm -W
643(3) 5' C A G CT W-3' Py-(3-ImPyHp-y-PyIm-~3-Hplm -W
644(3) 5' C A G CA W-3' Py-(3-ImPyPy-y-HpIm-(3-HpIm -W
645(3) 5' C A G GG W-3' Py-(3-ImImIm-y-PyPy-(3-Hplm -W
6463) 5' C A G GC W-3' Py-(3-ImImPy-y-ImPy-(3-HpIm -W
647(3) 5' C A G CG W-3' Py-(3-ImPyIm-y-Pylm-(3-Hplm -W
6483) 5' C A G CC W-3' Py-(3-ImPyPy-y-Imlm-(3-Hplm -W
6493) 5'-W C A C TT W-3' PyPyPyHpHp-y-Py-(3-ImHpIm 649(3p) 5' C A C TT W-3' PyPyPy-(3-Hp-y-Py-~i-ImHpIm -W
6503) 5' C A C TA W-3' PyPyPyHpPy-y-Hp-(3-ImHpIm -W
650(3p) 5' C A C TA W-3' PyPyPy-(3-Py-y-Hp-~i-ImHpIm -W
651(3) 5' C A C TG W-3' PyPy-(3-HpIm-y-Py-(3-ImHpIm -W
652~i) 5' C A C TC W-3' PyPyPyHpPy-y-Im-~3-ImHpIm -W
652(3p) 5' C A C TC W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm -W
653(3) 5' C A C AT W-3' PyPyPyPyHp-y-Py-(3-ImHpIm -W
653(3p) 5' C A C AT W-3' PyPyPy-(3-Hp-y-Py-p-ImHpIm -W
654(3) 5' C A C AA W-3' PyPyPyPyPy-y-Hp-(3-ImHpIm -W
654(3p) 5' C A C AA W-3' PyPyPy-(3-Py-y-Hp-(3-ImHpIm -W
655(3) 5' C A C AG W-3' PyPy-(3-PyIm-y-Py-(3-ImHpIm -W
. TABLE 65 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 656(3) 5' C A C A C W-3' PyPyPyPyPy-y-Im-(3-ImHpIm -W
656(3p) 5' C A C A C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm -W
6573) '5' C A C G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpIm -W
658(3p) 5' C A C G A W-3' PyPy-~-ImPy-y-Hp-~_ImHpIm -W
6590 5' C A C C T W-3' PyPyPyPyHp-y-PyImIm-(3-Im -W
659(3p) 5' C A C C T W-3' Py-(3-PyPyHp-r-PyImIm-(3-Im -W
660(3) 5' C A C C A W-3' PyPyPyPyPy-y-HpImIm-~-Im -W
660(3p) 5' C A C C A W-3' Py-/3-PyPyPy-y-HpImIm-(3-Im -W
6613) 5' C A C G G W-3' PyPy-/3-ImIm-y-Py-(3-ImHpIm -W
662(3) 5' C A C G C W-3' PyPy-(3-ImPy-y-Im-j3-ImHpIm -W
6633} 5' C A C C G W-3' PyPy-(3-pylm-y-PyImIm-(i-Im -W
664(3} 5' C A C C C W-3' PyPyPyPyPy-y-ImImIm-(3-Im -W
664~3p) 5' C A C C C W-3' Py-p-Pypypy-y-ImImIm-(3-Im -W
TABLE 66:
10-ring Hairpin Polyamides for recognition of 7-by S'-WCCWNNW-3' with ~
substitutions.
DNA aromatic amino acid sequence sequence 665(3) 5' C C TT T W-3' PyPyHpHpHp-y-PyPy-(3-ImIm -W
665(3p) '5' C C TT T W-3' PyPy-(3-HpHp-y-PyPy-~3-ImIm -W
666(3) 5' C C TT A W-3' PyPyHpHpPy-y-HpPy-~-ImIm -W
666(3p) 5' C C TT A W-3' PyPy-(3-HpPy-y-HpPy-p-ImIm -W
667(3) 5' C C TT G W-3' PyPy-(3-HpIm-y-PyPy-(3-ImIm -W
668(3) 5' C C TT C W-3' PyPyHpHpPy-y-ImPy-~3-Imlm -W
668(3p) 5' C C TT C W-3' PyPy-(3-HpPy-y-ImPy-(3-ImIm -W
669(3) 5' C C TA T W-3' PyPyHpPyHp-y-PyHp-(3-ImIm -W
669(3p) 5' C C TA T W-3' PyPy-[3-PyAp-y-PyHp-(3-ImIm -W
670(3) 5' C C TA A W-3' PyPylipPyPy-y-HpHp-(3-ImIm -W
670~3p) 5' C C TA A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImIm -W
671(3) 5' C C TA G W-3' PyPy-(3-PyIm-y-PyHp-(3-ImIm -W
672(3) 5' C C TA C W-3' PyPyHpPyPy-y-ImHp-(3-ImIm -W
672(3p) 5' C C TA C W-3' PyPy-[3-PyPy-y-ImHp-~3-ImIm -W
673(3) 5' C C TG T W-3' PyPy-(3-ImHp-y-PyPy-(3-Imlm -W
674(3) 5' C C TG A W-3' PyPy-~-ImPy-y-HpPy-(3-ImIm -W
6753) 5' C C TG G W-3' PyPy-~3-ImIm-y-PyPy-(3-ImIm -W
676(3) 5' C C TG C W-3' PyPy-p-ImPy-y-ImPy-(3-ImIm -W
677(3) 5' C C TC T W-3' PyPyHpPyHp-y-PyIm-(3-ImIm -W
677(3p) 5' C C TC T W-3' PyPy-(3-PyHp-y-PyIm-/3-ImIm -W
678(3) 5'-W C C TC A W-3' PyPyHpPyPy-y-Hplm-(3-ImIm 678(3p) 5' C C TC A W-3' PyPy-p-PyPy-y-Hplm-~i-ImIm -W
679p) 5' C C TC G W-3' PyPy-p-PyIm-y-Pylm-(3-ImIm -W
680(3) 5' C C TC C W-3' PyPyHpPyPy-y-Imlm-~i-Imlm -W
680~3p) 5' C C TC C W-3' PyPy-(3-PyPy-y-Imlm-(3-Imlm -W
681R) 5' C C AT T W-3' PyPyPyHpHp-y-PyPy-~3-ImIm -W
681~p) 5' C C AT T W-3' PyPy-(1-HpHp-y-PyPy-~-ImIm -W
682(3) 5' C C AT A W-3' PyPyPyHpPy-y-HpPy-~3-ImIm -W
682(3p) 5' C C AT A W-3' PyPy-~i-HpPy-y-HpPy-(3-ImIm -W
TABLE 66: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 683(3) 5' C C A TG W-3' Pypy-(3-HpIm-y-PyPy-~-ImIm -W
684(3) '5'-WC C A TC W-3' PyPyPyHpPy-y-ImPy-~3-ImIm 684(3p) 5' C C A TC W-3' PyPy-~i-HpPy-y-ImPy-(3-ImIm -W
6853) 5' C C A AT W-3' PyPyPyPyHp-y-PyHp-(3-ImIm -W
685(3p) 5' C C A AT W-3' PyPy-(3-PyHp-y-PyHp-p-ImIm -W
686(3) 5' C C A AA W-3' PyPyPyPyPy-y-HpHp-(3-ImIm -W
686(3p) 5' C C A AA W-3' PyPy-~3-PyPy-y-HpHp-~-ImIm -W
687(3) 5' C C A AG W-3' PyPy-p-PyIm-y-PyHp-(3-ImIm -W
6883) 5' C C A AC W-3' PyPyPyPyPy-y-ImHp-(3-ImIm -W
688~3p) 5' C C A AC W-3' PyPy-(3-pypy-y-I~p_~_ImIm -W
689(3) 5' C C A GT W-3' PyPy-j3-ImHp-y-PyPy-/3-ImIm -W
690(3) 5' C C A GA W-3' PyPy-(3-ImPy-y-HpPy-(3-ImIm -W
691(3) 5' C C A GG W-3' PyPy-(3-ImIm-y-PyPy-(3-ImIm -W
6923) 5' C C A GC W-3' PyPy-(3-ImPy-y-ImPy-(3-Imlm -W
693(3) 5' C C A CT W-3' PyPyPyPyHp-y-PyIm-(3-ImIm -W
693~ip) 5' C C A CT W-3' Pypy-(3-PyHp-y-Pylm-(3-ImIm -W
694(3) 5' C C A CA W-3' PyPyPyPyPy-y-Hplm-/3-ImIm -W
694(3p) 5' C C A CA W-3' PyPy-~i-PyPy-y-Hplm-[3-Imlm -W
695(3) 5' C C A CG W-3' PyPy-(3-PyIm-y-Pylm-~3-ImIm -W
696(3) 5' C C A CC W-3' PyPyPyPyPy-y-ImIm-p-ImIm -W
696~ip) 5' C C A CC W-3' PyPy-(3-PyPy-y-ImIm-(3-Imlm -W
TABLE
67: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 697(3) 5' C C G T TW-3' Py-~3-ImHpHp-y-PyPy-~3-ImIm -W
698(3) '5' C C G T AW-3' Py-~3-ImHpPy-y-HpPy-(3-ImIm -W
6993) 5' C C G T GW-3' Py-~i-ImHpIm-y-PyPy-p-Imlm -W
700(3) 5' C C G T CW-3' Py-~3-ImHpPy-y-ImPy-(3-ImIm -W
701(3) 5' C C G A TW-3' Py-[3-ImPyHp-y-PyHp-(3-ImIm -W
702(3) 5' C C G A AW-3' Py-(3-ImPyPy-y-HpHp-p-ImIm --W
703(3) 5' C C G A GW-3' Py-~i-ImPyIm-y-PyHp-p-Imlm -W
7043? 5'-W C C G A CW-3' p y-p-ImPyPy-y-ImHp-(3-ImIm 705(3) 5' C C G G TW-3' p -W y-(3-ImImHp-y-PyPy-(3- ImIm 706(3) 5' C C G G AW-3' Py-~-ImImPy-y-HpPy-(3-ImIm -W
707(3) 5' C C G C TW-3' Py-(3-ImPyHp-y-PyIm-R-ImIm -W
708(3) 5' C C G C AW-3' Py-(3-ImPyPy-y-Hplm-~i-Imlm -W
709~i) 5' C C C T TW-3' PyPypyHpHp-y-Py-(3-ImImIm -W
709~ip) 5' C C C T TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm -W
710(3) 5'-W C C C T AW-3' PyPyPyHpPy-y-Hp-~i-ImImIm 710(3p) 5' C C C T AW-3' PyPyPy-~3-Py-y-Hp-~i-ImImIm -W
7113) 5'-W C C C T GW-3' PyPy-(3-HpIm-y-Py-(3-ImImIm 7123) 5' C C C T CW-3' PyPyPyHpPy-y-Im-(3-ImImIm -W
712(3p) 5' C C C T CW-3' PyPyPy-~i-Py-y-Im-~3-ImImIm -W
713(3) 5' C C C A TW-3' PyPyPyPyHp-y-Py-(3-ImImIm -W
713~3p) 5' C C C A TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm -W
714(3) 5' C C C A AW-3' PyPyPyPyPy-y-Hp-(3-ImImIm -W
714(3p) 5' C C C A AW-3' PyPyPy-(3-Py-y-Hp-~i-ImImIm -W
715(3) 5' C C C A GW-3' PyPy-~3-Pylm-y-Py-(3-ImImIm -W
716(3) 5' C C C A CW-3' PyPypypypy-y-Im-(3-ImImIm -W
716(3p) 5' C C C A CW-3' PyPyPy-(3-Py-y-Im-~i-ImImIm -W
717(3) 5' C C C G TW-3' PyPy-(3-ImHp-y-Py-(3-ImImIm -W
718)3) 5' C C C G AW-3' PyPy-p-ImPy-y-Hp-(3-ImImIm -W
WO 98!37067 PCT/US98/01714 TABLE 67 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' with ~3 substitutions.
DNA sequence aromatic amino acid sequence G4l~i) 5' C C G G G W-3' Py-(~-ImImIm-y-PyPy-(3-ImIm -W
G42~3) 5' C C G G C W-3' Py-(3-ImImPy-y-ImPy-(3-ImIm -W
G43(3) '5' C C G C G W-3' Py-[3-ImPyIm-y-Pylm-p-Imlm -W
G44(3) 5' C C G C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImIm -W
645(3) 5' C C C G G W-3' PyPy-p-ImIm-y-Py-(3-ImImIm -W
G46~3) 5' C C C G C W-3' PyPy-(3-ImPy-y-Im-~3-ImImIm -W
G47(3) 5'-W C C C C G W-3' PyPy-(3-Pylm-y-PyImImImIm TABLE 68:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 7230 5'-W A G TT G W-3' Pylm-(3-HpIm-y-PyPyPyPyHp 723(3p) '5'-W A G TT G W-3' PyIm-~3-HpIm-y-PyPy-(3-PyHp 727(3) 5'-W A G TA G W-3' PyIm-(3-Pylm-y-PyHpPyPyHp 727~3p) 5'-W A G TA G W-3' PyIm-(3-PyIm-y-PyHp-(3-PyHp 729(3) 5'-W A G TG T W-3' Pylm-~3-ImHp-y-PyPyPyPyHp 729(3p) 5'-W A G TG T W-3' PyIm-(3-ImHp-y-PyPy-(3-PyHp 730(3) 5'-W A G TG A W-3' PyIm-[3-ImPy-y-HpPyPyPyHp 730(3p) 5'-W A G TG A W-3' PyIm-~i-ImPy-y-HpPy-~-PyHp 7313) 5'-W A G TG G W-3' PyIm-(3-ImIm-y-PyPyPyPyHp 731(3p) 5'-W A G TG G W-3' PyIm-~i-Imlm-y-PyPy-(3-PyHp 732(3) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPyPyPyHp 732(3p) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPy-J3-PyHp 735(3) 5'-W A G TC G W-3' Pyim-~-PyIm-y-PyImPyPyHp 735(3p) 5'-W A G TC G W-3' Pylm-(3-Pylm-y-Pylm-(3-PyHp 739(3) 5'-W A G AT G W-3' PyIm-p-HpIm-y-PyPyHpPyIip 739~p) 5'-W A G AT G W-3' PyIm-~3-HpIm-y-PyPy-~3-PyHp 743(3) 5'-W A G AA G W-3' PyIm-(3-PyIm-y-PyHpHpPyHp 743~ip) 5'-W A G AA G W-3' PyIm-(3-Pylm-y-PyHp-p-PyHp 745(3) 5'-W A G AG T W-3' PyIm-(3-ImHp-y-PyPyHpPyHp 745(3p) 5'-W A G AG T W-3' PyIm-~i-ImHp-y-PyPy-(3-PyHp 7463) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPyHpPyHp 746(3p) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPy-~3-PyHp 747(3) 5'-W A G AG G W-3' PyIm-~i-ImIm-y-PyPyHpPyHp 747~3p) 5'-W A G AG G W-3' PyIm-p-ImIm-y-PyPy-(3-PyHp 748(3) 5'-W A G AG C W-3' PyIm-p-ImPy-y-ImPyHpPyHp 748(3p) 5'-W A G AG C W-3' Pylm-(3-ImPy-y-ImPy-~3-PyHp 751(3) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-PyImHpPyHp 751(3p) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-Pylm-~i-PyHp TABLE :
69 10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 753(3) 5' A G G T TW-3' PyImIm-(3-Hp-y-pypypypyHp -W
753~3P) '5'-WA G G T TW-3' PyIrttIm-J3-Hp-y-py-(3-pypyHp 754(3) 5' A G G T AW-3' PyImIm-~3-Py-y-HpPyPyPyHp -W
754~3p) 5' A G G T AW-3' PyImIm-(3-Py-y-Hp-~-PypyHp -W
755(3) 5' A G G T GW-3' PyImIm-(3-Im-y-PyPypypyHp -W
755pp) 5' A G G T GW-3' PyImIm-(3-Im-y-Py-~3-pypyHp -W
7563) 5' A G G T CW-3' PyImIm-~3-py-y-ImPyPyPyHp -W
756(3p) 5' A G G T CW-3' PyImIm-(3-Py-y-Im-(3-PyPyHp -W
757(3) 5' A G G A TW-3' PyImIm-~3-Hp-y-PyHpPyPyHp -W
757~3P) 5' A G G A TW-3' PyImIm-(3-Hp-y-Py-(3-pypyHp -W
7583) 5' A G G A AW-3' PyImIm-(3-Py-y-HpHpPyPyHp -W
758(3p) 5' A G G A AW-3' PyImIm-(3-Py-y-Hp-(3-PyPyHp -W
759(3) 5' A G G A GW-3' PyImIm-p-Im-y-PyHpPyPyHp -W
759~3p) 5' A G G A GW-3' PyImIm-~3-Im-y-Py-~-pypygp -W
760(3) 5' A G G A CW-3' PyImIm-(3-Py-y-ImHpPyPyHp -W
760~p) 5' A G G A CW-3' PyImIm-(3-Py-y-Im-~-PyPyHp -W
763(3) 5' A G G C TW-3' PyImIm-(3-Hp-y-PyImPyPyHp -W
7643) 5' A G G C AW-3' Pylmim-(3-Py-y-HpImPyPyHp -W
765(3) 5' A G C T TW-3' PyImPyHpHp-y-Py-~3-ImPyHp -W
765pp) 5' A G C T TW-3' PyImPy-(3-Hp-y-py-(3-ImPyHp -W
7663) 5' A G C T AW-3' PyImPyHpPy-y-Hp-(3-ImPyHp -W
766(3p) 5' A G C T AW-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp -W
7673) 5' A G C T GW-3' PyIm-(3-HpIm-y-Py-(3-ImPyAp -W
768(3) 5' A G C T CW-3' PyImPyHpPy-y-Im-~3-ImPyHp -W
768~ip) 5' A G C T CW-3' PyImPy-(3-Py-y-Im-~-ImPyHp -W
769(3) 5' A G C A TW-3' PyImPyPyHp-y-Py-p-ImPyHp -W
769(3p) 5' A G C A TW-3' PyImPy-~i-Hp-y-py-(3-ImPyHp -W
770(3) 5' A G C A AW-3' PyImPyPyPy-y-Hp-(3-ImPyHp -W
lAIiLL by (cont):
IU-ring Hairpin Polyamides for recognition of 7-by 5'-WAGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 770~3p) 5'-WA G C A A W-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp 771(3) .5'-WA G C A G W-3' PyIm-~3-PyIm-y-Py-(3-ImPyHp 772(3) 5'-WA G C A C W-3' PyImPyPyPy-y-Im-(3-ImPyHp 772(3p) 5'-WA G C A C W-3' PyImPy-(3-Py-y-Im-~3-ImPyHp 7733) 5'-WA G C G T W-3' PyIm-(3-ImHp-y-Py-~-ImPyHp 7743) 5'-WA G C G A W-3' Pylm-(3-ImPy-y-Hp-(3-ImPyHp 775(3) 5'-WA G C C T W-3' PyImPyPyHp-y-PyImIm-/3-Hp 776~i) 5'-WA G C C A W-3' PyImPyPyPy-y-HpImIm-~3-Hp 7793) 5'-WA G G C G W-3' PyImIm-(3-Im-y-PyImPyPyHp 780(3) 5'-WA G G C C W-3' PyImIm-~3-Py-y-ImImPyPyHp 781(3) 5'-WA G C G G W-3' PyIm-~-ImIm-y-Py-~i-ImPyHp 782(3) 5'-WA G C G C W-3' Pylm-/3-ImPy-'y-Im-~-ImPyHp 783(3) 5'-WA G C C G W-3' Pylm-(3-Pylm-y-PyImIm-(3-Hp 784(3) 5'-WA G C C C W-3' PyImPyPyPy-y-ImImIm-a-Hp TABLE 70:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WATWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 7873) 5'-WA T T T G W-3' PyHp_R_Hplm-y-PypyPypyHp 787(3p) . -WA T T T G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyHp 5' 791(3) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHpPyPyHp 791(~p) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHp-p-PyHp 793(3) 5'-WA T T G T W-3' PyHp-~i-ImHp-y-PyPyPyPyHp 793~P) 5'-WA T T G T W-3' pyHp-~_I~p_y_pypy-~j-pyHp 7943) 5'-WA T T G A W-3' PyHp-p-ImPy-y-HpPyPyPyHp 794(3p) 5'-WA T T G A W-3' PyHp-~-ImPy-y-HpPy-~3-PyHp 795(3) 5'-WA T T G G W-3' PyHp-~3-Imlm-y-PypypypyHp 795~3P) 5'-WA T T G G W-3' PyHp-~-ImPy-y-ImPyPyPyHp 796(3p) 5'-WA T T G C W-3' Pylip-p-ImPy-y-ImPy-/3-PyHp 799(3) 5'-WA T T C G W-3' PyHp-p-pyIm-y-PyImPyPyHp 799(3p) 5'-WA T T C G W-3' PyHp-(3-Pylm-y-PyIm-p-PyHp 803~i) 5'-WA T A T G W-3' PyHp-/3-HpIm-y-PypyHpPyHp 803(3p) 5'-WA T A T G W-3' PyHp-~3-HpIm-y-PyPy-~3-PyHp 8073) 5'-WA T A A G W-3' PyHp-~-PyIm-y-PyHpHpPyHp 807(3p) 5'-WA T A A G W-3' PyHp-(3-PyIm-y-PyHp-~3-PyHp 8093) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPYHpPyHp 809(3p) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPy-p-PyHp 810(3) 5'-WA T A G A W-3 ' PyHp-(3-ImPy-y-HpPyHpPyHp 810~3p) 5'-WA T A G A W-3' PyHp-~-ImPy-y-HpPy-(3-PyHp 811~i) 5'-WA T A G G W-3' PyHp-[3-ImIm-y-pypyHpPyHp 811~3P) 5'-WA T A G G W-3' PyHp-/3-ImIm-y-PyPy-(3-PyHp 812~i) 5'-WA T A G C W-3' p H
Y P-p-ImPy-y-ImPyHpPyHp 812~ip) 5'-WA T A G C W-3' PyHp-(3-Impy-y-Impy-p-PyHp 815(3) 5'-WA T A C G W-3' PyHp-(3-pylm-y-PyImHpPyHp 815~3p) 5'-WA T A C G W-3' PyHp-p-PyIm-y-Pylm-~i-PyHp TABLE 71:
I 0-ring Hairpin Polyamides for recognition of 7-by S'-WATSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 817~i) 5'-W A T GT T W-3' Py-J3-ImHpHp-y-PyPyPyPyHp 817(3p) ' -W A T GT T W-3' py-(3-I~pgp_y_pypypy_p-Hp S' 8183) 5'-W A T GT A W-3 Py-(3-ImHpPy-y-HpPyPyPyHp 818(3p) 5'-W A T GT A W-3' Py-(3-ImHpPy-y-HpPyPy-~3-Hp 8193) 5'-W A T GT G W-3' Py-(3-ImHpIm-y-PyPyPyPyHp 819~3p) 5'-W A T GT G W-3' Py-/3-ImHpIm-y-PyPyPy-(3-Hp 820(3) 5'-W A T GT C W-3' Py-~3-ImHppy-y-ImPyPyPyHp 820(3p) 5'-W A T GT C W-3' py-(3-ImHpPy-y-ImPyPy-~3-Hp 821(3) 5'-W A T GA T W-3' Py-(3-ImPyHp-y-PyHpPyPyHp 821(3p) 5'-W A T GA T W-3' Py-/3-ImPyHp-y-PyHpPy-(3-Hp 822(3} 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHppyPyHp 822(3p) 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHpPy-~3-Hp 823(3) 5'-W A T GA G W-3' Py-p-ImPyIm-y-PyHpPyPyHp 823(3p) 5'-W A T GA G W-3' Py-/3-ImPyIm-y-PyHpPy-~i-Hp 824(3) 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPyPyHp 824(3p} 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPy-(3-Hp 825(3) 5'-W A T GG T W-3' Py-(3-ImImHp-y-PypyPyPyHp 825~3p} 5'-W A T GG T W-3' Py-(3-ImImHp-y-PyPyPy-(3-Hp 826(3) 5'-W A T GG A W-3' Py-~3-ImImPy-y-HpPyPyPyHp 826(3p) 5'-W A T GG A W-3' Py-(3-ImImPy-y-HpPyPy-p-Hp 8273) 5'-W A T GC T W-3' Py-p-ImPyHp-y-PyImPyPyHp 827(3p) 5'-W A T GC T W-3' Py-~3-ImPyHp-y-PyImPy-p-Hp 8283) 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPyPyHp 828(3p} 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPy-~3-Hp 8290 5'-W A T GG G W-3' Py-(3-ImImIm-y-PypyPyPyHp 829~p) 5'-W A T GG G W-3' Py-(3-ImImIm-y-PyPyPy-(3-Hp 830(3) 5'-W A T GG C W-3' Py-j3-ImImPy-y-ImPyPyPyHp 830(3p) 5'-W A T GG C W-3' Py-(3-ImImPy-y-ImPyPy-(3-Hp 831(3) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPyPyHp 831(3p) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPy-~3-Hp TABLE 71:
I 0-ring Hairpin Polyamides for recognition of 7-by 5'-WATSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 8323) 5'-W A TG C C W-3' Py-~-ImPyPy-y-ImImPyPyHp 832~3p) ' -W A TG C C W-3' Py-~-ImPyPy-y-ImImPy-~3-Hp 5' 833(3) 5'-W A TC T T W-3' PyHpPyHpHp-y-Py-~3-ImPyHp 833~p) 5'-W A TC T T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp 8340 5'-W A TC T A W-3' PyHpPyHpPy-y-Hp-(3-ImPyHp 834~3p) 5'-W A TC T A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp 8353) 5'-W A TC T G W-3' PyHp-(3-HpIm-y-Py-(3-ImPyHp 836~i) 5'-W A TC T C W-3' PyHpPyHpPy-y-Im-(3-ImPyHp 836(3p) 5'-W A TC T C W-3' PyHpPy-~3-py-y-Im-(3-ImPyHp 837(3) 5'-W A TC A T W-3' PyHpPyPyHp-y-Py-(3-ImPyHp 837~3p) 5'-W A TC A T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp 8383) 5'-W A TC A A W-3' PyHpPyPyPy-y-Hp-(3-ImPyHp 838(3p) 5'-W A TC A A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp 839(3) 5'-W A TC A G W-3' PyHp-~3-PyIm-y-Py-(3-ImPyHp $40(3) 5'-W A TC A C W-3' PyHpPyPyPy-y-Im-p-ImPyHp 840~p) 5'-W A TC A C W-3' PyHpPy-~i-Py-y-Im-~3-ImPyHp 841(3) 5'-W A TC G T W-3' PyHp-(3-ImHp-y-Py-(3-ImPyHp 842(3) 5'-W A TC G A W-3' PyHp-~-ImPy-y-Hp-~-ImPyHp 8430 5'-W A TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Hp 843(3p) 5'-W A TC C T W-3' py-(3-pypygp-y-pylmIm-~3-Hp 8443) 5'-W A TC C A W-3' PyHppyPyPy-y-HpImIm-(3-Hp 844(3p) 5'-W A TC C A W-3' py-p-pypypy-y-HpImIm-(3-Hp 845 ) 5'-W A TC G G W-3' PyHp-(3-ImIm-y-Py-(3-ImPyHp 8463) 5'-W A TC G C W-3' PyHp-(3-ImPy-y-Im-(3-ImPyHp 8473) 5'-W A TC C G W-3' PyHp-(3-PyIm-y-PyImIm-(3-Hp - 8483) 5'-W A TC C C W-3' PyHpPyPyPy-y-ImImIm-~3-Hp 848(3p) 5'-W A TC C C W-3' Py-(3-PyPyPy-y-ImImIm-(3-Hp TABLE 72:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAAWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 851(3) 5' -WA AT T G W-3' PyPy-~3-Hp lm-y-PyPyPyHpHp 851~3p) ' -WA AT T G W-3' PyPy-J3-Hplm-y-PyPy-~3-HpHp 5' 8553) 5' -WA AT A G W-3' PyPy-~3-Pylm-y-PyHppyHpHp 855(3p) 5' -WA AT A G W-3' Pypy-p-PyIm-y-PyHp-~3-HpHp 857(3) 5' -WA AT G T W-3' PyPy-~3-ImHp-y-PyPyPyHpHp 857(3p) 5' -WA AT G T W-3' PyPy-~-ImHp-y-PyPy-(3-HpHp 858(3) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-HpPyPyHpHp 858(3p) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-Hppy-(3-HpHp 8593) 5' -WA AT G G W-3' Pypy-(3-Imlm-y-PyPyPyHpHp 859~3p) 5' -WA AT G G W-3' PyPy-(3-Imlm-y-Pypy-~-HpHp 8603) 5' -WA AT G C W-3' PyPy-(3-ImPy-y-ImPyPyHpHp 860(3p) 5' -WA AT G C W-3' PyPy-[3-ImPy-y-ImPy-(3-HpHp 8633) 5' -WA AT C G W-3' PyPy-(3-PyIm-y-PyImPyHpHp 863(3p) 5' -WA AT C G W-3' PyPy-(3-Pylm-y-PyIm-(3-HpHp 8673) 5' -WA AA T G W-3' PyPy-(3-HpIm-y-PyPyHpHpHp 867(3p) 5' -WA AA T G W-3' PyPy-(3-Hplm-y-PyPy-(3-HpHp 871(3) 5' -WA AA A G W-3' PyPy-(3-PyIm-y-PyHpHpHpHp 871~3p) 5' -WA AA A G W-3' PyPy-p-PyIm-y-PyHp-(3-HpAp 8733) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPyHpHpHp 873(3p) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpHp 874(3) 5' -WA AA G A W-3' PyPy-p-ImPy-y-HpPyHpHpHp 874~p) 5' -WA AA G A W-3' PyPy-(i-ImPy-y-HpPy-(3-HpHp 875(3) 5' -WA AA G G W-3' PyPy-p-ImIm-y-PyPyHpHpHp 875(3p) 5' -WA AA G G W-3' PyPy-~3-Imlm-y-PyPy-~i-HpHp 876(3) 5' -WA AA G C W-3' Pypy-(3-ImPy-y-ImPyHpHpHp 876~ip) 5' -WA AA G C W-3' PyPy-~i-ImPy-y-ImPy-(3-HpHp 8793) 5' -WA AA C G W-3' PyPy-~i-PyIm-y-PyImHpHpHp 879(3p) 5' -WA AA C G W-3' PyPy-(3-PyIm-y-PyIm-(3-HpHp TABLE
73: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WAASNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence ' 881) 5' A A GT T W-3' Py--IrnHpHp-y-PyPyPyHpHp -W
881p) '5' A A GT T W-3' py__I~pHp-y-pyPypy--Hp -W
882) 5' A A GT A W-3' Py--ImHpPy-y-HpPyPyHpHp -W
882P) 5' A A GT A W-3' py--I~ppy_y-Hppypy--Hp -W
883) 5' A A GT G W-3' Py--ImHpIm-y-PyPypyHpHp -W
883(3p) 5'-W A A GT G W-3' Py--ImHpIm-y-PyPyPy--Hp 884) 5'-W A A GT C W-3' p y--ImHpPy-y-ImPyPyHpHp 884(3p) 5' A A GT C W-3' p -W y--ImHppy-y-ImPyPy--Hp 8853) 5' A A GA T W-3' -W Py--ImPyHp-y-PyHpPyHpHp 885p) 5' A A GA T W-3' Py--ImPyHp-y-PyHpPy--Hp -W
886(3) 5' A A GA A W-3' -W Py--ImPyPy-y-HpHpPyHpHp 886p) 5'-W A A GA A W-3' Py--ImPyPy-y-HpHpPy--Hp 887) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPyHpHp -W
887(3p) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPy--Hp -W
888) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPyI-IpHp -W
888~iP) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPy--Hp -W
889) 5'-W A A GG T W-3' Py--ImImHp-y-PyPyPyHpHp 889p) 5'-W A A GG T W-3' Py--ImImHp-y-PyPyPy--Hp 890(3) 5'-W A A GG A W-3' Py--ImImPy-y-HpPyPyHpHp 890p) 5'-W A A GG A W-3' Py--ImImPy-y-HpPyPy--Hp 891) 5' A A GC T W-3' Py--ImPyHp-y-PyTmPyHpHp -W
891p) 5' A A GC T W-3' Py--ImPyHp-y-PyImPy--Hp -W
892) 5'-W A A GC A W-3' Py--ImPyPy-y-HpImPyHpHp 892p) 5'-W A A GC A W-3' Py--ImPyPy-y-HpImPy--HP
893(3) 5' A A GG G W-3' Py--ImImIm-y-PyPyPyHpHp -W
893p) 5' A A GG G W-3' Py--ImImIm-y-PyPyPy--Hp -W
894) 5' A A GG C W-3' Py--ImImPy-y-ImPyPyHpHp -W
894p) 5'-W A A GG C W-3' Py--ImImPy-y-ImPyPy--Hp 895(3) 5' A A GC G W-3' Py--ImPyIm-y-PyImPyHpHp -W
895p) 5'-W A A GC G W-3' Py--ImPyIm-y-PyImPy--Hp TABLE 73 (cont); Polyamides 10-ring Hairpin for recognition of 7-by 5'-WAASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 896(3) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPyHpHp 896(3p) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPy-(3-Hp 8973) ~ -W A AC T T W-3' PyPyPyHpHp-y-Py-~i-ImHpHp 5' 897(3p) 5'-W A AC T T W-3' pypypy_R_Hp_y_py_~_I~pHp 898(3) 5'-W A AC T A W-3' PyPyPyHpPy-y-Hp-(3-ImHpHp 898~3p) 5'-W A AC T A W-3' PyPyPy-(3-py-y-Hp_(3-ImApHp 899(3) 5'-W A AC T G W-3' PyPy-(3-HpIm-y-Py-(3-ImHpHp 900(3) 5'-W A AC T C W-3' PyPyPyHpPy-y-Im-~3-ImHpHp 900(3p) 5'-W A AC T C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpHp 901(3) 5'-W A AC A T W-3' PyPyPyPyHp-y-Py-(3-ImHpHp 901(3p) 5'-W A AC A T W-3' PyPyPy-(3-Hp-y-py_~3-ImHpHp 902(3) 5'-W A AC A A W-3' PyPyPypypy-y-Hp_~-ImHpHp 902~3p) 5'-W A AC A A W-3' pypypy_~_py_y_Hp-~-I~pHp 903~i) 5'-W A AC A G W-3' PyPy-(3-pylm_y_py_~_I~pHp 904(3) 5'-W A AC A C W-3' PyPyPyPyPy-y-Im-~3-ImHpHp 904(3p) 5'-W A AC A C W-3' PyPyPy-~3-Py-y-Im-(3-ImHpHp 905(3) 5'-W A AC G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpHp 9063) 5'-W A AC G A W-3' PyPy-(3-ImPy-y-Hp-(3-ImHpHp 9073) 5'-W A AC C T W-3' PyPypypyHp-y-PyImIm-p-Hp 907(3p) 5'-W A AC C T W-3' Py-(3-PyPyHp-y-PyImIm-(3-Hp 908(3) 5'-W A AC C A W-3' PyPyPyPyPy-y-HpImIm-(3-Hp 908~3p) 5'-W A AC C A W-3' Py-(3-PyPyPy-y-HpImIm-p-Hp 9093) 5'-W A AC G G W-3' PyPy-(3-Imlm-y-Py-(3-ImHpHp 910(3) 5'-W A AC G C W-3' PyPy-(3-ImPy-y-Im-(3-ImHpHp 9113) 5'-W A AC C G W-3' PyPy-~3-PyIm-y-PyImIm-(3-Hp 912(3) 5'-W A AC C C W-3' PyPyPyPyPy-y-ImImIm-(3-Hp 912~3p) 5'-W A AC C C W-3' Py-(3-pypypy-y-ImImIm-p-Hp ' TABLE
74: 30-ring Hairpin Polyamides for recognition of 7-by 5'-WACWNNW-3' with ~3 substitutions .
DNA aromatic amino acid sequence sequence 913(3) 5' -WA C T TT W-3' PyPyHpHpHp-y-PyPy-(3-ImFip 913(3p) .5'-WA C T TT W-3' PyPy-(3-HpHp-y-Pypy-(3-ImHp 914(3) 5' -WA C T TA W-3' PyPyHpHpPy-y-HpPy-(3-ImHp 914(3p) 5' -WA C T TA W-3' pyPy-p-HpPy-y-HpPy-j3-ImHp 9153) 5' -WA C T TG W-3' PyPy-(3-HpIm-y-PyPy-(3-ImHp 916(3) 5' -WA C T TC W-3' PyPyHpHpPy-Y-ImPy-(3-ImHp 916(3p) 5' -WA C T TC W-3' PyPy-(3-HpPy-y-ImPy-(3-ImHp 9173) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-~3-ImHp 9I7(3p) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-(3-ImHp 918~i) 5' -WA C T AA W-3' PyPyHpPyPy-y-HpHp-(3-ImHp 918~3p) 5' -WA C T AA W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp 9193) 5' -WA C T AG W-3' PyPy-p-pylm-y-PyHp-~i-ImHp 920(3) 5' -WA C .TAC W-3' PyPyHpPyPy-Y-ImHp-(3-ImHp 920(3p) 5' -WA C T AC W-3' PyPy-(3-PyPy-y-ImIip-(3-ImHp 921(3) 5' -WA C T GT W-3' pypy-~-Imp-y_pypy-a_I~p 922(3) 5' -WA C T GA W-3' PyPy-~3-ImPy-y-HpPy-(3-ImHp 923(3) 5' -WA C T GG W-3' PyPy-(3-Imlm-y-PyPy-(3-ImHp 924(3) 5' -WA C T GC W-3' PyPy-~3-ImPy-y-ImPy-(3-ImHp 925(3) 5' -WA C T CT W-3' PyPyHpPyHp-y-PyIm-~3-ImHp 925~3p) 5' -WA C T CT W-3' PyPy-(1-PyHp-Y-pylm-(3-ImHp 9260 5' -WA C T CA W-3' PyPyHpPyPy-y-HpIm-(3-ImHp 926(3p) 5' -WA C T CA W-3' PyPy-(3-PyPy-Y-Hplm-~3-ImHp 927(3) 5' -WA C T CG W-3' PyPy-(3-PyIm-y-PyIm-(3-ImHp 928(3) 5' -WA C T CC W-3' PyPyHpPyPy-y-ImIm-[3-ImHp 928~3p) 5' -WA C T CC W-3' PyPy-(3-pypy-y-Imlm-~3-ImHp 929(3) 5' -WA C A TT W-3' PyPyPyHpHp-y-PyPy-/3-ImHp ' 30 929~3p) 5' -WA C A TT W-3' pypy-(3-gpgp_y_pypy_~_I~p 9303) 5' -WA C A TA W-3' PyPyPyHpPy-Y-HpPy-(3-ImHp 930~3p) 5' -WA C A TA W-3' pypy-(3-Hppy-y-HpPy-p-ImHp 9313) 5' -WA C A TG W-3' Pypy-(3-Hplm-Y_pypy_p-I~p TABLE 74 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WACWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 932(3) 5'-W A CA T C W-3' PyPyPyHpPy-y-ImPy-(3-ImHp 932(3p) '5'-W A CA T C W-3' PyPy-(3-HpPy-y-ImPy-[3-ImHp 9333) 5'-W A CA A T W-3' PyPyPyPyHp-y-PyHp-(3-ImHp 933(3p) 5'-W A CA A T W-3' PyPy-(3-PyHp-y-PyHp-(3-ImHp 934(3) 5'-W A CA A A W-3' PyPyPyPyPy-y-HpHp-(3-ImHp 934(3p) 5'-W A CA A A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp 1(? 935~i) 5'-W A CA A G W-3' PyPy-(3-PyIm-y-PyHp-p-ImHp 936(3) 5'-W A CA A C W-3' PyPypypypy-y-I~p-~-I~p 936(3p) 5'-W A CA A C W-3' PyPy-(3-PyPy-y-ImHp-(i-ImHp 937(3) 5'-W A CA G T W-3' PyPy-(3-ImHp-y-PyPy-p-ImHp 938(3) 5'-W A CA G A W-3' PyPy-(3-ImPy-y-HpPy-~3-ImHp 9393) 5'-W A CA G G W-3' PyPy-~3-Imlm-y-PyPy-(3-ImHp 940(3) 5'-W A CA G C W-3' PyPy-(3-ImPy-y-ImPy-(3-ImHp 941(3) 5'-W A CA C T W-3' PyPyPyPyHp-y-PyIm-(3-ImAp 941~p) 5'-W A CA C T W-3' PyPy-(3-PyHp-y-Pylm-(i-ImFip 942(3) 5'-W A CA C A W-3' PyPyPyPyPy-y-HpIm-(3-ImHp 942(3p) 5'-W A CA C A W-3' PyPy-(3-PyPy-y-HpIm-~3-ImHp 943(3) 5'-W A CA C G W-3' PyPy-(3-PyIm-y-PyIm-~-ImHp 9443) 5'-W A CA C C W-3' PyPyPyPyPy-y-ImIm-(3-ImHp 944(3p) 5'-W A CA C C W-3' PyPy-(3-Pypy-y-ImIm-(3-ImHp TABLE
75: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' with (3 substitutions.
D1~1A aromatic amino acid sequence sequence 9453) 5' -WA C GT T W-3' Py-(3-ImHpHp-Y-Pypy-(3-Imp 9463) '5'-WA C GT A W-3' py_~3_I~ppy_y-Hppy_~-I~p 9473) 5' -WA C GT G W-3' Py-(3-ImHpIm-y-Pypy-a-ImHp 948(3) 5' -WA C GT C W-3' Py-(3-ImHpPy-y-ImPy-~3-ImHp 949(3) 5' -WA C GA T W-3' Py-(3-ImPyHp-y-pyHp-/3-ImHp 950(3) 5' -WA C GA A W-3' Py-~3-ImPyPy-y-HpHp-~-ImHp 9513) 5' -WA C GA G W-3' Py-J3-ImPyIm-y-PyHp-[3-ImHp 952(3) 5' -WA C GA C W-3' Py-(3-ImPyPy-Y-ImHp-(3-ImHp 9533) 5' -WA C GG T W-3' Py-(3-ImImHp-y-PyPy-p-I~p 954(3) 5' -WA C GG A W-3' Py-(3-ImImPy-y-Hppy-(3-ImHp 9553) 5' -WA C GC T W-3' Py-(3-ImPyHp-y-Pylm-(3-ImHp 9563) 5' -WA C GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-ImHp 9573) 5' -WA C CT T W-3' PyPypyHpHp-y-Py-(3-ImImHp 957(3p) 5' -WA C CT T W-3' PyPyPy-~3-Hp-Y-Py-~3-ImImHp 958(3) 5' -WA C CT A W-3' PyPyPyHpPy-y-Hp-(3-ImImHp 958~3p) 5' -WA C CT A W-3' PyPypy-~3-py-y-Hp-~-ImImHp 959p) 5' -WA C CT G W-3' PyPy-j3-HpIm-y-Py-(3-ImImHp 960(3) 5' -WA C CT C W-3' PyPyPyHpPy-y-Im-~-ImImHp 960pp) 5' -WA C CT C W-3' Pypypy-(3-py-y-Im_~-ImImHp 961~i) 5' -WA C CA T W-3' PyPyPyPyHp-y-Py-~3-ImImHp 961(3p) 5' -WA C CA T W-3' PyPyPy-/3-Hp-y-Py-(3-ImImHp 9623) 5' -WA C CA A W-3' pypypypypy_y_Hp_~-ImImHp 962~3p) 5' -WA C CA A W-3' pypypy-(3-py-y-Hp-~-ImImHp 9633) 5' -WA C CA G W-3' PyPy-(3-pylm-y-Py-(3-ImImHp 964) 5' -WA C CA C W-3' PyPyPyPyPy-y-Im-~3-ImImHp 964(3p) 5' -WA C CA C W-3' PyPypy-(3-Py-y-Im_~3-ImImHp 965(3) 5' -WA C CG T W-3' PyPy-~3_ImHp-y-Py-~i-ImImHp 966(3) 5' -WA C CG A W-3' Pypy-~-Impy-y-Hp-~3-ImImHp 969(3) 5' -WA C GG G W-3' Py-(3-ImImIm-y-Pypy-~3-I~p 970~i) 5' -WA C GG C W-3' Py-(3-ImImPy-y-ImPy-~3-ImHp TABLE 75 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' with (3 substitutions.
DNA sequence aromatic amino acid sequence 9713) 5' -W A C G W-3' Py-(3-ImPyIm-y-PyIm-~-ImHp C G
972(3) 5' -W A C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImHp C G
973(3) ' 5' -W G G W-3' PyPy-(3-Imlm-y-Py-~-ImImHp A C C
974(3) 5' -W A G C W-3' PyPy-~-ImPy-y-Im-(3-ImImHp C C
9753) 5' -W A C G W-3' PyPy-(3-PyIm-y-PyImImImHp C C
TABLE 76:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 979(3) 5' -WT G T T GW-3' Hplm-(3-HpIm-y-PyPyPyPyPy 979(3p) ~ -WT G T T GW-3' HpIm-~3-HpIm-y-PyPy-(3-PyPy 5' 9833) 5' -WT G T A GW-3' HpIm-/3-PyIm-y-PyHpPypyPy 983(3p) 5' -WT G T A GW-3' Hplm-~3-PyIm-y-PyHp-(3-PyPy 985(3) 5' -WT G T G TW-3' HpIm-p-ImHp-y-PyPyPyPyPy 985(3p) 5' -WT G T G TW-3' HpIm-(3-ImHp-y-PyPy-~i-PyPy 9863) 5' -WT G T G AW-3' HpIm-~3-ImPy-y-HpPypypypy 986~3p) 5' -WT G T G AW-3' HpIm-(3-ImPy-~y-HpPy-~3-PyPy 987(3) 5' -WT G T G GW-3' Hplm-p-Imlm-y-PyPyPyPyPy 987(3p) 5' -WT G T G GW-3' HpIm-(3-Imlm-y-PyPy-p-PyPy 988(3) 5' -WT G T G CW-3' HpIm-(3-ImPy-y-ImPyPYPyPy IS 988(3p) 5' -WT G T G CW-3' Hplm-~-ImPy-y-ImPy-p-Pypy 9913) 5' -WT G T C GW-3' Hplm-~i-Pylm-y-PyImPypyPy 991(3p) 5' -WT G T C GW-3' Hplm-(3-Pylm-y-Pylm-~3-PyPy 9953) 5' -WT G A T GW-3' Hplm-(3-HpIm-y-PyPyHpPyPy 995~p) 5' -WT G A T GW-3' HpIm-(3-HpIm-y-PyPy-(3-PyPy 999(3) 5' -WT G A A GW-3' HpIm-(3-Pylm-y-PyHpHpPyPy 999~3p) 5' -WT G A A GW-3' HpIm-(3-PyIm-y-PyHp-~3-PyPy 1001(3) 5' -WT G A G TW-3' HpIm-(3-ImHp-y-PyPyHpPyPy 1001~3p) 5' -WT G A G TW-3' HpIm-p-ImHp-y-PyPy-(3-PyPy 1002(3) 5' -WT G A G AW-3' Hplm-(3-ImPy-y-HpPyHpPyPy 1002~3p) 5' -WT G A G AW-3' HpIm-(3-ImPy-y-HpPy-(3-PyPy 1003(3) 5' -WT G A G GW-3' HpIm-~3-Imlm-y-PyPyHpPyPy 1003~3p) 5' -WT G A G GW-3' HpIm-~3-ImIm-y-PyPy-(3-PyPY
10043) 5' -WT G A G CW-3' HpIm-(3-ImPy-y-ImPyHpPyPy - 1004~ip) 5' -WT G A G CW-3' Hplm-~3-ImPy-y-ImPy-(3-PyPy 10073) 5' -WT G A C GW-3' HpIm-(3-PyIm-y-PyImHpPyPy 1007(3p) 5' -WT G A C GW-3' Hplm-(3-PyIm-y-Pylm-(3-PyPy TABLE 77:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGSNNW-3' with substitutions.
DNA sequence aromatic amino acid sequence 1009(3) 5'-W T GG T T W-3' HpImIm--Hp-y-PyPyPyPyPy 1009p)' 5'-W T GG T T W-3' HpImIm--Hp-y-Py--PyPyPy 1010(3) 5'-W T GG T A W-3' HpImIm--Py-y-HpPyPyPyPy 1010(3p) 5'-W T GG T A W-3' HpImIm--Py-y-Hp--PyPyPy 10113) 5'-W T GG T G W-3' HpImIm--Im-y-PyPyPyPyPy 1011(3p) 5'-W T GG T G W-3' HpImIm--Im-y-Py--PyPyPy 1012(3) 5'-W T GG T C W-3' HpImIm--Py-y-ImPyPyPyPy 1012~p) 5'-W T GG T C W-3' HpImIm--Py-y-Im--PyPyPy 1013(3) 5'-W T GG A T W-3' HpImIm--Hp-y-PyHpPyPyPy 1013p) 5'-W T GG A T W-3' HpImIm--Hp-y-Py--PyPyPy 1014(3) 5'-W T GG A A W-3' HpImIm--Py-y-HpHpPyPyPy 1014p) 5'-W T GG A A W-3' HpImIm--Py-y-Hp--PyPyPy 10153) 5'-W T GG A G W-3' HpImIm--Im-y-PyHpPyPyPy 1015(3p) 5'-W T GG A G W-3' HpImIm--Im-y-Py-(3-PyPyPy 10163) 5'-W T GG A C W-3' HpImIm--Py-y-ImHpPyPyPy 1016(3p) 5'-W T GG A C W-3' HpImIm-(3-Py-y-Im--PyPyPy 1019(3) 5'-W T GG C T W-3' HpImIm--Hp-y-PyImPyPyPy 10203) 5'-W T GG C A W-3' HpImIm--Py-y-HpImPyPyPy 1021(3) 5'-W T GC T T W-3' HpImPyHpHp-y-Py--ImPyPy 1021(3p) 5'-W T GC T T W-3' HpImPy--Hp-y-Py--ImPyPy 1022(3) 5'-W T GC T A W-3' HpImPyHpPy-y-Hp--ImPyPy 1022(3p) 5'-W T GC T A W-3' HpImPy-(3-Py-y-Hp--ImPyPy 1023) 5'-W T GC T G W-3' HpIm--Hplm-y-Py--ImPyPy 10243) 5'-W T GC T C W-3' HpImPyHpPy-y-Im-/3-ImPyPy 1024p) 5'-W T GC T C W-3' HpImPy--Py-y-Im--ImPyPy 1025(3) 5'-W T GC A T W-3' HpImPyPyHp-y-Py-(i-ImPyPy 1025(3p) 5'-W T GC A T W-3' HpImPy--Hp-y-Py--ImPyPy 1026(3) 5'-W T GC A A W-3' HpImPyPyPy-y-Hp--ImPyPy 1026~p) 5'-W T GC A A W-3' HpImPy--Py-y-Hp--ImPyPy 10273) 5'-W T GC A G W-3' HpIm--PyIm-y-Py--ImPyPy TABLE 77 (cont): Polyamides 10-ring Hairpin for recognition of 7-by 5'-WTGSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 1028(3) 5' -WT G C A C W-3' HpImPyPyPy-y-Im-~3-ImPyP
1028(3p)' 5' -WT G C A C W-3' HpImPy-(3-Py-y-Im-~i-ImPyPy 1029(3) 5' -WT G G G T W-3' HpIm-(3-ImHp-y-py-(3-ImPypy 1030(3) 5' -WT G C G A W-3' Hplm-~-ImPy-y-Hp-(3-ImPyPy 1031(3) 5' -WT G C C T W-3' HpImPyPyHp-y-PyImIm-~i-Py 1031(3p) 5' -WT G C C T W-3' HpImPy-p-Hp-y-PyImIm-(3-Py 10323) 5' -WT G C C A W-3' HpImPyPyPy-y-HpImIm-(3-Py 1032~3p) 5' -WT G C C A W-3' HpImPy-(3-Py-y-HpImIm-(3-Py 1035(3) 5' -WT G G C G W-3' HpImIm-(3-Im-y-PyImPyPyPy 1036) 5' -WT G G C C W-3' HpImIm-~3-Py-y-ImImPyPyPy 1037(3) 5' -WT G C G G W-3' HpIm-(3-ImIm-y-Py-(3-ImPyPy 1038(3) 5' -WT G C G C W-3' Hplm-(3-ImPy-y-Im-(3-ImPyPy 1039~i) 5' -WT G C C G W-3' Hplm-(3-Pylm-y-pylmlm-(3-Py 1040(3) 5' -WT G C C C W-3' HpImPyPyPy-y-ImImIm-~3-Py TABLE 78:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTWIVNW-3' with p substitutions.
DNA sequence aromatic amino acid sequence 10433) 5'-WT T T T G W-3' HpHp-(3-Hplm-y-PyPyPyPyPy 1043(3p)' 5'-WT T T T G W-3 HpHp-(3-HpIm-y-PyPy-(3-PyPy T
10473) 5'-WT T T A G W-3' HpHp-(3-PyIm-y-PyHpPyPyPy 1047(3p) 5'-WT T T A G W-3' HpHp-~i-Pylm-y-PyHp-(3-PyPy 1049(3) 5'-WT T T G T W-3' HpHp-~i-ImHp-y-PyPyPyPyPy 1049~3p) 5'-WT T T G T W-3' HpHp-p-ImHp-y-PyPy-(3-PyPy 1050(3) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPyPyPyPy 1050(3p) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPy-p-PyPy 1051(3) 5'-WT T T G G W-3' HpHp-(3-Imlm-y-PyPyPyPyPy 1051(3p) 5'-WT T T G G W-3' HpHp-(i-ImIm-y-PyPy-(3-PyPy 1052(3) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPyPyPyPy 1052(3p) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPy-(3-PyPy 1055(3) 5'-WT T T C G W-3' HpHp-(3-Pylm-y-PyImPyPyPy 1055~3p) 5'-WT T T C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy 1059~i) 5'-WT T A T G W-3' HpHp-(3-HpIm-y-PyPyHpPyPy 1059(3p) 5'-WT T A T G W-3' HpHp-~3-HpIm-y-PyPy-R-PyPy 1063(3) 5'-WT T A A G W-3' HpHp-~3-Pylm-y-PyHpHpPyPy 1063~3p) 5'-WT T A A G W-3' HpHp--PyIm-y-PyHp-(3-PyPy 1065(3) 5'-WT T A G T W-3' HpHp-(3-ImHp-y-PyPyHpPyPy 1065(3p) 5'-WT T A G T W-3' HpHp-~-ImHp-y-PyPy-p-PyPy 1066~i) 5'-WT T A G A W-3' HpHp-p-ImPy-y-HpPyHpPyPy 1066(3p) 5'-WT T A G A W-3' HpHp-J3-ImPy-y-HpPy-/3-PyPy 1067(3) 5'-WT T A G G W-3' ~ HpHp-(3-Imlm-y-PyPyHpPyPy 1067(3p) 5'-WT T A G G W-3' HpHp-(3-ImIm-y-PyPy-(3-PyPy 1068(3) 5'-WT T A G C W-3' HpHp-(3-ImPy-y-ImPyHpPyPy 1068(3p) 5'-WT T A G C W-3' HpHp-~3-ImPy-y-ImPy-(3-PyPy 1071(3) 5'-WT T A C G W-3' HpHp-(3-PyIm-y-PyImHpPyPy 1071~ip) 5'-WT T A C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy n TABLE 79:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' with ~i substitutions DNA aromatic amino acid sequence sequence 1073R) 5' -WT T G T TW-3' Hp-~3-I,~pgp-y-pypypypypy 1073~3p)' 5' -WT T G T TW-3' Hp-(3-ImHpAp-y-PyPYPy-(3-py 1074(3) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HppypypypY
1074(3p) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HpPYPy-~3_py 1075(3) 5' -WT T G T GW-3' Hp-~3-ImHpIm-y-PyPYPyPyPy 1075(3p) 5' -WT T G T GW-3' Hp-p-ImHpIm-y-PyPYPy-(3-Py 10763) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPyPyPy 1076(3p) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPy-~-Py 1077(3) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PyHpPyPyPy 1077(3p) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PYHpPy-(3-Py 1078(3) 5' -WT T G A AW-3' Hp-(3-ImPyPy-y-HpHpPyPyPy I5 1078~3p) 5' -WT T G A AW-3' Hp-~3-ImPyPy-y-HpHpPy-p-Py 1079(3) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PyHpPyPyPy 1079~3p) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PYHpPy-~-Py 1080(3) 5' -WT T G A CW-3' Hp-~3-ImPyPy-y-ImHpPyPYPy 1080(3p} 5' -WT T G A CW-3' Hp-(3-ImPyPy-y-ImHpPy-/3-Py 1081(3) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PyPypypypY
1081(3p) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PYPypy-(3-py 10820 5' -WT T G G AW-3' Hp-(3-ImImPy-y-HpPypyPyPy 1082~p) 5' -WT T G G AW-3' Hp-~-ImImPy-y-HpPYPy-~3-Py 1083(3) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPyPyPy 1083~3p) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPy-~-Py 10843) 5' -WT T G C AW-3' Hp-~i-ImPyPy-y-HpImPYPyPy 1084(3p) 5' -WT T G C AW-3' Hp-~3-ImPyPy-y-HpImPy-~3-Py 10850 5' -WT T G G GW-3' Hp-(3-ImImIm-y-PYPypypypy - 1085(3p) 5' -WT T G G GW-3' Hp-J3-ImImIm-y-PyPyPy-~3-Py 10863) 5' -WT T G G CW-3' Hp-~i-ImImPy-y-ImPyPyPyPy 1086(3p) 5' -WT T G G CW-3' Hp-(3-ImImPy-y-ImPyPy-~i-Py 1087) 5' -WT T G C GW-3' Hp-~3-ImPYIm-y-PyImPyPyPy 1087(3p) 5' -WT T G C GW-3' Hp-(3-ImPYIm-y-PyImPy-/3-Py WO 98/370b7 PCT/US98/01714 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1088(3) 5'-W T T G CC W-3' Hp-p-ImPyPy-y-ImImPyPyPy 1088(3p)' 5'-W T T G CC W-3' Hp-(3-ImPyPy-y-ImImPy-(3-Py 1089(3) 5'-W T T C TT W-3' HpHpPyHpHp-y-Py-(3-ImPyPy 1089(3p) 5'-W T T C TT W-3' HpHpPy-p-Hp-y-Py-(3-ImPyPy 1090(3) 5'-W T T C TA W-3' HpHpPyHpPy-y-Hp-(3-ImPyPy 1090(3p) 5'-W T T C TA W-3' HpHpPy-(3-Py-y-Hp-(3-ImPyPy 1091~i) 5'-W T T C TG W-3' HpHp-(3-HpIm-y-Py-~i-ImPyPy 10923) 5'-W T T C TC W-3' HpHpPyApPy-y-Im-(3-ImPyPy 1092(3p) 5'-W T T C TC W-3' HpHpPy-(3-Py-y-Im-(3-ImPyPy 10933) 5'-W T T C AT W-3' HpHpPyPyHp-y-Py-~3-ImPyPy 1093(3p) 5'-W T T C AT W-3' HpHpPy-~i-Hp-y-Py-/3-ImPyPy 10943) 5'-W T T C AA W-3' HpHpPyPyPy-y-Hp-(3-ImPyPy 1094(3p) 5'-W T T C AA W-3' HpHpPy-~3-Py-y-Hp-~i-ImPyPy 10953) 5'-W T T C AG W-3' HpHp-(3-Pylm-y-Py-(3-ImPyPy 10963) 5'-W T T C AC W-3' HpHpPyPyPy-y-Im-/3-ImPyPy 1096(3p) 5'-W T T C AC W-3' HpHpPy-(3-Py-y-Im-(i-ImPyPy 1097(3) 5'-W T T C GT W-3' HpHp-(3-ImHp-y-Py-[3-ImPyPy 1098(3) 5'-W T T C GA W-3' HpHp-~3-ImPy-y-Hp-p-ImPyPy 1099) 5'-W T T C CT W-3' HpHpPyPyHp-y-PyimIm-~3-Py 1099(3p) 5'-W T T C CT W-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py 1100(3) 5'-W T T C CA W-3 HpHpPyPyPy-y-HpImIm-p-Py ' 1100~ip) 5'-W T T C CA W-3' Hp-~i-PyPyPy-y-HpImIm-~-Py 1101(3) 5'-W T T C GG W-3' HpHp-(3-ImIm-y-Py-(3-ImPyPy 1102(3) 5'-W T T C GC W-3' HpHp-(3-ImPy-y-Im-~i-ImPyPy 1103(3) 5'-W T T C CG W-3' HpHp-(3-PyIm-y-PyImIm-(3-Py TABLE 80:
10-ring Hairpin Polyamides for recognition of 7-by S'-WTAWNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 11073) 5'-W T A TT G W-3' HpPy-(3-HpIm-y-PypypyHppy S I107(3p)' S'-W T A TT G W-3' HpPy-p-Hplm-y-Pypy-(3-HpPy 1111(3) 5'-W T A TA G W-3' HpPy-~3-Pylm-y-PyHpPyHpPy 1111~p) 5'-W T A TA G W-3' HpPy-~3-PyIm-y-PyHp-(3-HpPy 11133) 5'-W T A TG T W-3' HpPy-(3-ImHp-y-Pypypygppy 1113(3p) 5'-W T A TG T W-3' HpPy-p_ImHp_y_p~,p~,_~_HppY
11143) 5'-W T A TG A W-3' HpPy-p-ImPy-y-HpPYPyHpPy 1114(3p) 5'-W T A TG A W-3' HpPy-(3-ImPy-y-HpPy-(3-HpPy 1115(3) 5'-W T A TG G W-3' HpPy-(3-Imlm-y-Pypypygppy 1115(3p) 5'-W T A TG G W-3' HpPy-(3-ImIm-y-PyPy-(3-HpPy 1116(3) 5'-W T A TG C W-3' HpPy-~3-ImPy-y-ImPyPyHpPy 1S 1116~3p) 5'-W T A TG C W-3' HpPy-R-ImPy-y-ImPy-J3-HpPy 11193) 5'-W T A TC G W-3' HpPy-~i-PYim-y-PyImPyHpPy 1119(3p) 5'-W T A TC G W-3' HpPy-(3-PyIm-y-PyIm-(3-HpPy 11233) 5'-W T A AT G W-3' HpPy-(3-HpIm-y-PyPyHpHpPy 1123(3P) 5'-W T A AT G W-3' HpPy-p-HpIm-y-PyPy-(3-HpPY
1127(3) 5'-W T A AA G W-3' HpPy-(3-PYIm-y-PyHpHpHpPy 1127(3p) 5'-W T A AA G W-3' HpPy-(3-Pylm-y-PyHp-(3-HpPy 1129(3) 5'-W T A AG T W-3' HpPy-(3-ImHp-y-PyPyHpHpPy 1129(3p) 5'-W T A AG T W-3' Hppy-(3_I~p_y_p~,py_a-Hppy 1130(3) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPyHpHpPy 1130(3p) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPy-(3-HpPy 1131(3) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-PyPyI-IpHppy 1131~p) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-Pypy-(3-Hppy 1132(3) 5'-W T A AG C W-3' HpPy-(3-ImPy-y-ImPyHpHpPy 1132(3p) 5'-W T A AG C W-3' HpPy-~i-ImPy-y-ImPy-p-HpPy 1135~i) 5'-W T A AC G W-3' Hppy_~_pylm_y_pYImHpHppy 1135~p) 5'-W T A AC G W-3' HpPy-(3-PyIm-y-PYIm-~i-HpPy TABLE 81: in 10-ring Polyamides Hairp for recognition of 7-by 5'-WTASNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1137(3) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPyHpPy 1137(3p) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPy-~3-Py 1138(3) 5' -W T A GT A W-3' Hp-(3-ImHpPy-y-HpPyPyHpPy 1138~ip) 5' -W T A GT A W-3' Hp-p-ImHpPy-y-HpPyPy-(3-Py 1139(3) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPyHpPy 1139(3p) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPy-(3-Py 11403) 5' -W T A GT C W-3' Hp-~3-ImHpPy-y-ImPyPyHpPy 1140(3p) 5' -W T A GT C W-3' Hp-(3-ImHpPy-y-ImPyPy-(3-Py 1141(3) 5' -W T A GA T W-3' Hp-~3-ImPyHp-y-PyHpPyHpPy 1141(3p) 5' -W T A GA T W-3' Hp-(3-ImPyHp-y-PyHpPy-(3-Py 1142(3) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPyHpPy 1142~ip) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPy-(3-Py 11433) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPyHpPy 1143(3p) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPy-~3-Py 11443) 5' -W T A GA C W-3' Hp-(3-ImPyPy-y-ImHpPyHpPy 1144(3p) 5' -W T A GA C W-3' Hp-~-ImPyPy-y-ImHpPy-~3-Py 11453) 5' -W T A GG T W-3' Hp-~-ImImHp-y-PyPyPyHpPy 1145~3p) 5' -W T A GG T W-3' Hp-p-ImImHp-y-PyPyPy-(3-Py 1146(3) 5' -W T A GG A W-3' Hp-(3-ImImPy-y-HpPyPyHpPy 1146(3p) 5' -W T A GG A W-3' Hp-~-ImImPy-y-HpPyPy-(3-Py 1147(3) 5' -W T A GC T W-3' Hp-~3-ImPyHp-y-PyImPyHpPy 1147~ip) 5' -W T A GC T W-3' Hp-(3-ImPyHp-y-PyImPy-(3-Py 1148(3) 5' -W T A GC A W-3' ~ Hp-~i-ImPyPy-y-HpImPyHpPy 1148(3p) 5' -W T A GC A W-3' Hp-p-ImPyPy-y-HpImPy-~i-Py 11493) 5' -W T A GG G W-3' Hp-(3-ImImIm-y-PyPyPyHpPy 1149(3p) 5' -W T A GG G W-3' Hp-~i-ImImIm-y-PyPyPy-(3-Py 1150(3) 5' -W T A GG C W-3' Hp-(3-ImImPy-y-ImPyPyHpPy 1150(3p) 5' -W T A GG C W-3' Hp-~3-ImImPy-y-ImPyPy-~i-Py 1151(3) 5' -W T A GC G W-3' Hp-p-ImPyIm-y-PyImPyHpPy 1151~3p) 5' -W T A GC G W-3' Hp-(3-ImPyIm-y-PyImPy-~-Py (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTASNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1152(3) 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPyHpPy 1152(3p). 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPy-~3-Py 1153(3) 5' -WT A C T TW-3' HpPyPyHpHp-y-Py-(3-ImHpPy 1153(3p) 5' -WT A C T TW-3' HpPyPy-(3-Hp-y-Py-(3-ImHpPy 1154(3) 5' -WT A C T AW-3' HpPyPyHpPy-y-Hp-~3-ImHpPy 1154~ip) 5' -WT A C T AW-3' HpPyPy-p-py-y-Hp_p_I~ppy 11553) 5' -WT A C T GW-3' HpPy-(3-HpIm-y-Py-~3-ImHpPy 1156(3) 5' -WT A C T CW-3' HpPyPyHpPy-y-Im-(3-ImHpPy 1156(3p) 5' -WT A C T CW-3' HpPyPy-(3-Py-y-Im-~i-ImApPy 11573) 5' -WT A C A TW-3' HpPyPyPyHp-y-Py-(3-ImHpPy 1157(3p) 5' -WT A C A TW-3' HpPyPy-(3-Hp-y-Py-~3-ImHppy IS 1158~i) 5' -WT A C A AW-3' HpPyPyPyPy-y-Hp-(3-ImHpPy 1158(3p) 5' -WT A C A AW-3' HpPypy-(3-Py-y-Hp-/3-ImHpPy 1159(3) 5' -WT A C A GW-3' HpPy-(i-PyIm-y-Py-(3-ImHpPy 11603) 5' -WT A C A CW-3' HpPyPyPyPy-y-Im-(3-ImHpPy 1160(3p) 5' -WT A C A CW-3' HpPyPy-(3-Py-y-Im-(3-ImHpPy 1161) 5' -WT A C G TW-3' Hppy-~3-I~p_y-py-~_I~ppy 1162(3) 5' -WT A C G AW-3' HpPy-(3-ImPy-y-Hp-~-ImHpPy 1163(3) 5' -WT A C C TW-3' HpPyPyPyHp-y-PyImIm-(3-Py 1163(3p) 5' -WT A C C TW-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py 1164(3) 5' -WT A C C AW-3' HpPyPyPyPy-y-HpImIm-p-Py 1164(3p) 5' -WT A C C AW-3' Hp-~3-PyPyPy-y-HpImIm-(3-Py 1165~i) 5' -WT A C G GW-3' HpPy-(3-ImIm-y-Py-(3-ImHpPy 1166(3) 5' -WT A C G CW-3' HpPy-(3-ImPy-y-Im-~3-ImHpPy 1167(3) 5' -WT A C C GW-3' HpPy-(3-PyIm-y-PyImIm-(3-Py TABLE 82:
10-ring Hairpin Polyamides for recognition of ?-by 5'-WTCWNNW-3' with R
substitutions DNA sequence aromatic amino acid sequence 11703) 5'-W T CT T A W-3' HpPyHpHpPy-y-HpPy-p-ImPy S 1170(3p)' S'-W T CT T A W-3' HpPy-~3-HpPy-y-HpPy-(3-ImPy 1171~i) 5'-W T CT T G W-3' HpPy-(3-HpIm-y-PyPy-~i-ImPy 1I72~i) 5'-W T CT T C W-3' HpPyHpHpPy-y-ImPy-(3-ImPy 1172(3p) 5'-W T CT T C W-3' HpPy-(3-HpPy-y-ImPy-(3-ImPy 1173(3) 5'-W T CT A T W-3' HpPyHpPyHp-y-PyHp-(3-ImPy 1173(3p) 5'-W T CT A T W-3' HpPy-~3-PyHp-y-PyHp-(3-ImPy 1174(3) 5'-W T CT A A W-3' HpPyHpPyPy-y-HpHp-(3-ImPy 1I74(3p) 5'-W T CT A A W-3' HpPy-~3-PyPy-y-HpHp-(3-ImPy 1175(3) 5'-W T CT A G W-3' HpPy-(3-PyIm-y-PyHp-(3-ImPy 1176J3) 5'-W T CT A C W-3' HpPyHpPyPy-y-ImHp-p-ImPy 1176(3p) 5'-W T CT A C W-3' HpPy-(3-PyPy-y-ImHp-(3-ImPy 1177(3) 5'-W T CT G T W-3' HpPy-(3-ImHp-y-PyPy-(3-ImPy 1178(3) 5'-W T CT G A W-3' HpPy-[3-ImPy-y-HpPy-[3-ImPy 11793) 5'-W T CT G G W-3' HpPy-(3-Imlm-y-PyPy-(3-ImPy 1180(3) 5'-W T CT G C W-3' HpPy-(3-ImPy-y-ImPy-(3-ImPy 1181(3) 5'-W T CT C T W-3' HpPyHpPyHp-y-PyIm-p-ImBy 1181~3p) 5'-W T CT C T W-3' HpPy-(3-PyHp-y-PyIm-p-ImPy 1182(3) 5'-W T CT C A W-3' HpPyHpPyPy-y-HpIm-[3-ImPy 1182~3p) 5'-W T CT C A W-3' HpPy-(3-PyPy-y-HpIm-p-ImPy 1183(3) 5'-W T CT C G W-3' HpPy-p-Pylm-y-PyIm-(3-ImPy 1184(3) 5'-W T CT C C W-3' HpPyHpPyPy-y-Imlm-(3-ImPy 1184~3p) 5'-W T CT C C W-3' ~ HpPy-j3-PyPy-y-Imlm-(3-ImPy 1185(3) 5'-W T CA T T W-3' HpPyPyHpHp-y-PyPy-(3-ImPy 1185~3p) 5'-W T CA T T W-3' HpPy-(3-HpHp-y-PyPy-~3-ImPy 1186(3) 5'-W T CA T A W-3' HpPyPyHpPy-y-HpPy-p-ImPy 1186(3p) 5'-W T CA T A W-3' HpPy-(3-HpPy-y-HpPy-(3-ImPy 11873) 5'-W T CA T G W-3' HpPy-p-HpIm-y-PyPy-(3-ImPy TABLE 82 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCWNNW-3' with substitutions DNA sequence aromatic amino acid sequence 1188) 5'-WT C A T CW-3' HpPyPyHpPy-y-ImPy--ImPy 1188p)~ 5'-WT C A T CW-3' HpPy--HpPy-y-ImPy--Impy 1189) 5'-WT C A A TW-3' HpPyPyPyHp-y-PyHp--ImPy 1189p) 5'-WT C A A TW-3' HpPy--pyHp-y-pyHp--ImPy 1190(3) 5'-WT C A A AW-3' HpPyPyPyPy-y-HpHp--ImPy 1190p) 5'-WT C A A AW-3' HpPy--PyPy-y-HpHp--ImPy 1191) 5'-WT C A A GW-3' HpPy--pyIm-y-PyHp--ImPy 1192) 5'-WT C A A CW-3' HppypyPyPy-y-ImHp--ImPy 1192p) 5'-WT C A A CW-3' HpPy--pypy-y-ImHp--ImPy 1193(3) 5'-WT C A G TW-3' HpPy--ImHp-y-PyPy--ImPy 1194) 5'-WT C A G AW-3' HpPy--ImPy-y-HpPy--ImPy IS 11953) 5'-WT C A G GW-3' HpPy--Imlm-y-PyPy--ImPy 1196) 5'-WT C A G CW-3' HpPy--ImPy-y-ImPy--ImPy 1197(3) 5'-WT C A C TW-3' HpPyPyPyHp-y-PyIm--ImPy 1197p) 5'-WT C A C TW-3' HpPy--PyHp-y-Pylm--ImPy 1198) 5'-WT C A C AW-3' HpPyPyPyPy-y-HpIm--ImPy 1198p) 5'-WT C A C AW-3' HpPy--PyPy-y-Hplm--ImPy 1199) 5'-WT C A C GW-3' HpPy--PyIm-y-PyIm--ImPy 1200) 5'-WT C A C CW-3' HpPyPyPyPy-y-ImIm--ImPy 1200p) 5'-WT C A C CW-3' HpPy--pypy-y-ImIm--ImPy TABLE 83:
10-ring Hairpin Polyamides for recognition of 7-by S'-WTCSNNW-3' with ~i substitutions DNA aromatic amino acid sequence sequence 1201(3) 5' -W TC G T T W-3' Hp-(3-ImHpHp-y-PyPy-J3-ImPy 1202(3) 5''-W TC G T A W-3' Hp-(3-ImHpPy-y-HpPy-(3-ImPy 12033) 5' -W TC G T G W-3' Hp-~3-ImHpIm-y-PyPy-/3-ImPy 1204(3) 5' -W TC G T C W-3' Hp-(3-ImHpPy-y-ImPy-(3-ImPy 1205(3) 5' -W TC G A T W-3' Hp-(3-ImPyHp-y-PyHp-~i-ImPy 1206(3) 5' -W TC G A A W-3' Hp-(3-ImPyPy-y-HpHp-(3-ImPy 1207(3) 5' -W TC G A G W-3' Hp-(3-ImPyIm-y-PyHp-~3-ImPy 1208~i) 5' -W TC G A C W-3' Hp-(3-ImPyPy-y-ImHp-(3-ImPy 12093) 5' -W TC G G T W-3' Hp-(3-ImImHp-y-PyPy-(3-ImPy 1210(3) 5' -W TC G G A W-3' Hp-~3-ImImPy-y-HpPy-R-ImPy 1211(3) 5' -W TC G C T W-3' Hp-(3-ImPyHp-y-Pylm-p-ImPy 12123) 5' -W TC G C A W-3' Hp-~3-ImPyPy-y-Hplm-(3-ImPy 12133) 5' -W TC C T T W-3' HpPyPyHpHp-y-Py-p-ImImPy 1213(3p) 5' -W TC C T T W-3' HpPyPy-~i-Hp-y-Py-(3-ImImPy 12143) 5' -W TC C T A W-3' HpPyPyHpPy-y-Hp-~-ImImPy 1214(3p) 5' -W TC C T A W-3' HpPyPy-(3-Py-y-Hp-(3-ImImPy 12153) 5' -W TC C T G W-3' HpPy-(3-HpIm-y-Py-(3-ImImPy 1216(3) 5' -W TC C T C W-3' HpPyPyHpPy-y-Im-~3-ImImPy 1216(3p) 5' -W TC C T C W-3' HpPyPy-~3-Py-y-Im-~3-ImImPy 1217(3) 5' -W TC C A T W-3' HpPyPyPyHp-y-Py-~3-ImImPy 1217~3p) 5' -W TC C A T W-3' HpPyPy-(3-Hp-y-Py-p-ImImPy 1218(3) 5' -W TC C A A W-3' HpPyPyPyPy-y-Hp-[3-ImImPy 1218(3p) 5' -W TC C A A W-3' HpPyP-(3-Py-y-Hp-~-ImImPy 12193) 5' -W TC C A G W-3' HpPy-[3-PyIm-y-Py-(3-ImImPy 1220(3) 5' -W TC C A C W-3' HpPyPyPyPy-y-Im-R-ImImPy 1220~3p) 5' -W TC C A C W-3' HpPyPy-~i-Py-y-Im-~3-ImImPy 1221(3) 5' -W TC C G T W-3' HpPy-p-ImHp-y-Py-(3-ImImPy 1222(3) 5' -W TC C G A W-3' HpPy-~3-ImPy-y-Hp-(3-ImImPy 1225(3) 5' -W TC G G G W-3' Hp-(3-ImImIm-y-PyPy-(3-ImPy TABLE 83 (cont): 10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCSNNW-3' with (3 substitutions DNA sequence aromatic amino acid sequence 1226(3) 5' -W T C G G C W-3' Hp-~3-ImImPy-y-ImPy-(3-ImPy 12273) 5' -W T C G C G W-3' Hp-(3-ImPyIm-y-Pyim-(3-ImPy 12280 5' -W T C G C C W-3' Hp-(3-ImPyPy-y-Imlm-y-ImPy 1229(3) 5' -W T C C G G W-3' H p P Yrj-ImIm-y-Py-(3-ImImPy 1230~i) 5' -W T C C G C W-3' HpPy-(3-ImPy-y-Im-~i-ImImPy 1231(3) 5' -W T C C C G W-3' HpPy-(3-pyIm-y-PyImImImPy If the process described above of designing a preferred polyamide molecule comprising four or five carboxamide binding pairs does not produce a selective polyamide that binds to the target identified DNA sequence with subnanomolar affinity and with a selectivity over mismatch sequences of greater than a factor of ten, a polyamide molecule X1X2X3X4XSX6-Y-X7X8X9X1OX11X12 having six carboxamide binding pairs can be designed that is selective for an eight base pair identified target 5'-WNTI~JNNNW-3' sequence.
The design and synthesis of six binding pair polyamides is essentially the same as that of the 2o four and five binding pair polyamides described above.
The polyamide design process for six carboxamide binding pair polyamides is shown schematically in Figure 10 A and the upper half of l OB. The method for chosing the residues that can be replaced by a (3-alanine residue is shown schematically in the lower half of Figure 10 B and in Figure 11. The 1024 possible 12-ring hairpins which target the 1024 5'-GNNNNN-3' core sequences are listed in Tables 84-I 15. Each DNA sequence entry can be correlated to its corresponding polyamide recognition sequence using the process outlined in this figure. The 1024 possible I2-ring hairpins which target the 1024 5'-CNNNNN-3' core sequences are listed in Tables 116-147. Each DNA sequence entry can be correlated to its corresponding polyamide 3o recognition sequence using the process outlined in this figure.
Figure 11 shows a process for replacement of aromatic amino acid residues with aliphatic (3-aIanine 'spring' residues in order to enhance the DNA binding properties of 12-ring hairpin polyamides. Selective placement of an aliphatic (3-alanine (/3) residue paired side-by-side with either a pyrrole (Py) or imidazoIe (Im) aromatic amino acid or another (3-alanine residue is found to compensate for sequence composition effects for recognition of the minor groove of DNA by hairpin pyrrole-imidazole polyamides. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be tuned out by replacement of an aromatic amino acid with an aliphatic j3-alanine spring.
Rules have been determined to help determine the exact placement of the (3-spring residues.
For example, within the 12-ring template, it is only beneficial to place ~3-alanine within positions X2, X3, X4, XS, Xg, X9, and X10 X11,. No more than two (3-alanine residues may be placed within a single hairpin structure. No more than a single (3-residue may be placed within each individual to poiyamide subunit. Tables 148-1079 list derivatives of sequences (1233-2224) labeled (1223(3-2224[3) which contain two (3-alanine residues assigned according to the process outlined in Figure 11A & B.
WO 98/37067 , PCT/US98/01714 1 AtiLl; 12-ring 84: Hairpin Polyamides for recognition of 8-by 5'-WGGGWNNW-3' DNA aromatic amino acid sequence sequence 1233) 5'-W GG G T T T W-3' ImImImHpHpHp-y-PYPYPYPYPYpy 1234) 5'~-W GG G T T A W-3' ImImImHpHpPy-y-HpPyPYPyPyPy 1235) 5'-W GG G T T G W-3' ImImImHpHpIm-y-Pypypypypypy 1236) 5'-W GG G T T C W-3' ImTmImHpHppy-y-ImpyPYPypypy 1237) 5'-W GG G T A T W-3' ImImImHpPYHp-y-PyHpPyPyPyPy 1238) 5' GG G T A A W-3' ImImImHpPyPy-y-HpHpPyPYPYPy -W
1239) 5'-W GG G T A G W-3' ImImImHpPyIm-y-PyHpPYpypypY
1240) 5'-W GG G T A C W-3' ImImImHpPyPy-y-ImHpPYPYPYPy 1241) 5'-W GG G T G T W-3' ImImImHpImHp-y-pypypypypypy 1242} 5'-W GG G T G A W-3' ImImImHpImPy-y-HpPyPyPyPyPy 1243) 5'-W GG G T G G W-3' ImImImHpImIm-y-PyPYPyPyPYPy 1244) 5' GG G T G C W-3' ImImImHpImPy-y-ImPyPYPyPyPy -W
1245) 5' GG G T C T W-3' ImImImHpPyHp-y-PyImPyPyPyPy -W
1246) 5'-W GG G T C A W-3' ImImImHpPYPy-y-HpImPYPYPYPy 1247) 5'-W GG G T C G W-3' ImImImHpPyIm-y-pyImPyPyPYPy 1248) 5'-W GG G T C C W-3' ImImImHpPYPy-y-ImImPyPYPyPy 1249) 5'-W GG G A T T W-3' ImImImPyHpHp-y-PYPyHpPyPyPy 1250) 5'-W GG G A T A W-3' ImImImPyHpPy-y-HpPyHpPyPyPy 1251) 5'-W GG G A T G W-3' TmImImPyHpIm-y-PypyHpPyPyPy 1252) 5'-W GG G A T C W-3' ImImImPyHpPy-y-ImPyHpPyPyPy 1253) 5'-W GG G A A T W-3' ImImImPyPyHp-y-PyHpHpPYPyPy 1254) 5'-W GG G A A A W-3' ImImImPyPyPy-y-HpHpHppyPyPy 1255) 5'-W GG G A A G W-3' ImImImPyPyIm-y-PyHpHpPYPyPy 1256) 5'-W GG G A A C W-3' ImImImPyPYPy-y-ImHpHpPYPyPy 1257) 5'-W GG G A G T W-3' ImImImPyImHp-y-PyPyHpPyPYPy 1258) 5'-W GG G A G A W-3' ImImImPyImPy-y-HpPyHpPyPyPy 1259) 5'-W GG G A G G W-3' ImImImPyImIm-y-P
P
H
P
P
p y y p y y y 12 60 5' GG G A G C W-3 ImImImPyImPy-y- ImPYHpPyPyPy ) -W ' 1261) 5'-W GG G A C T W-3' ImImImPyPyHp-y-PyImHpPYPYPY
1262) 5'-W GG G A C A W-3' ImImImPyPypy-y-HpImHpPyPyPy 1263) 5'-W GG G A C G W-3' ImImImPyPyIm-y-PyImHpPypypy 1264) 5'-W GG G A C C W-3' ImImImPyPYPy-y-ImImHpPyPYPy TABLE
85:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGGSNNW-3' ' DNA aromatic amino acid sequence sequence 1265) 5' -W GG G G T T W-3' ImImImImHpHp-y-PyPyPyPyPyPy 1266) 5' -W GG G G T A W-3' ImImImImHpPy-y-HpPyPyPyPyPy S 1267) 5'~-W GG G G T G W-3' ImImImImHpIm-y-PyPyPyPyPyPy 1268} 5' -W GG G G T C W-3' ImImImImHpPy-y-ImPyPyPyPyPy 1269) 5' -W GG G G A T W-3' ImImImImPyHp-y-PyHpPyPyPyPy 1270) 5' -W GG G G A A W-3' ImImImImPyPy-y-HpHpPyPyPyPy 1271) 5' -W GG G G A G W-3' ImImImImPyIm-y-PyHpPyPyPyPy 1272) 5' -W GG G G A C W-3' ImImImImPyPy-y-ImHpPypyPyPy 1273} 5' -W GG G G G T W-3' ImImImImImHp-y-PyPypypypypy 1274) 5' -W GG G G G A W-3' ImImImImImPy-y-HpPyPyPyPyPy 1275) 5' -W GG G G C T W-3' ImImImImPyHp-y-PyImPyPyPyPy 1276) 5' -W GG G G C A W-3' ImImImImPyPy-y-HpImPyPyPyPy 1277) 5' -W GG G C T T W-3' ImImImPyHpHp-y-PyPyImPyPyPy 1278} 5' -W GG G C T A W-3' ImImImPyHpPy-y-HpPyImPyPyPy 1279) 5' -W GG G C T G W-3' ImImImPyHpIm-y-PyPyImPyPyPy 1280) 5' -W GG G C T C W-3' ImImImPyHpPy-y-ImPyImPyPyPy 1281) 5' -W GG G C A T W-3' ImImImPypyHp-y-PyHpImPyPyPy 1282) 5' -W GG G C A A W-3' ImImImPyPyPy-y-HpHpImPyPyPy 1283) 5' -W GG G C A G W-3' ImImImPyPyIm-y-PyHpImPyPyPy 1284) 5' -W GG G C A C W-3' ImImImPyPyPy-y-ImHpImPyPyPy 1285) 5' -W GG G C G T W-3' ImImImPyImHp-y-PyPyImPyPyPy 12 86 5' -W GG G C G A W-3 ImImImPyImPy-y-HpPyImPyPyPy ) ' 1287) 5' -W GG G C C T W-3' ImImImPyPyHp-y-PyImImPyPyPy 1288) 5' -W GG G C C A W-3' ImImImPyPyPy-y-HpImImPyPyPy G4 9 5' -W GG G G G G W-3 ImImImImImIm-y-PyPyPyPyPyPy ) ' G50) 5' -W GG G G G C W-3' ImImImImImPy-y-ImPyPyPyPyPy G51) 5' -W GG G G C G W-3' ImImImImPyIm-y-PyImPyPyPyPy G52) 5' -W GG G G C C W-3' ImImImImPyPy-y-ImImPyPyPyPy G53) 5' -W GG G C G G W-3' ImImImPyImIm-y-PyPyImPyPyPy G54 ) 5' -W GG G C G C W-3 ImImImPyImPy-y-ImPyImPyPyPy ' G55) 5' -W GG G C C G W-3' ImImImPyPyIm-y-PyImImPyPyPy G56) 5' -W GG G C C C W-3' ImImImPypyPy-y-ImImImPyPyPy TABLE
86:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGTWNNW-3' DNA aromatic amino acid sequence sequence 1289) 5' -WG G T T TT W-3' ImImHpHpHpHp-y-PyPyPyPyPypy 1290) 5' '-WG G T T TA W-3' ImImHpHpHpPy-y-HpPyPyPyPyPy 1291) 5' -WG G T T TG W-3' ImImHpHpHpIm-y-PyPyPyPyPyPy 1292) 5' -WG G T T TC W-3' ImImHpApHpPy-y-ImPyPyPyPyPy 1293) 5' -WG G T T AT W-3' ImImHpHpPyHp-y-PyHpPyPyPyPy 12 94 5' -WG G T T AA W-3 ImImHpHpPyPy-y-HpHpPyPyPyPy ) ' 1295) 5' -WG G T T AG W-3' ImImHpHpPyIm-y-PyHpPyPyPyPy 1296) 5' -WG G T T AC W-3' ImImHpHpPyPy-y-ImHppyPyPyPy 1297) 5' -WG G T T GT W-3' ImImHpHpImHp-y-PyPyPyPyPyPy 1298) 5' -WG G T T GA W-3' ImImHpHpImPy-y-HpPypyPyPyPy 1299) 5' -WG G T T GG W-3' ImImHpHpImIm-y-PyPyPyPypypy 1300) 5' -WG G T T GC W-3' ImImHpHpImPy-y-ImpyPyPyPypy 1301) 5' -WG G T T CT W-3' ImImHpHpPyHp-y-PyImPyPyPyPy 1302) 5' -WG G T T CA W-3' ImImHpHpPyPy-y-HpImPyPyPyPy 1303) 5' -WG G T T CG W-3' ImImHpHppylm-y-PyImPyPyPyPy 1304) 5' -WG G T T CC W-3' ImImHpHpPyPy-y-ImImPypyPyPy 1305) 5' -WG G T A TT W-3' ImImHpPyHpHp-y-PyPyHpPyPyPy 1306) 5' -WG G T A TA W-3' ImImHpPyHpPy-y-HpPyHpPyPyPy 1307) 5' -WG G T A TG W-3' ImImHpPyHpIm-y-PyPyHpPyPyPy 1308) 5' -WG G T A TC W-3' ImImHpPyHpPy-y-ImPyHpPyPyPy 1309) 5' -WG G T A AT W-3' ImImHpPyPyHp-y-PyHpHpPyPyPy 1310 5' -WG G T A AA W-3 ImImHpPyPyPy-y-HpHpHpPyPyPy ) ' 1311) 5' -WG G T A AG W-3' ImImHpPyPyIm-y-PyHpHpPyPyPy 1312) 5' -WG G T A AC W-3' ImImHpPyPyPy-y-ImHpHpPyPyPy 1313) 5' -WG G T A GT W-3' ImImHpPyImHp-y-PyPyHpPyPyPy a 1314) 5' -WG G T A GA W-3' ImImHpPyImPy-y-HpPyHpPyPyPy 1315) 5' -WG G T A GG W-3' ImImHpPyImIm-y-PyPyHpPyPyPy 1316) 5' -WG G T A GC W-3' ImImHpPyImPy-y-ImPyHpPyPyPy 1317) 5' -WG G T A CT W-3' ImImHpPyPyHp-y-pyImHpPyPyPy 1318) 5' -WG G T A CA W-3' ImImHpPyPyPy-y-HpImHppyPyPy 1319) 5' -WG G T A CG W-3' ImImHpPyPyIm-y-PyImHpPyPyPy 1320) 5' -WG G T A CC W-3' ImImHpPyPyPy-y-ImImHpPyPyPy TABLE
87:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGTSNNW-3' DNA aromatic amino acid sequence sequence 1321) 5' -W G GT G T T W-3' ImImHpImHpHp-y-PyPyPyPyPyPy 1322) 5' -W G GT G T A W-3' ImImHpImHpPy-y_Hppypypypypy 1323) 5' -W G GT G T G W-3' ImImHpImHpIm-y-PyPyPyPyPyPy 1324) 5' -W G GT G T C W-3' ImImHpImHpPy-y-ImPyPyPyPyPy 1325) 5' -W G GT G A T W-3' ImImHpImPyHp-y-PyHpPyPyPyPy 1326) 5' -W G GT G A A W-3' ImImHpImPyPy-y-HpHpPyPyPyPy 1327) 5' -W G GT G A G W-3' ImImHpImPyIm-y-PyHpPyPyPyPy 1328) 5' -W G GT G A C W-3' ImImHpImPyPy-y-ImHpPyPyPyPy 1329) 5' -W G GT G G T W-3' ImImHpImImHp-y-PyPyPyPyPyPy 1330) 5' -W G GT G G A W-3' ImImHpImImPy-y-HpPyPyPyPyPy 1331) 5' -W G GT G C T W-3' ImImHpImPyHp-y-PyImPyPyPyPy 1332) 5' -W G GT G C A W-3' ImImHpImPyPy-y-HpImPyPyPyPy 1333) 5' -W G GT G G G W-3' ImImApImImIm-y-PyPyPyPyPyPy 1334) 5' -W G GT G G C W-3' ImImHpImImPy-y-ImPyPyPyPyPy 1335) 5' -W G GT G C G W-3' ImImHpImPyIm-y-PyImPyPyPyPy 1336) 5' -W G GT G C C W-3' ImImHpImPyPy-y-ImImPyPyPyPy 1337) 5' -W G GT C T T W-3' ImImHpPyHpHp-y-PyPyImPyPyPy 1338) 5' -W G GT C T A W-3' ImImHpPyHpPy-y-HpPyImPyPyPy 1339) 5' -W G GT C T G W-3' ImImHpPyHpIm-y-PyPyImPyPyPy 1340) 5' -W G GT C T C W-3' ImImHpPyHpPy-y-ImPyImPyPyPy 1341) 5' -W G GT C A T W-3' ImImHpPyPyHp-y-PyHpImPyPyPy 1342) 5' -W G GT C A A W-3' ImImHpPyPyPy-y-HpHpImPyPypy 1343) 5' -W G GT C A G W-3' ImImHpPyPyIm-y-PyHpImPyPyPy 1344) 5' -W G GT C A C W-3' ImImHpPyPyPy-y-ImHpImPyPyPy 1345) 5' -W G GT C G T W-3' ImImHpPyImHp-y-PyPyImPyPyPy 1346) 5' -W G GT C G A W-3' ImImHpPyImPy-y-HpPyImPyPyPy 1347) 5' -W G GT C C T W-3' ImImHpPyPyHp-y-PyImImPyPyPy 1348) 5' -W G GT C C A W-3' ImImHpPyPyPy-y-HpImImPyPyPy 1349) 5' -W G GT C G G W-3' ImImHpPyImIm-y-PyPyimPyPyPy 1350) 5' -W G GT C G C W-3' ImImHpPyImPy-y-ImPyImPyPyPy 1351) 5' -W G GT C C G W-3' ImImHpPyPyIm-y-PyImImpyPyPy 1352) 5' -W G GT C C C W-3' ImImHpPyPyPy-y-ImImImPyPyPy lAt3Ll;
~i8:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGAWNNW-3' DNA aromatic amino acid sequence sequence 1353) 5'-W G G A T TT W-3' ImImPyHpHpHp-y-PyPyPyHpPyPy 1354) 5' G G A T TA W-3' ImImPyHpHpPy-y-HpPyPyHpPyPy -W
1355) 5' G G A T TG W-3' ImImPyHpHpIm-y-PyPyPyHpPyPy -W
1356) 5' G G A T TC W-3' ImImPyHpHpPy-y-ImPyPyHpPyPy -W
1357 5' G G A T AT W-3 ImImPyHpPyHp-y-PyHpPyHpPyPy ) -W ' 1358) 5' G G A T AA W-3' ImImPyHpPyPy-y-HpHpPyHppyPy -W
1359) 5' G G A T AG W-3' ImImPyHpPyIm-y-PyHpPyHpPyPy -W
1360) 5'-W G G A T AC W-3' ImImPyHpPyPy-y-ImHpPyHpPyPy 1361) 5' G G A T GT W-3' ImImPyHpImHp-y-pypypyHpPyPy -W
1362) 5' G G A T GA W-3' ImImPyHpImPy-y-HpPyPyHpPyPy -W
1363) 5'-W G G A T GG W-3' ImImPyHpImIm-y-PyPyPyHpPyPy IS 1364) 5'-W G G A T GC W-3' ImImPyHpImPy-y-ImPyPyHpPyPy 1365) 5' G G A T CT W-3' ImImPyHpPyHp-y-PyImPyHpPyPy -W
1366) 5' G G A T CA W-3' ImImPyHpPyPy-y-HpImPyHpPyPy -W
1367) 5'-W G G A T CG W-3' imImPyHpPyIm-y-PyImPyHpPyPy 1368) 5'-W G G A T CC W-3' ImImPyHpPyPy-y-ImImPyHpPyPy 1369) 5' G G A A TT W-3' ImImPyPyHpHp-y-PyPyHpHpPyPy -W
1370) 5'-W G G A A TA W-3' ImImPyPyHpPy-y-HpPyHpHpPyPy 1371) 5' G G A A TG W-3' ImImPyPyHpIm-y-PyPyHpHpPyPy -W
1372) 5' G G A A TC W-3' ImImPyPyHpPy-y-ImPyHpHpPyPy -W
1373) 5'-W G G A A AT W-3' ImImPyPyPyHp-y-PyHpHpHpPyPy 1374) 5'-W G G A A AA W-3' ImImPyPypypy-y-HpHpHpHpPyPy 1375) 5' G G A A AG W-3' ImImPyPypyIm-y-PyHpHpHpPyPy -W
1376) 5' G G A A AC W-3' ImImPyPyPyPy-y-ImHpHpHpPyPy -W
1377) 5'-W G G A A GT W-3' ImImPyPyImHp-y-PyPyHpHpPyPy 1378) 5' G G A A GA W-3' ImImPyPyImPy-y-HpPyHpHpPyPy -W
1379) 5' G G A A GG W-3' ImImPyPyImIm-y-PyPyHpHpPyPy -W
13 8 5' G G A A GC W- 3 ImImPyPyImPy-y- ImPyHpHpPyPy 0 ) -W ' 1381) 5' G G A A CT W-3' ImImPyPyPyHp-y-PyImApHpPyPy -W
1382) 5' G G A A CA W-3' ImImPypypypy-y_HpI~pHppyPy -W
1383} 5' G G A A CG W-3' ImImPyPyPyIm-y-PyImHpHpPyPy -W
1384) 5'-W G G A A CC W-3' ImImPyPyPyPy-y-ImImHpHpPyPy TABLE
89:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGASNNW-3' DNA aromatic amino acid sequence sequence 1385} 5' -WG G A G TT W-3' ImImPyImHpHp-y-PyPypyHpPyPy 1386) 5' -WG G A G TA W-3' ImImPyImHpPy-y-HpPyPyHpPyPy 1387} 5' -WG G A G TG W-3' ImImPyImHpIm-y-PyPyPyHpPyPy 1388) 5' -WG G A G TC W-3' ImImPyImHpPy-y-ImPyPyHpPyPy 1389) 5' -WG G A G AT W-3' Im3mPyImPyHp-y-PyHpPyHpPyPy 1390} 5' -WG G A G AA W-3' ImImPyImPyPy-y-HpHpPyHpPyPy 1391) 5' -WG G A G AG W-3' ImImPyImPyIm-y-PyHpPyHpPyPy 1392) 5' -WG G A G AC W-3' ImImPyImPyPy-y-ImHpPyHpPyPy 1393) 5' -WG G A G GT W-3' ImImPyImImHp-y-PyPyPyHpPyPy 13 94 5' -WG G A G GA W-3 ' ImImPyImImPy-y-HpPyPyHppyPy ) 1395) 5' -WG G A G CT w-3' ImImPyImPyHp-y-PyImPyHpPyPy 1396) 5' -WG G A G CA W-3' ImImPyImPyPy-y-HpImPyHpPyPy 1397) 5' -WG G A G GG W-3' ImImPyImImIm-y-PyPyPyHppyPy 13 9 5' -WG G A G GC W-3 ' ImImPyImImPy-y- ImPyPyHpPyPy 8 ) 1399) 5' -WG G A G CG W-3' ImImPyImPyIm-y-PyImPyHpPyPy 1400) 5' -WG G A G CC W-3' ImImPyImPyPy-y-ImImPyHpPyPy 1401) 5' -WG G A C TT W-3' ImImPyPyHpHp-y-PyPyImHpPyPy 1402) 5' -WG G A C TA W-3' ImImPyPyHpPy-y-HpPyImHpPyPy 1403 5' -WG G A C TG W-3' ImImPyPyHpIm-y-PyPyImHpPyPy ) 1404) 5' -WG G A C TC W-3' ImImPyPyHpPy-y-ImPyImHpPyPy 1405) 5' -WG G A C AT W-3' ImImPyPyPyHp-y-PyHpImHpPyPy 1406) 5' -WG G A C AA W-3' ImImPyPyPyPy-y-HpHpImHpPyPy 1407) 5' -WG G A C AG W-3' ImImPyPyPyIm-y-PyHpImHpPyPy 1408} 5' -WG G A C AC W-3' ImImPyPyPyPy-y-ImHpImHpPyPy 1409} 5' -WG G A C GT W-3' ImImPyPyImHp-y-PypyImHpPyPy 1410 5' -WG G A C GA W-3 ' ImImPyPyImPy-y-HpPyImHpPyPy ) 1411) 5' -WG G A C CT W-3' ImImPyPyPyHp-y-PyImImHpPyPy 1412 5' -WG G A C CA W- 3 ImImPyPyPyPy-y-HpImImHpPypy ) ' 1413) 5' -WG G A C GG W-3' ImImPyPyImIm-y-PyPyImHpPyPy 1414) 5' -WG G A C GC W-3' ImImPyPyImPy-y-ImPyImHpPypy 1415) 5' -WG G A C CG W-3' ImImPyPyPyIm-y-PyImImHpPyPy 1416) 5' -WG G A C CC W-3' ImImPyPyPyPy-y-ImImImFippyPy TABLE
90:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGCWNNW-3' DNA aromatic amino acid sequence sequence 1417) 5' -W GG C T T T W-3' ImImPyHpHpHp-y-PyPyPyImPyPy 1418 5' -W GG C T T A W-3 ImImPyHpHpPy-y-HpPyPyImPyPy ) ' 1419) 5' -W GG C T T G W-3' ImImPyHpHpIm-y-PyPyPyImPyPy 1420) 5' -W GG C T T C W-3' ImImPyHpHpPy-y-ImPyPyImPyPy 1421) 5' -W GG C T A T W-3' ImImPyHpPyHp-y-PyHpPyImPyPy 1422) 5' -W GG C T A A W-3' ImImPyHpPyPy-y-HpHpPyImPyPy 1423) 5' -W GG C T A G W-3' ImImPyHpPyIm-y-PyHpPyImPyPy 1424) 5' -W GG C T A C W-3' ImImPyHpPyPy-y-ImHpPyImPyPy 1425) 5' -W GG C T G T W-3' ImImPyHpImHp-y-PyPyPyImPyPy 1426) 5' -W GG C T G A W-3' ImImPyHpImPy-y-HpPyPyImPyPy 1427) 5' -W GG C T G G W-3' ImImPyHpImIm-y-PyPyPyImPyPy 1428) 5' -W GG C T G C W-3' ImImPyHpImPy-y-ImPyPyImPyPy 1429) 5' -W GG C T C T W-3' ImImPyHpPyHp-y-PyImPyImPyPy 1430) 5' -W GG C T C A W-3' ImImPyHpPyPy-y-HpImPyImPyPy 143I) 5' -W GG C T C G W-3' ImImPyHpPyIm-y-PyImPyImPyPy 1432) 5' -W GG C T C C W-3' ImImPyHpPyPy-y-ImImPyImPyPy 1433) 5' -W GG C A T T W-3' ImImPyPyHpHp-y-PyPyHpImPyPy 1434) 5' -W GG C A T A W-3' ImImPyPyHpPy-y-HpPyHpImPyPy 1435) 5' -W GG C A T G W-3' ImImPyPyHpIm-y-PyPyHpImPyPy 1436) 5' -W GG C A T C W-3' ImImPyPyHpPy-y-ImPyHpImPyPy 1437) 5' -W GG C A A T W-3' ImImpyPyPyHp-y-PyHpHpImPyPy 1438) 5' -W GG C A A A W-3' ImImPyPyPyPy-y-HpHpHpImPyPy 1439) 5' -W GG C A A G W-3' ImImPyPyPyIm-y-PyHpHpImPyPy 1440) 5' -W GG C A A C W-3' ImImPyPyPyPy-y-ImHpHpImPyPy 1441) 5' -W GG C A G T W-3' ImImPyPyImHp-y-PyPyHpImPyPy 1442) 5' -W GG C A G A W-3' ImImPyPyImPy-y-HpPyHpImPyPy 1443) 5' -W GG C A G G W-3' ImImPyPyImIm-y-PyPyHpImPyPy 1444) 5' -W GG C A G C W-3' ImImPyPyimPy-y -ImPyHpImPyPy 1445) 5' -W GG C A C T W-3' ImImPyPyPyHp-y-PyImHpImPyPy 1446) 5' -W GG C A C A W-3' ImImPyPyPyPy-y-HpImHpImPyPy 1447) 5' -W GG C A C G W-3' ImImPyPyPyIm-y-PyImHpImPyPy 1448) 5' -W GG C A C C W-3' ImImPyPyPyPy-y-ImImHpImPyPy TABLE
91:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGCSNNW-3' DNA aromatic amino acid sequence sequence 1449) 5' GG C G T T W-3' ImImPyImHpHp-y-PyPyPyImPyPy -W
1450) 5' GG C G T A W-3' ImImPyImHpPy-y-HpPyPyImPyPy -W
1451) 5' GG C G T G W-3' ImImPyImHpIm-y-PyPyPyImPyPy -W
1452) 5' GG C G T C W-3' ImImPyImHpPy-y-ImPyPyImPyPy -W
1453) 5' GG C G A T W-3' ImImPyImPyHp-y-PyHpPyImPyPy -W
1454) 5'-W GG C G A A W-3' ImImPyImPyPy-y-HpHpPyImPyPy 1455) 5' GG C G A G W-3' ImImPyImPyIm-y-PyHpPyImPyPy -W
1456) 5' GG C G A C W-3' ImImPyImPyPy-y-ImHpPyImPyPy -W
1457) 5'-W GG C G G T W-3' ImImPyImImHp-y-PyPyPyImPyPy 1458) 5' GG C G G A W-3' ImImPyImImPy-y-HpPyPyImPyPy -W
1459) 5' GG C G C T W-3' ImImPyImPyHp-y-PyImPyImPyPy -W
1460) 5' GG C G C A W-3' ImImPyImPyPy-y-HpImPyImPyPy -W
1461) 5' GG C C T T W-3' ImImPyPyHpHp-y-PyPyImImPyPy -W
1462) 5' GG C C T A W-3' ImImPyPyHpPy-y-HpPyImImPyPy -W
1463 5' GG C C T G W-3' ImImPyPyHpIm-y-PyPyImImPyPy ) -W
1464) 5' GG C C T C W-3' ImImPyPyHpPy-y-ImPyImImPyPy -W
1465) 5' GG C C A T W-3' ImImPyPyPyHp-y-PyHpImImPyPy -W
1466) 5' GG C C A A W-3' ImImPyPyPyPy-y-HpHpImImPyPy -W
1467) 5'-W GG C C A G W-3' ImImPyPyPyIm-y-PyHpImImPyPy 1468) 5' GG C C A C W-3' ImImPyPyPyPy-y-ImHpImImPyPy -W
1469) 5' GG C C G T W-3' ImImPyPyImHp-y-PyPyImImPyPy -W
1470) 5' GG C C G A W-3' ImImPyPyImPy-y-HpPyImImPyPy -W
1471) 5' GG C C C T W-3' ImImPyPyPyHp-y-PyImImImPyPy -W
1472) 5' GG C C C A W-3' ImImPyPyPyPy-y-HpImImImPyPy -W
G57) 5' GG C G G G W-3' ImImPyImImIm-y-PyPyPyImPyPy -W
G58) 5' GG C G G C W-3' ImImPyImImPy-y-ImPyPyImPyPy -W
G59) 5' GG C G C G W-3' ImImPyImPyIm-y-PyImPyImPyPy -W
G60) 5' GG C G C C W-3' ImImPyImPyPy-y-ImImPyImPyPy -W
G61) 5' GG C C G G W-3' ImImPyPyImIm-y-PyPyImImPyPy -W
G62) 5' GG C C G C W-3' ImImPyPyImPy-y-ImPyImImPyPy -W
G63) 5' GG C C C G W-3' ImImPyPyPyIm-y-PyImImImPyPy -W
G64) 5' GG C C C C W-3' ImImPyPyPyPy-y-ImImImImPyPy -W
WO 98!37067 PCT/US98/01714 TABLE
92:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCGWNNW-3' DNA aromatic amino acid sequence sequence 1473) 5' -W G C GT T T W-3' ImPyImHpHpHp-y-PyPyPyPyImPy .
1474) 5' -W G C GT T A W-3' ImPyImHpHpPy-y-HppypyPyImPy 1475) 5' -W G C GT T G W-3' ImPyImHpHpIm-y-PyPypypylmpy 1476) 5' -W G C GT T C W-3' ImPyImHpHpPy-y-ImPyPyPyImPy 1477) 5' -W G C GT A T W-3' ImPyImHpPyHp-y-PyHpPyPyImPy 1478) 5' -W G C GT A A W-3' ImPyImHpPyPy-y-HpHpPyPyImPy 1479) 5' -W G C GT A G W-3' ImPyImHpPyIm-y-PyHpPyPyImPy 1480) 5' -W G C GT A C W-3' ImPyImHpPyPy-y-ImHpPyPyImPy 1481} 5' -W G C GT G T W-3' ImPyImHpImHp-y-PyPyPypyImPy 1482) 5' -W G C GT G A W-3' ImPyImHpImPy-y-HpPyPypyImPy 1483) 5' -W G C GT G G W-3' ImPyImHpImIm-y-PypyPyPyImPy 1484) 5' -W G C GT G C W-3' ImPyImfipImPy-y-ImPyPyPyImPy 1485) 5' -W G C GT C T W-3' ImPyImHpPyHp-y-PyImPyPyImPy 1486 5' -W G C GT C A W-3' ImpyImHpPyPy-y-HpImPyPyImPy ) 1487) 5' -W G C GT C G W-3' ImPyImHpPyIm-y-PyImpyPyImPy 1488) 5' -W G C GT C C W-3' ImPyImHpPyPy-y-ImimPyPyImPy 1489) 5' -W G C GA T T W-3' ImPyImPyHpHp-y-PyPyHpPyImPy 1490) 5' -W G C GA T A W-3' ImPyImPyHpPy-y-HpPyHpPyImPy 1491) 5' -W G C GA T G W-3' ImPyImPyHpIm-y-PyPyHpPyImPy 1492) 5' -W G C GA T C W-3' ImPyImPyHpPy-y-ImPyHpPyImPy 1493) 5' -W G C GA A T W-3' ImPyImPyPyHp-y-pyHpHpPyImPy 1494) 5' -W G C GA A A W-3' ImPyImPyPypy-y-HpHpHpPyImPy 1495) 5' -W G C GA A G W-3' ImPyImpypylm-y-PyHpHpPyImPy 1496) 5' -W G C GA A C W-3' ImPyImPyPyPy-y-ImHpHppyImPy 1497) 5' -W G C GA G T W-3' ImpyImPyImHp-y-PypyHpPyImPy 1498) 5' -W G C GA G A W-3' ImPyImPyImpy-y-HpPyHpPyImPy 1499) 5' -W G C GA G G W-3' ImPyImPyImIm-y-PyPyHpPyImPy 1490) 5' -W G C GA G C W-3' ImPyImPyImpy-y-ImPyHpPyImPy 1501) 5' -W G C GA C T w-3' ImPyImPyPyHp-y-PyImHpPyImPy 1502) 5' -W G C GA C A W-3' ImPyImPyPyPy-y-HpImHpPyImPy _ 1503) 5' -W G C GA C G W-3' ImPyImPyPyIm-y-PyImHpPyImPy 1504) 5' -W G C GA C C W-3' ImPyImPyPyPy-y-ImImHpPyImPy TABLE
93:
I2-ring Hairpin Polyamides for recognition of 8-by 5'-WGCGSNNW-3' DNA aromatic amino acid sequence sequence 1505) 5' -WG C G G T T W-3' ImPyImImHpHp-y-PyPyPyPyImPy 1506) 5' -WG C G G T A W-3' ImPyImImHpPy-y-HpPyPyPyImPy 1507) 5' -WG C G G T G W-3' ImPyImImHpIm-y-PyPyPyPyImPy 1508) 5' -WG C G G T C W-3' ImPyImImHpPy-y-ImPyPyPyImPy 1509) 5' -WG C G G A T W-3' ImPyImImPyHp-y-PyHpPyPyImPy 1510) 5' -WG C G G A A W-3' ImPyImImPyPy-y-HpHpPyPyImPy 1511) 5' -WG C G G A G W-3' ImPyImImPyIm-y-PyHpPyPyImPy 1512) 5' -WG C G G A C W-3' ImPyImImPyPy-y-ImHpPyPyImPy 1513) 5' -WG C G G G T W-3' ImPyImImImHp-y-PyPyPyPyImPy 1514 5' -WG C G G G A W-3 ImPyImImImPy-y-HpPyPyPyImPy ) ' 1515) 5' -WG C G G C T W-3' ImPyImImPyHp-y-PyImPyPyImPy IS 1516) 5' -WG C G G C A W-3' ImPyImImPyPy-y-HpImPyPyImPy 1517) 5' -WG C G C T T W-3' ImPyImPyHpHp-y-PyPyImPyImPy 1518) 5' -WG C G C T A W-3' ImPyImPyHpPy-y-HpPyImPyImPy 1519) 5' -WG C G C T G W-3' ImPyImPyHpIm-y-PyPyImPyImPy 1520) 5' -WG C G C T C W-3' ImPyImPyHpPy-y-ImPyImPyImPy 1521) 5' -WG C G C A T W-3' ImPyImPyPyHp-y-PyHpImPyImPy 1522) 5' -WG C G C A A W-3' ImPyImPyPyPy-y-HpHpImPyImPy 1523) 5' -WG C G C A G W-3' ImPyImPyPyIm-y-PyHpImPyImPy 1524) 5' -WG C G C A C W-3' ImPyImPyPyPy-y-ImHpImPyImPy 1525) 5' -WG C G C G T W-3' ImPyImPyImHp-y-PyPyImPyImPy 1526) 5' -WG C G C G A W-3' ImPyImPyImPy-y-HpPyImPyImPy 1527) 5' -WG C G C C T W-3' ImPyImPyPyHp-y-PyImImPyImPy 1528) 5' -WG C G C C A W-3' ImPyImPyPyPy-y-HpImImPyImPy G65) 5' -WG C G G G G W-3' ImPyImImIrnIm-y-PyPyPyPyImPy G66) 5' -WG C G G G C W-3' ImPyImImImPy-y-ImPyPyPyImPy G67 ) 5' -WG C G G C G W-3 ImPyImImPyIm-y-PyImPyPyImPy ' G68) 5' -WG C G G C C W-3' ImPyImImPyPy-y-ImImPyPyImPy G69) 5' -WG C G C G G W-3' ImPyimPyImIm-y-PyPyImPyImPy G70) 5' -WG C G C G C W-3' ImPyImPyImPy-y-ImPyImPyImPy G71) 5' -WG C G C C G W-3' ImPyImPyPyIm-y-PyImImPyImPy G72) 5' -WG C G C C C W-3' ImPyImPyPyPy-y-ImImImPyImPy WO 98137067 , PCT/US98/01714 1A13L1;
94:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCTWNNW-3' DNA aromatic amino acid sequence sequence 1529) 5'-W G C TT T T W-3' ImPyHpHpHpHp-y-PypypypylmPy 1530) 5''-W G C TT T A W-3' ImPyHpHpHpPy-y-HppyPyPyImPy 1531) 5' G C TT T G W-3' ImPyHpHpHpIm-y-PypypypylmPy -W
1532) 5' G C TT T C W-3' ImPyHpHpHpPy-y-ImPyPyPyImPy -W
1533 5' G C TT A T W-3 ImPyHpHpPyHp-y-PyHpPyPyImPy ) -W ' 1534) 5'-W G C TT A A W-3' ImpyHpHpPyPy-y-HpHpPyPyImPy 1535) 5' G C TT A G W-3' ImPyHpHpPyIm-y-PyHpPyPyImPy -W
1536) 5'-W G C TT A C W-3' ImPyHpHpPyPy-y-ImHpPyPyImPy 1537) 5'-W G C TT G T W-3' ImPyHpHpImHp-y-PyPyPyPyImPy 1538) 5' G C TT G A W-3 ImPyHpHpImPy-y-HpPyPyPyImPy -W T
1539) 5'-W G C TT G G W-3' ImPyHpHpImIm-y-pypypypylmPy 1540) 5' G C TT G C W-3' ImPyHpHpImPy-y-ImPyPyPyImPy -W
154I) 5' G C TT C T W-3' ImPyHpHpPyHp-y-pyImPyPyImPy -W
1542) 5'-W G C TT C A W-3' ImPyHpHpPyPy-y-HpImPyPyImPy 1543) 5' G C TT C G W-3' ImPyHpHpPyIm-y-PyImPyPyImPy -W
1544) 5'-W G C TT C C W-3' ImPyHpHpPyPy-y-ImImPypyImPy 1545) 5' G C TA T T W-3' ImPyHpPyHpHp-y-PyPyHpPyImPy -W
1546) 5'-W G C TA T A W-3' ImPyHpPyHpPy-y-HpPyHpPyImPy 1547 5' G C TA T G W-3 ImPyHpPyHpim-y-PyPyHppyImPy ) -W ' 154 B 5' G C TA T C W-3 ImPyHpPyHpPy-y- ImPyHpPyImPy ) -W ' 1549) 5' G C TA A T W-3' ImpyHppyPyHp-y-PyHpHpPyImPy -W
1550 5' G C TA A A W-3 ImPyHpPyPyPy-y-HpHpHpPyImPy ) -W ' 1551) 5' G C TA A G W-3' ImPyHpPypyIm-y-PyHpHpPyImPy -W
1552) 5' G C TA A C W-3' ImPyHpPyPyPy-y-ImHpHpPyImPy -W
1553) 5' G C TA G T W-3' ImPyHpPyImHp-y-PyPyHpPyImPy -W
1554) 5'-W G C TA G A W-3' ImPyHpPyImPy-y-HpPyHpPyImPy 1555) 5'-W G C TA G G W-3' ImPyHpPyImIm-y-PyPyHpPyImPy 1556) 5'-W G C TA G C W-3' ImPyHpPyImPy-y-ImPyHpPyImPy 1557) 5'-W G C TA C T W-3' ImPyHpPyPyHp-y-PyImHpPyImPy 1558) 5' G C TA C A W-3' ImPyHpPyPyPy-y-HpImHpPyTmPy -W
1559) 5' G C TA C G W-3' ImPyHpPyPyIm-y-PyImHpPyImPy -W
1560) 5' G C TA C C W-3' ImPyHpPyPyPy-y-ImImHpPyImPy -W
TABLE 95: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCTSNNW-3' DNA sequence aromatic amino acid sequence 1561) 5'-W G C T G T T W-3' ImPyHpImHpHp-y-PyPyPyPyImPy 1562) 5'-W G C T G T A W-3' ImPyHpImHpPy-y-HpPyPyPyImPy 1563) 5'-W G C T G T G W-3' ImPyHpImHpIm-y-PyPyPyPyImPy 1564) 5'-W G C T G T C W-3' ImPyHpImHpPy-y-ImPyPyPyImPy 1565) 5' -W G C T G A T W-3' ImPyHpImPyHp-y-PyHpPyPyImPy 1566) 5'-W G C T G A A W-3' ImPyHpImPyPy-y-HpHpPyPyImPy 1567) 5'-W G C T G A G W-3' ImPyHpImPyIm-y-PyHpPyPyImPy 1568) 5' -W G C T G A C W-3' ImPyHpImPyPy-y-ImHpPyPyImPy 1569) 5'-W G C T G G T W-3' ImPyHpImImHp-y-PyPyPyPyImPy 1570) 5'-W G C T G G A W-3' ImPyHpImImPy-y-HpPyPyPyImPy 1571) 5'-W G C T G C T W-3' ImPyHpImPyHp-y-PyImPyPyImPy 1572) 5'-W G C T G C A W-3' ImPyHpImPyPy-y-HpImPyPyImPy 1573) 5'-W G C T G G G W-3' ImPyHpImImIm-y-PyPyPyPyImPy 1574) 5' -W G C T G G C. W-3' ImPyHpImImPy-y-ImPyPyPyImPy 1575) 5'-W G C T G C G W-3' ImPyHpImPyIm-y-PyImPyPyImPy 1576) 5'-W G C T G C C W-3' ImPyHpImPyPy-y-ImImPyPyImPy 1577) 5' -WG C TC T T W-3' ImPyHpPyHpHp-y-PyPyImPyImPy 1578) 5' -WG C TC T A W-3' ImPyHpPyHpPy-y-HpPyImPyImPy 1579) 5' -WG C TC T G W-3' ImPyHpPyHpIm-y-PyPyImPyImPy 1580) 5' -WG C TC T C W-3' ImPyHpPyHpPy-y-ImPyImPyImPy 1581) 5' -WG C TC A T W-3' ImPyHpPyPyHp-y-PyHpImPyImPy 1582) 5' -WG C TC A A W-3' ImPyHpPyPyPy-y-HpHpImPyImPy 1583) 5' -WG C TC A G W-3' ImPyHpPyPyIm-y-PyHpImPyImPy 1584) 5' -WG C TC A C W-3' ImPyHpPyPyPy-y-ImHpImPyImPy 1585) 5' -WG C TC G T W-3' ImPyHpPyImHp-y-PyPyImPyImPy 1586) 5' -WG C TC G A W-3' ImPyHpPyImPy-y-HpPyImPyImPy 1587) 5' -WG C TC C T W-3' ImPyHpPyPyHp-y-PyImImPyImPy 1588) 5' -WG C TC C A W-3' ImPyHpPyPyPy-y-HpImImPyImPy 1589) 5' -WG C TC G G W-3' ImPyHpPyImIm-y-PyPyImPyImPy 1590) 5' -WG C TC G C W-3' ImPyHpPyImPy-y-ImPyImPyImPy 1591) 5' -WG C TC C G W-3' ImPyHpPyPyIm-y-PyImImPyImPy 1592) 5' -WG C TC C C W-3' ImPyHpPyPyPy-y-ImImImPyImPy WO 98/37067 PCTlUS98/01714 TABLE
96:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCAWNNW-3' DNA aromatic amino acid sequence sequence 1593) 5'-W G C A TT T W-3' ImPyPyHpHpHp-y-pypypyHpImPy 1594) 5''-W G C A TT A W-3' ImPyPyHpHpPy-y-HpPyPyHpImPy 1595) 5' -W G C A TT G W-3' ImPyPyHpHpIm-y-PypypygplmPy 1596) 5' -W G C A TT C W-3' ImPyPyHpHpPy-y-ImPyPyHpImPy 1597) 5' -W G C A TA T W-3' ImPyPyHpPyHp-y-PyHpPyHpImPy 1598) 5' -W G C A TA A W-3' ImPyPyHpPyPy-y-HpHpPyHpImPy 1599) 5' -W G C A TA G W-3' ImPyPyHpPyIm-y-PyHpPyHpImPy 1600) 5' -W G C A TA C W-3' ImPyPyHpPyPy-y-ImHpPyHpImPy 1601) 5' -W G C A TG T W-3' ImPyPyHpImAp-y-PyPyPyHpImPy 1602) 5' -W G C A TG A W-3' ImPyPyHpImPy-y-HpPyPyHpImPy 1603) 5' -W G C A TG G W-3' ImPyPyHpImIm-y-PyPyPyHpImPy 1604) 5' -W G C A TG C W-3' ImPyPyHpImPy-y-ImPyPyHpImPy 1605) 5' -W G C A TC T W-3' ImPyPyHpPyHp-y-PyImPyHpImPy 1606) 5' -W G C A TC A W-3' ImPyPyHpPyPy-y-HpImPyHpImPy 1607) 5' -W G C A TC G W-3' ImPyPyHpPyIm-y-PyImPyHpImPy 1608) 5' -W G C A TC C W-3' ImPyPyHpPyPy-y-ImImPyHpImPy 1609) 5' -W G C A AT T W-3' ImPyPyPyHpHp-y-PyPyHpHpImPy 1610) 5' -W G C A AT A W-3' ImPyPyPyHpPy-y-HpPyHpHpimPy 1611) 5' -W G C A AT G W-3' ImPyPyPyHpIm-y-PyPyHpHpImPy 1612) 5' -W G C A AT C W-3' ImPyPyPyHpPy-y-ImPyHpHpImPy 1613) 5' -W G C A AA T W-3' ImPyPyPyPyHp-y-PyHpHpHpImPy 1614) 5' -W G C A AA A W-3' ImPyPyPyPyPy-y-HpHpHpFipImPy 1615) 5' -W G C A AA G W-3' ImPyPyPyPyIm-y-PyHpHpHpImPy 1616 5' -W G C A AA C W-3' ImPyPyPyPyPy-y-ImHpHpHpImPy ) 1617) 5' -W G C A AG T W-3' ImPyPyPyImHp-y-PypyHpHpImPy 1618) 5' -W G C A AG A W-3' ImPyPyPyImPy-y-HpPyHpHpImPy 1619) 5' -W G C A AG G W-3' ImPyPyPyImIm-y-PyPyFipHpImPy 1620) 5' -W G C A AG C W-3' ImPyPyPyImPy-y-ImPyHpHpImPy 1621) 5' -W G C A AC T W-3' ImPyPyPyPyHp-y-pyImHpHpImPy 1622) 5' -W G C A AC A W-3' ImPyPyPypypy-y-HpI~pHpImPy 1623) 5' -W G C A AC G W-3' ImPyPyPyPyIm-y-PyImHpHpImPy 1624) 5' -W G C A AC C W-3' ImPyPyPypyPy-y-ImImHpHpImPy TABLE
97:
12-ring Hairpin PoIyamides for recognition of 8-by 5'-WGCASNNW-3' DNA aromatic amino acid sequence sequence 1625) 5' -W G CA G T T W-3' ImPyPyImHpHp-y-PyPyPyHpImPy 1626) 5' ~-WG CA G T A W-3' ImPyPyImHpPy-y-HpPyPyHpItaPy 1627) 5' -W G CA G T G W-3' ImPyPyImHpIm-y-PyPyPyHpImPy 1628) 5' -W G CA G T C W-3' ImPyPyImHpPy-y-ImPyPyHpImPy 1629) 5' -W G CA G A T W-3' ImPyPyImPyHp-y-PyHpPyHpImPy 1630) 5' -W G CA G A A W-3' ImPyPyImPyPy-y-HpHpPyHpImPy 1631) 5' -W G CA G A G W-3' ImPyPyImPyIm-y-PyHpPyHpImPy 1632) 5' -W G CA G A C W-3' ImPyPyImPyPy-y-ImHpPyHpImPy 1633} 5' -W G CA G G T W-3' ImPyPyImImHp-y-PyPyPyHpImPy 1634) 5' -W G CA G G A W-3' ImPyPyImImPy-y-HpPyPyHpImPy 1635) 5' -W G CA G C T W-3' ImPyPyImPyHp-y-PyImPyHpImPy 1636) 5' -W G CA G C A W-3' ImPyPyImPyPy-y-HpImPyHpImPy 1637) 5' -W G CA G G G W-3' ImPyPyImImIm-y-PyPyPyHpImPy 1638} 5' -W G CA G G C W-3' ImPyPyImImPy-y-ImPyPyHpImPy 1639) 5' -W G CA G C G W-3' ImPyPyImPyIm-y-PyImPyHpImPy 1640) 5' -W G CA G C C W-3' ImPyPyImPyPy-y-ImImPyHpImPy 1641) 5' -W G CA C T T W-3' ImPyPyPyHpHp-y-PyPyImHpImPy 1642) 5' -W G CA C T A W-3' ImPyPyPyHpPy-y-HpPyImHpImPy 1643) 5' -W G CA C T G W-3' ImPyPyPyHpIm-y-PyPyImHp3mPy 1644) 5' -W G CA C T C W-3' ImPyPyPyHpPy-y-ImPyImHpImPy 1645) 5' -W G CA C A T W-3' ImPyPyPyPyHp-y-PyHpImHpImPy 1646) 5' -W G CA C A A W-3' ImPyPyPyPyPy-y-HpHpImHpImPy 1647) 5' -W G CA C A G W-3' ImPyPyPyPyIm-y-PyHpImHpImPy 1648) 5' -W G CA C A C W-3' ImPyPyPyPyPy-y-ImHpImHpImPy 1649) 5' -W G CA C G T W-3' ImPyPyPyImHp-y-PyPyImHpImPy 1650) 5' -W G CA C G A W-3' ImPyPyPyImPy-y-HpPyImHpImPy 1651) 5' -W G CA C C T W-3' ImPyPyPyPyHp-y-PyImImHpImPy 1652) 5' -W G CA C C A W-3' ImPyPyPyPyPy-y-HpImImHpImPy 1653) 5' -W G CA C G G W-3' ImPyPyPyImim-y-PyPyImHpImPy 1654) 5' -W G CA C G C W-3' ImPyPyPyImPy-y-ImPyImHpImPy 1655) 5' -W G CA C C G W-3' ImPyPyPyPyIm-y-PyImImHpImPy 1656) 5' -W G CA C C C W-3' ImPyPyPyPyPy-y-ImImImHpImPy 1'A13LE
98:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCCWNNW-3' DNA aromatic amino acid sequence sequence 1657) 5' -WG C CT T T W-3' ImPyPyHpHpHp-y-PyPypyImImPy 1658) 5' -WG C CT T A W-3' ImPyPyHpHpPy-y-HpPyPyImImPy 1659) 5' -WG C CT T G W-3' ImPyPyHpHpIm-y-PyPyPyImImPy 1660) 5' -WG C CT T C W-3' ImPyPyHpHpPy-y-ImPyPyImImPy 1661) 5' -WG C CT A T W-3' ImPyPyHpPyHp-y-PyHpPyImImPy 1662) 5' -WG C CT A A W-3' ImPyPyHpPyPy-y-HpHpPyImImPy 1663) 5' -WG C CT A G W-3' ImPypyHpPyIm-y-PyHpPyImImPy 1664) 5' -WG C CT A C W-3' ImPyPyHpPyPy-y-ImHppyImImPy 1665) 5' -WG C CT G T W-3' ImPyPyHpImHp-y-PyPyPyImImPy 1666) 5' -WG C CT G A W-3' ImPyPyHpImPy-y-HpPyPyImImPy 1667) 5' -WG C CT G G W-3' ImPyPyHpImIm-y-PyPyPyImImpy 1668) 5' -WG C CT G C W-3' ImPyPyHpImPy-y-ImPyPyImImPy 1669) 5' -WG C CT C T W-3' ImPyPyHpPyHp-y-PyImPyImImPy 1670) 5' -WG C CT C A W-3' ImPyPyHpPyPy-y-HpImPyImImPy 1671) 5' -WG C CT C G W-3' ImPyPyHpPyIm-y-PyImPyImImPy 1672) 5' -WG C CT C C W-3' ImPyPyHpPyPy-y-ImImPyImImPy 1673) 5' -WG C CA T T W-3' ImPyPyPyHpHp-y-PyPyHpImImPy 1674) 5' -WG C CA T A W-3' ImPyPyPyHpPy-y-HpPyHpImImPy 1675) 5' -WG C CA T G W-3' ImPyPyPyHpIm-y-PyPyHpImImPy 1676) 5' -WG C CA T C W-3' ImPyPyPyHpPy-y-ImPyHpImImPy 1677) 5' -WG C CA A T W-3' ImPyPyPyPyHp-y-PyHpHpImImPy 1678) 5' -WG C CA A A W-3' ImPyPyPypypy-y-HpHpHpImImPy 1679) 5' -WG C CA A G W-3' ImPyPyPyPyIm-y-PyApHpImImPy 1680) 5' -WG C CA A C W-3' ImPyPyPyPyPy-y-ImHpHpImImPy 1681) 5' -WG C CA G T W-3' ImPyPyPyImHp-y-pypyHpImImPy 1682) 5' -WG C CA G A W-3' ImPyPyPyImPy-y-HpPyHpImImPy 1683 ) 5' -WG C CA G G W-3' ImPyPyPyImIm-y-pypyHpImImPy 1684) 5' -WG C CA G C W-3' mPyPyPyImPy-y-ImPyHpImImPy I
1685) 5' -WG C CA C T W-3' ImPyPyPyPyHp-y-PyImHpImImPy 1686) 5' -WG C CA C A W-3' ImPyPyPyPyPy-y-HpImHpImImPy 1687) 5' -WG C CA C G W-3' ImPyPyPyPyIm-y-PyImHpImImPy 1688) 5' -WG C CA C C W-3' ImPyPyPyPyPy-y-ImImIipImImPy TABLE
99:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCCSNNW-3' DNA aromatic amino acid sequence sequence 1689) 5' -WG C C G T T W-3' ImPyPyImHpHp-y-PyPyPyImImPy 1690) 5' -WG C C G T A W-3' ImPyPyImHpPy-y-HpPyPyImImPy 1691) 5' -WG C C G T G W-3' ImPyPyImHpIm-y-PyPyPyImImPy 1692) 5' -WG C C G T C W-3' ImPyPyImHpPy-y-ImPyPyImImPy 1693) 5' -WG C C G A T W-3' ImPyPyImPyHp-y-PyHpPyImImPy 1694) 5' -WG C C G A A W-3' ImPyPyImPyPy-y-HpHpPyImImPy 16 9 5 5' -WG C C G A G W-3 ImPyPyImPyIm-y-PyHpPyImImPy ) ' 1696) 5' -WG C C G A C W-3' ImPyPyImPyPy-y-ImHpPyImImPy 1697) 5' -WG C C G G T W-3' ImPyPyImImHp-y-PyPyPyImImPy 1698) 5' -WG C C G G A W-3' ImPyPyImImPy-y-HpPyPyImImPy 1699) 5' -WG C C G C T W-3' ImPyPyImPyHp-y-PyImPyImImPy 1700) 5' -WG C C G C A W-3' ImPyPyImPyPy-y-HpImPyImImPy 1701) 5' -WG C C C T T W-3' ImPyPyPyHpHp-y-PyPyImImImPy 1702) 5' -WG C C C T A W-3' ImPyPyPyHpPy-y-HpPyImImImPy 1703) 5' -WG C C C T G W-3' ImPyPyPyHpIm-y-PyPyImImImPy 1704) 5' -WG C C C T C W-3' ImPyPyPyHpPy-y-ImPyImImImPy 1705) 5' -WG C C C A T W-3' ImPyPyPyPyHp-y-PyHpImImImPy 1706) 5' -WG C C C A A W-3' ImPyPyPyPyPy-y-HpHpImImImPy 1707) 5' -WG C C C A G W-3' ImPyPyPyPyIm-y-PyHpImImImPy 1708) 5' -WG C C C A C W-3' ImPyPyPyPyPy-y-ImHpImImImPy 1709) 5' -WG C C C G T W-3' ImPyPyPyImHp-y-PyPyImImImPy 1710 ) 5' -WG C C C G A W-3 ImPyPyPyImPy-y-HpPyImImImPy ' 1711) 5' -WG C C C C T W-3' ImPyPyPyPyHp-y-PyImImImImPy 1712) 5' -WG C C C C A W-3' ImPyPyPyPyPy-y-HpImImImImPy G73) 5' -WG C C G G G W-3' ImPyPyImImIm-y-PyPyPyImImPy G74 ) 5' -WG C C G G C W- 3 ImPyPyImImPy-y- ImPyPyImImPy ' G75) 5' -WG C C G C G W-3' ImPyPyImPyIm-y-PyImPyImImPy G7 6 ) 5' -WG C C G C C W- 3 ImPyPyImPyPy-y-ImImPyImImPy ' G77) 5' -WG C C C G G W-3' ImPyPyPyImIm-y-PyPyImImImPy G7 8 ) 5' -WG C C C G C W- 3 ImPyPyPyImPy-y- ImPyImImImPy ' G7 9 ) 5' -WG C C C C G W- 3 ImPyPyPyPyIm-y-PyImImImImPy ' G80) 5' -WG C C C C C W-3' ImPyPyPyPyPy-y-ImImImImImPy WO 98/37067 PCTIUS98/Oi714 TABLE
100:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAGWNNW-3' DNA aromatic amino acid sequence sequence 1713) 5' -WG A G T T TW-3' ImPyImHpHpHp-y-PyPypypyHppy 1714) 5' -WG A G T T AW-3' ImPyImHpHpPy-y-HpPyPyPyHpPy 1715) 5' -WG A G T T GW-3' ImPyImHpHpIm-y-PyPyPyPyHpPy 1716) 5' -WG A G T T CW-3' ImPyImHpHpPy-y-ImPyPyPyHpPy 1717) 5' -WG A G T A TW-3' ImPyImHpPyHp-y-PyHpPyPyHpPy 1718) 5' -WG A G T A AW-3' ImPyImHpPyPy-y-HpHpPyPyHpPy 1719) 5' -WG A G T A GW-3' ImPyImHpPyIm-y-PyHpPyPyHpPy 17 2 0 5' -WG A G T A CW-3 ImPyImHpPyPy-y- ImHpPyPyFipPy ) ' 1721) 5' -WG A G T G TW-3' ImPyImHpImHp-y-PyPyPyPyHpPy 1722) 5' -WG A G T G AW-3' ImPyImHpImPy-y-HpPyPyPyHpPy 1723) 5' -WG A G T G GW-3' ImPyImHpImIm-y-PyPyPyPyHpPy 1724) 5' -WG A G T G CW-3' ImPyImHpImPy-y-ImPyPypyHpPy 1725) 5' -WG A G T C TW-3' ImPyImHpPyHp-y-PyImPyPyHpPy 1726) 5' -WG A G T C AW-3' ImPyImHpPyPy-y-HpImPyPyHpPy 1727) 5' -WG A G T C GW-3' ImPyImHpPyIm-y-PyImPyPyHpPy 1728) 5' -WG A G T C CW-3' ImPyImHpPyPy-y-ImImPyPyHpPy 1729) 5' -WG A G A T TW-3' ImPyImPyHpHp-y-PyPyHpPyHpPy 1730) 5' -WG A G A T AW-3' ImPyImPyHpPy-y-HpPyHpPyHpPy 1731) 5' -WG A G A T GW-3' ImPyImPyHpIm-y-PyPyHpPyHpPy 1732) 5' -WG A G A T CW-3' ImPyImPyHpPy-y-ImPyHpPyHpPy 1733) 5' -WG A G A A TW-3' ImPyImPyPyHp-y-PyHpHpPyHpPy 1734) 5' -WG A G A A AW-3' ImPyImPyPyPy-y-HpHpHpPyHpPy 1735) 5' -WG A G A A GW-3' ImPyImPyPyIm-y-PyHpHpPyHpPy 1736) 5' -WG A G A A CW-3' ImPyImPyPyPy-y-ImHpHpPyHpPy 1737) 5' -WG A G A G TW-3' ImPyImPyImHp-y-PyPyHpPyHpPy 1738) 5' -WG A G A G AW-3' ImPyImPyImPy-y-HpPyHpPyHpPy 1739) 5' -WG A G A G GW-3' ImPyImPyImIm-y-PyPyHpPyHpPy 1740) 5' -WG A G A G CW-3' ImPyImPyImPy-y-ImPyHpPyHpPy 1741) 5' -WG A G A C TW-3' ImPyImPyPyAp-y-PyImHpPyHpPy 1742) 5' -WG A G A C AW-3' ImPyImPyPyPy-y-HpImHpPyHpPy 1743) 5' -WG A G A C GW-3' ImPyImPyPyIm-y-PyImHpPyHpPy 1744) 5' -WG A G A C CW-3' ImPyImPyPyPy-y-ImImHpPyHpPy TABLE
101:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAGSNNW-3' DNA aromatic amino acid sequence sequence 1745) 5'-W G A GG T T W-3' ImpyImImHpHp-y-PyPypypyHpPy 1746) 5''-W G A GG T A W-3' ImPyImImHpPy-y-HpPyPyPyHpPy 1747) 5'-W G A GG T G W-3' ImPyImImHpIm-y-PyPyPypyHpPy 1748) 5'-W G A GG T C W-3' ImPyImImHpPy-y-ImPyPyPyHppy 1749) 5'-W G A GG A T W-3' ImPyImImPyHp-y-PyHpPyPyHpPy 1750) 5'-W G A GG A A W-3' ImPyImImPyPy-y-HpHpPyPyHpPy 1751) 5'-W G A GG A G W-3' ImPyImImPyIm-y-PyHpPyPyHpPy 1752) 5'-W G A GG A C W-3' ImPyImImPyPy-y-ImHpPyPyHpPy 1753} 5'-W G A GG G T W-3' ImPyImImImHp-y-PyPyPyPyHpPy 1754) 5'-W G A GG G A W-3' ImPyImImImPy-y-HpPyPyPyHpPy 1755} 5'-W G A GG C T W-3' ImPyImImPyHp-y-PyImPyPyHpPy 1756) 5'-W G A GG C A W-3' ImPyImImPyPy-y-HpImPyPyHpPy 1757) 5'-W G A GC T T W-3' ImPyImPyHpHp-y-PyPyImPyFipPy 1758) 5'-W G A GC T A W-3' ImPyImPyHpPy-y-HpPyImPyHpPy 1759) 5'-W G A GC T G W-3' ImPyImPyHpIm-y-PyPyImPyHpPy 1760) 5'-W G A GC T C W-3' ImPyImPyHpPy-y-ImPyImPyHpPy 1761} 5'-W G A GC A T W-3' ImPyImPyPyHp-y-PyHpImPyHpPy 1762) 5'-W G A GC A A W-3' ImPyImPyPyPy-y-HpHpImPyHpPy 1763) 5'-W G A GC A G W-3' ImPyImPyPyIm-y-PyHpImpyHpPy 1764) 5'-W G A GC A C W-3' ImPyImPyPyPy-y-ImHpImPyHpPy 1765) 5'-W G A GC G T W-3' ImPyImPyImHp-y-PyPyImPyHpPy 1766) 5'-W G A GC G A W-3' ImPyImPyImPy-y-HpPyImPyHpPy 1767) 5'-W G A GC C T W-3' ImpyImPyPyHp-y-PyImImPyHpPy 1768) 5'-W G A GC C A W-3' ImPyImPyPyPy-y-HpImImPyHpPy 1769) 5'-W G A GG G G W-3' ImPyImImImIm-y-PyPyPyPyHpPy 1770) 5'-W G A GG G C W-3' ImPyImImImPy-y-ImPyPyPyHpPy 1771) 5'-W G A GG C G W-3' ImPyImImPyIm-y-PyImPyPyHpPy 1772) 5'-W G A GG C C W-3' ImPyImImPyPy-y-ImImPyPyHpPy 1773) 5'-W G A GC G G W-3' ImPyImPyImIm-y-PyPyImPyHpPy 1774) 5'-W G A GC G C W-3' ImPyImPyImPy-y-ImPyImPyHppy 1775) 5'-W G A GC C G W-3' ImPyImPyPyIm-y-PyImImPyHpPy 1776) 5'-W G A GC C C W-3' ImPyImPyPyPy-y-ImImImPyHpPy WO 98/37067 , PCT/US98/01714 TABLE
102:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGATWNNW-3' DNA aromatic amino acid sequence sequence 1777) 5'-W G A T TT T W-3' ImPyHpHpHpHp-y-PyPyPyPyHpPy 1778) 5'~-W G A T TT A W-3' ImPyHpHpHppy-y-HpPyPyPyHpPy 1779) 5' G A T TT G W-3' ImPyHpHpHpIm-y-PyPyPyPyHpPy -W
1780) 5'-W G A T TT C W-3' ImPyHpHpHpPy-y-ImPyPyPyHpPy 1781) 5'-W G A T TA T W-3' ImPyHpHpPyHp-y-PyHpPyPyHpPy 1782) 5'-W G A T TA A W-3' ImPyHpHpPypy-y-HpHppypyHpPy 1783 ) 5'-W G A T TA G W-3 ImPyHpHpPyIm-y-PyApPyPyHpPy ' 1784) 5'-W G A T TA C W-3' ImPyHpHpPypy-y-I~ppypygppy 1785) 5'-W G A T TG T W-3' ImPyHpHpImHp-y-pypypypyHppy 1786) 5'-W G A T TG A W-3' ImPyHpHpImPy-y-HpPyPyPyHpPy 1787) 5'-W G A T TG G W-3' ImPyHpHpImIm-y-PyPypypygpPy 1788) 5'-W G A T TG C W-3' ImpyHpHpImPy-y-ImPyPypyHppy 1789) 5'-W G A T TC T W-3' ImPyHpHpPyHp-y-PyImPyPyHpPy 1790) 5'-W G A T TC A W-3' ImPyHpHpPyPy-y-HpImPyPyHpPy 1791) 5'-W G A T TC G W-3' ImPyHpHpPyIm-y-pyImPyPyHpPy 1792) 5'-W G A T TC C W-3' ImPyHpHpPyPy-y-ImImPyPyHpPy 1793) 5'-W G A T AT T W-3' ImPyHpPyHpHp-y-PypyHpPyHpPy 1794) 5'-W G A T AT A W-3' ImPyHpPyHpPy-y-HpPyHpPyHpPy 1795) 5'-W G A T AT G W-3' ImPyHpPyHpIm-y-PyPyHpPyHpPy 1796) 5'-W G A T AT C W-3' ImPyHpPyHpPy-y-ImPyHpPyHpPy 1797) 5'-W G A T AA T W-3' ImPyHpPyPyHp-y-PyHpHpPyHpPy 1798) 5'-W G A T AA A W-3' ImPyHpPyPyPy-y-HpHpHpPyHpPy 1799) 5'-W G A T AA G W-3' ImPylipPypyIm-y-PyHpHpPyHpPy 1800) 5'-W G A T AA C W-3' ImPyHpPyPyPy-y-ImHpHppyHpPy 1801) 5'-W G A T AG T W-3' ImPyHpPyImHp-y-pyPyHppyHpPy 1802) 5'-W G A T AG A W-3' ImPyHpPyImPy-y-HpPyHpPyHpPy 1803) 5'-W G A T AG G W-3' ImPyHpPyImIm-y-PyPyHpPyHpPy 1804) 5'-W G A T AG C W-3' ImPyHpPyImPy-y-ImPyHpPyHpPy 1805) 5'-W G A T AC T W-3' ImPyHpPyPyHp-y-PyImHpPyHpPy 1806) 5'-W G A T AC A W-3' ImPyHpPyPyPy-y-HpImHpPyHpPy _ 1807) 5'-W G A T AC G W-3' ImPyHpPyPyIm-y-PyImHpPyHpPy 1808) 5'-W G A T AC C W-3' ImPyHpPyPyPy-y-ImImHpPyHpPy TABLE
103:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGATSNNW-3' DNA aromatic amino acid sequence sequence 1809) 5' -WG A T G TT W-3' ImPyHpImHpHp-y-PyPyPyPyHpPy 1810) 5' -WG A T G TA W-3' ImPyHpImHpPy-y-HpPyPyPyHpPy 1811) 5' -WG A T G TG W-3' ImPyHpImHpIm-y-PyPyPyPyHpPy 1812) 5' -WG A T G TC W-3' ImPyHpImHpPy-y-ImPyPyPyHpPy 1813) 5' -WG A T G AT W-3' ImPyHpImPyHp-y-PyHpPyPyHpPy 1814) 5' -WG A T G AA W-3' ImPyHpImPyPy-y-HpHpPyPyHpPy 1815) 5' -WG A T G AG W-3' ImPyHpImPyIm-y-PyF-IpPyPyHpPy 1816) 5' -WG A T G AC W-3' ImPyHpImPyPy-y-ImHpPyPyHpPy 1817) 5' -WG A T G GT W-3' ImPyHpImImHp-y-PyPyPyPyHpPy 1818) 5' -WG A T G GA W-3' ImPyHpImImPy-y-HpPyPyPyHpPy 1819) 5' -WG A T G CT W-3' ImPyHpImPyHp-y-PyImPyPyHpPy 1820) 5' -WG A T G GA W-3' ImPyHpImPyPy-y-HpImPyPyHpPy 1821) 5' -WG A T G GG W-3' ImPyHpImImIm-y-PyPyPyPyHpPy 1822) 5' -WG A T G GC W-3' ImPyHpImImPy-y-ImPyPyPyHpPy 1823) 5' -WG A T G CG W-3' ImPyHpImPyIm-y-PyImPyPyHpPy 1824) 5' -WG A T G CC W-3' ImPyHpImPyPy-y-ImImPyPyHpPy 1825) 5' -WG A T C TT W-3' ImPyHpPyHpHp-y-PyPyImPyHpPy 1826) 5' -WG A T C TA W-3' ImPyHpPyHpPy-y-HpPyImPyHpPy 1827) 5' -WG A T C TG W-3' ImPyHpPyHpIm-y-PyPyImPyHpPy 1828) 5' -WG A T C TC W-3' ImPyHpPyHpPy-y-ImPyImPyHpPy 1829) 5' -WG A T C AT W-3' ImPyHpPyPyHp-y-PyHpImPyHpPy 1830) 5' -WG A T C AA W-3' ImPyHpPyPyPy-y-HpHpImPyHpPy 1831) 5' -WG A T C AG W-3' ImPyHpPyPyIm-y-PyHpImPyHpPy 1832) 5' -WG A T C AC W-3' ImPyHpPyPyPy-y-ImHpImPyHpPy 1833) 5' -WG A T C GT W-3' ImPyHpPyImHp-y-PyPyImPyHpPy 1834) 5' -WG A T C GA W-3' ImPyHpPyImPy-y-HpPyImPyHpPy 1835) 5' -WG A T C CT W-3' ImPyHpPyPyHp-y-PyImImPyHpPy 1836) 5' -WG A T C CA W-3' ImPyHpPyPyPy-y-HpImImPyHpPy 1837) 5' -WG A T C GG W-3' ImPyHpPyImIm-y-PyPyImPyHpPy 1838) 5' -WG A T C GC W-3' ImPyHpPyImPy-y-ImPyImPyHpPy 183 9 5' -WG A T C CG W-3' ImPyHpPyPyIm-y-PyImImPyHpPy ) 1840) 5' -WG A T C CC W-3' ImPyHpPyPyPy-y-ImImImPyHpPy TABLE
104:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAAWNNW-3' DNA aromatic amino acid sequence sequence 184I) 5'-W G A AT T T W-3' ImPyPyHpHpHp-y-PypypyHpHpPy 1842) 5'-W G A AT T A W-3' ImPyPyHpHpPy-y-HpPyPyHpHpPy 1843) 5'-W G A AT T G W-3' ImPyPyHpHpIm-y-PyPypyHpHpPy 1844) 5'-W G A AT T C W-3' ImPyPyHpHpPy-y-ImPyPyHpHpPy 1845) 5'-W G A AT A T W-3' ImPyPyHpPyHp-y-PyHpPyHpHpPy 1846) 5'-W G A AT A A W-3' ImPyPyHpPyPy-y-HpHpPyHpHpPy 1847 ) 5'-W G A AT A G W-3 ImPyPyHpPyIm-y-PyHpPyHpHpPy ' 1848) 5'-W G A AT A C W-3' ImPyPyHpPyPy-y-ImHpPyHpHpPy 1849) 5'-W G A AT G T W-3' ImPyPyHpImHp-y-PypypyHpHpPy 1850) 5'-W G A AT G A W-3' ImPyPyHpImPy-y-HpPyPyHpHpPy 1851) 5'-W G A AT G G W-3' ImPyPyHpImIm-y-PyPyPyHpHppy 1852) 5'-W G A AT G C W-3' ImPypyHpImPy-y-ImPyPyHpHpPy 1853) 5'-W G A AT C T W-3' ImPyPyHpPyHp-y-PyImPyHpHpPy 1854) 5'-W G A AT C A W-3' ImPyPyHpPyPy-y-HpImPyHpHpPy 1855) 5'-W G A AT C G W-3' ImPyPyHpPyIm-y-PyImPyHpHpPy 1856) 5'-W G A AT C C W-3' ImPyPyHpPyPy-y-ImImPyHpHpPy 1857 ) 5'-W G A AA T T W-3' ImPyPyPyHpHp-y-PyPyHpHpHpPy 1858) 5'-W G A AA T A W-3' ImPyPyPyHpPy-y-HpPyHpHpHpPy 1869) 5'-W G A AA T G W-3' ImPyPyPyHpIm-y-PyPyHpHpHpPy 1860) 5'-W G A AA T C W-3' ImPyPyPyApPy-y-ImPyHpHpHpPy 1861) 5'-W G A AA A T W-3' ImPyPyPypyHp-y-PyHpHpHpHpPy 1862 ) 5'-W G A AA A A W-3 ImPyPyPyPyPy-y-HpHpHpHpHpPy ' 1863) 5'-W G A AA A G W-3' ImPyPyPyPyIm-y-PyHpHpHpHpPy 1864) 5'-W G A AA A C W-3' ImPyPyPyPyPy-y-ImHpHpHpHpPy 1865) 5'-W G A AA G T W-3' ImPyPyPyImHp-y-pyPyHpHpHpPy 1866) 5'-W G A AA G A W-3' ImPyPypyImPy-y-HpPyHpHpHpPy 1867) 5'-W G A AA G G W-3' ImPyPyPyImIm-y-PyPyHpHpHpPy 1868) 5'-W G A AA G C W-3' ImPyPyPyImPy-y-ImPyHpHpHpPy 1869) 5'-W G A AA C T W-3' ImPyPyPypyHp-y-PyImHpHpHpPy 1870) 5'-W G A AA C A W-3' ImPyPyPypypy-y-HpI,~pHpgpPy _ 1871) 5'-W G A AA C G W-3' ImPyPypypyIm-y-PyImHpHpHpPy 1872) 5'-W G A AA C C W-3' ImPyPyPypypy-y-ImImHpHpHpPy TABLE 105:
12-ring I airpin Polyamides for recognition of 8-by 5'-WGAASNNW-3' DNA sequence aromatic amino acid sequence 1873) 5'-W G A GT T W-3' ImPyPyImHpHp-y-PyPypygpgppy A
1874) 5'-W G A GT A W-3' ImPyPyImHpPy-y-HpPyPyHpHpPy A
1875) 5' -W G GT G W-3' ImPyPyImHpIm-y-PyPyPyHpHpPy A A
1876) 5' -W G GT C W-3' ImPyPyImHpPy-y-ImPyPyHpHpPy A A
1877) 5'-W G A GA T W-3' ImPyPyImPyHp-y-PyHpPyHpHpPy A
1878) 5'-W G A GA A W-3' ImPyPyImPyPy-y-HpHpPyHpHpPy A
1879) 5'-W G AA G A G W-3' ImPyPyImPyIm-y-pyHpPyHpHppy 1880) 5'-W G AA G A C W-3' ImPyPyImPypy-y-ImHppyHpHpPy 1881) 5'-W G AA G G T W-3' ImPyPyImImHp-y-PyPyPyHpHpPy 1882) 5'-W G AA G G A W-3' ImPyPyImImPy-y-HpPyPyHpHpPy 1883) 5'-W G AA G C T W-3' ImPyPyImPyHp-y-PyImPyHpHpPy 1884) 5'-W G AA G C A W-3' ImPyPyImPyPy-y-HpImpyHpHpPy 1885) 5'-W G A A G G G W-3' ImPyPyImImIm-y-PyPyPyHpHpPy 1886) 5' -W G A A G G C W-3' ImPyPyImImPy-y-ImpyPyHpHpPy 1887) 5'-W G A A G C G W-3' ImPyPyImPyIm-y-PyImPyHpHpPy 1888) 5'-W G A A G C C W-3' ImPyPyImPypy-y-ImImPyHpHpPy 1889) 5'-W G A A CT T W-3' ImPyPyPyHpHp-y-PyPyImHpHpPy 1890) 5'-W G A A CT A W-3' ImPyPyPyHpPy-y-HpPyImHpHpPy 1891) 5'-W G A A CT G W-3' ImPyPyPyHpIm-y-PyPyImHpHpPy 1892) 5'-W G A A CT C W-3' ImPyPyPyHpPy-y-ImPyImHpHpPy 1893) 5'-W G A A CA T W-3' ImPyPyPypyHp-y-PyHpImHpHpPy 1894) 5'-W G A A CA A W-3' ImPyPyPyPyPy-y-HpHpImHpHpPy 1895) 5'-W G A A CA G W-3' ImPyPyPyPyIm-y-PyHpImHpHpPy 1896) 5'-W G A A CA C W-3' ImPyPyPyPyPy-y-ImHpImHpHpPy 1897) 5'-W G A A CG T W-3' ImPyPyPyImHp-y-PyPyImHpHpPy 1898) 5'-W G A A CG A W-3' ImPyPyPyImPy-y-HpPyImHpHpPy 1899) 5'-W G A A CC T W-3' ImPyPyPyPyHp-y-PyImImHpHpPy 1900) 5'-W G A A CC A W-3' ImPyPyPyPyPy-y-HpImImHpHpPy 1901) 5'-W G A A CG G W-3' ImPyPyPyImIm-y-PyPyImHpHpPy 1902) 5'-W G A A CG C W-3' ImPyPyPyImPy-y-ImPyImHpHpPy 1903) 5'-W G A A CC G W-3' ImPyPyPyPyIm-y-PyImImHpHpPy 1904) 5'-W G A A CC C W-3' ImPyPyPyPyPy-y-ImImImHpHpPy WO g8I37067 PCT/US98/01714 TABLE
lOG:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGACWNNW-3' DNA aromatic amino acid sequence sequence 1905} 5'-W GA C T T T W-3' ImPyPyHpHpHp-y-PypypyImHpPy 1906) 5'-W GA C T T A W-3' ImPyPyHpHpPy-y-HppyPyImHpPy 1907) 5'-W GA C T T G W-3' ImPyPyHpHpIm-y-PypypyImHpPy 1908) 5'-W GA C T T C W-3' ImPyPyHpHpPy-y-ImPyPyImHpPy 1909) 5'-W GA C T A T W-3' ImpyPyHpPyHp-y-PyHppyImHpPy 1910) 5'-W GA C T A A W-3' ImPyPyHpPyPy-y-HpHpPyImHpPy 1911) 5'-W GA C T A G W-3' ImPyPyHpPyIm-y-PyHpPyImHpPy 1912) 5'-W GA C T A C W-3 ImPyPyHpPyPy-y-ImHpPyImHpPy T
1913) 5'-W GA C T G T W-3' ImPyPyHpImHp-y-PyPyPyImHpPy 1914) 5'-W GA C T G A W-3' ImPyPyHpImPy-y-HpPyPyImHpPy 1915) 5'-W GA C T G G W-3' TmPyPyHpImIm-y-PyPyPyImHpPy 1916) 5'-W GA C T G C W-3' ImPyPyHpImPy-y-ImPyPyImHpPy 1917) 5'-W GA C T C T W-3' ImPyPyHpPyHp-y-PyImPyImHpPy 1918) 5'-W GA C T C A W-3' ImpyPyHpPyPy-y-HpImPyImHpPy 1919) 5'-W GA C T C G W-3' ImPyPyHpPyIm-y-PyImPyImHppy 1920) 5'-W GA C T C C W-3' ImPyPyHpPyPy-y-ImImPyImHpPy 1921) 5'-W GA C A T T W-3' ImPyPyPyHpHp-y-PypyHpImHpPy 1922) 5'-W GA C A T A W-3' ImPyPyPyHpPy-y-HppyHpImHpPy 1923) 5'-W GA C A T G W-3' ImPyPyPyHpIm-y-PyPyHpImHpPy 1924) 5'-W GA C A T C W-3' ImPyPyPyHpPy-y-ImPyHpImHpPy 1925} 5'-W GA C A A T W-3' ImPyPyPyPyHp-y-PyHpHpImHpPy 1926) 5'-W GA C A A A W-3' ImPyPyPyPyPy-y-HpHpHpImHpPy 1927) 5'-W GA C A A G W-3' ImPyPyPyPyIm-y-PyHpHpImHpPy 1928) 5'-W GA C A A C W-3' ImPyPypyPyPy-y-ImHpHpImHpPy 1929) 5'-W GA C A G T W-3' ImPyPyPyImHp-y-PypyHpImHpPy 1930) 5'-W GA C A G A W-3' ImPyPyPyImPy-y-HpPyHpImHpPy 1931) 5'-W GA C A G G W-3' ImPyPyPyImIm-y-PypyHpImHpPy 1932) 5'-W GA C A G C W-3' ImPyPyPyImPy-y-ImPyHpImHpPy . 1933) 5'-W GA C A C T W-3' ImPyPyPyPyHp-y-PyImHpImHppy 1934) 5'-W GA C A C A W-3' ImPyPyPyPyPy-y-HpImHpImHpPy 1935) 5'-W GA C A C G W-3' ImPyPyPyPyIm-y-PyImHpImHpPy 1936) 5'-W GA C A C C W-3' ImPyPyPyPyPy-y-ImImHpImHpPy WO 98/37067 PCT/~7598/01714 TABLE
107:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGACSNNW-3' DNA aromatic amino acid sequence sequence 1937) 5' -WG A C G T T W-3' ImPyPyImHpHp-y-PyPyPyImHpPy 1938) 5' -WG A C G T A W-3' ImPyPyImHpPy-y-HpPyPyImHpPy 1939) 5' -WG A C G T G W-3' ImPyPyImHpIm-y-PyPyPyImHpPy 1940) 5' -WG A C G T C W-3' ImPyPyImHpPy-y-ImPyPyImHpPy 1941) 5' -WG A C G A T W-3' ImPyPyImPyHp-y-PyHpPyImHpPy 1942) 5' -WG A C G A A W-3' ImPyPyImPyPy-y-HpHpPyImHpPy 1943) 5' -WG A C G A G W-3' ImPyPyImPyIm-y-PyHpPyImHpPy 1944 5' -WG A C G A C W-3' ImPyPyImPyPy-y-ImHpPyImHpPy ) 1945) 5' -WG A C G G T W-3' ImPyPyImImHp-y-PyPyPyImHpPy 1946) 5' -WG A C G G A W-3' ImPyPyImImPy-y-HpPyPyImHpPy 1947) 5' -WG A C G C T W-3' ImPyPyImPyHp-y-PyImPyImHpPy 1948) 5' -WG A C G C A W-3' ImPyPyImPyPy-y-HpImPyImHpPy 1949) 5' -WG A C C T T W-3' ImPyPyPyHpHp-y-PyPyImImHpPy 1950) 5' -WG A C C T A W-3' ImPyPyPyHpPy-y-HpPyImImHpPy 1951) 5' -WG A C C T G W-3' ImPyPyPyHpIm-y-PyPyImImHpPy 1952) 5' -WG A C C T C W-3' ImPyPyPyHpPy-y-ImPyImImHpPy 1953) 5' -WG A C C A T W-3' ImPyPyPyPyHp-y-PyHpImImHpPy 1954) 5' -WG A C C A A W-3' ImPyPyPyPyPy-y-HpHpImImHpPy 1955) 5' -WG A C C A G W-3' ImPyPyPyPyIm-y-PyHpImImHpPy 1956) 5' -WG A C C A C W-3' ImPyPyPyPyPy-y-ImHpImImHpPy 1957) 5' -WG A C C G T W-3' ImPyPyPyImHp-y-PyPyImImHpPy 1958) 5' -WG A C C G A W-3' ImPyPyPyImPy-y-HpPyImImHpPy 1959) 5' -WG A C C C T W-3' ImPyPyPyPyHp-y-PyImImImHpPy 1960) 5' -WG A C C C A W-3' ImPyPyPyPyPy-y-HpImImImHpPy 1961) 5' -WG A C G G G W-3' ImPyPyImImIm-y-PyPyPyImHpPy 1962) 5' -WG A C G G C W-3' ImPyPyImImPy-y-ImPyPyImHpPy 1963) 5' -WG A C G C G W-3' ImPyPyImPyIm-y-PyImPyImHpPy 1964) 5' -WG A C G C C W-3' ImPyPyImPyPy-y-ImImPyImHpPy 1965) 5' -WG A C C G G W-3' ImPyPyPyImIm-y-PyPyImImHpPy 19 6 5' -WG A C C G C W- ImPyPyPyImPy-y- ImPyimImHpPy 6 ) 3 ' 1967) 5' -WG A C C C G W-3' ImPyPyPyPyIm-y-PyImImImHpPy 1968) 5' -WG A C C C C W-3' ImPyPyPyPyPy-y-ImImImImHpPy TABLE
108:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTGWNNW-3' DNA aromatic amino acid sequence sequence 1969) 5'-W GT G T T T W-3' ImHpImHpHpHp-y-PYPyPYPyPyPy 1970) 5'-W GT G T T A W-3' ImHpImHpHppy-y-HpPYPyPyPyPy 1971) 5'-W GT G T T G W-3' ImHpImHpHpIm-y-PyPypypypypy 1972) 5'-W GT G T T C W-3' ImHpImHpHpPy-y-ImPyPyPypypy 1973) 5'-W GT G T A T W-3' ImHpImHpPyHp-y-PyHpPyPyPYPy 1974) 5'-W GT G T A A W-3' ImHpImHpPYPy-y-HpHpPyPyPYpy 1975) 5'-W GT G T A G W-3' ImHpImHpPyIm-y-PyHpPyPyPyPy 1976) 5'-W GT G T A C W-3' ImHpImHpPyPy-y-ImHpPyPyPYPY
1977) 5'-W GT G T G T W-3' ImHpImHpImHp-y-PyPYPyPyPyPy 1978) 5'-W GT G T G A W-3' ImHpImHpImPy-y-HpPYPyPyPyPy 1979) 5'-W GT G T G G W-3' ImHpImHpImIm-y-PyPYPyPyPyPy 1980) 5'-W GT G T G C W-3' ImHpImHpImPy-y-ImPyPyPYPyPy 1981) 5'-W GT G T C T W-3' ImHpImHpPYHp-y-PyImPYPYPyPy 1982} 5'-W GT G T C A W-3' ImHpImHpPYPy-y-HpImPyPyPyPy 1983) 5'-W GT G T C G W-3' ImHpImHpPyIm-y-PyImPyPyPyPy 1984) 5'-W GT G T C C W-3' ImHpImHpPYPy-y-ImImPYPyPypy 1985) 5'-W GT G A T T W-3' ImHpImPYHpHp-y-PyPyHpPyPyPy 1986) 5'-W GT G A T A W-3' ImHpImPyHpPy-y-HpPYHpPyPyPy 1987) 5'-W GT G A T G W-3' ImHpImPyHpIm-y-PYPyHpPyPyPy 1988) 5'-W GT G A T C W-3' ImHpImPyHpPy-y-ImPYHpPyPyPy 1989) 5'-W GT G A A T W-3' ImHpImPyPyHp-y-PYHpHpPyPyPy 19 9 0 5'-W GT G A A A W- 3 ImHpImPyPyPy-y-HpHpHpPyPyPy ) ' 1991) 5'-W GT G A A G W-3' ImHpImPyPyIm-y-PyHpHpPYPyPy 1992) 5'-W GT G A A C W-3' ImHpImPyPyPy-y-ImHpHpPyPyPy 1993) 5'-W GT G A G T W-3' ImHpImPyImHp-y-PYPyHpPYPYPy 1994) 5'-W GT G A G A W-3' ImHpImPyImPy-y-HpPyHpPyPyPy 1995) 5'-W GT G A G G W-3' ImHpImPYImIm-y-PypyHpPyPyPy . 1996) 5'-W GT G A G C W-3' ImHpImPyImPy-y-ImPyHpPyPyPy 1997) 5'-W GT G A C T W-3' ImHpImPyPyHp-y-PYImHpPyPYPy 1998) 5'-W GT G A C A W-3' ImHpImPyPyPy-y-HpImHpPypyPy 1999) 5'-W GT G A C G W-3' ImHpImPYPYIm-y-pyImHpPYPYPy 2000) 5'-W GT G A C C W-3' ImHpImPyPyPy-y-ImImHpPyPYPy TABLE
109:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTGSNNW-3' DNA aromatic amino acid sequence sequence 2001) 5' -WG T G G T T W-3' ImHpImImHpHp-y-pypypypypypy 2002) 5' =WG T G G T A W-3' ImHpImImHpPy-y-HpPyPyPyPyPy 2003) 5' -WG T G G T G W-3' ImHpImImHpIm-y-PyPyPyPyPyPy 2004) 5' -WG T G G T C W-3' ImHpImImHpPy-y-ImPyPyPyPyPy 2005) 5' -WG T G G A T W-3' ImHpImImPyHp-y-PyHpPyPyPyPy 2006) 5' -WG T G G A A W-3' ImHpImImPyPy-y-HpHpPyPyPyPy 2007) 5' -WG T G G A G W-3' ImHpImImPyIm-y-PyHpPyPyPyPy 2008) 5' -WG T G G A C W-3' ImHpImImPyPy-y-ImHpPypyPyPy 2009) 5' -WG T G G G T W-3' ImHpImImImHp-y-PyPyPyPyPyPy 2 010 5' -WG T G G G A W- 3 ImHpImImImPy-y-HpPyPyPyPyPy ) ' 2011) 5' -WG T G G C T W-3' ImHpImImPyHp-y-pyImPyPyPyPy 2 012 5' -WG T G G C A W-3 ImHpImImPyPy-y-HpImPyPyPyPy ) ' 2013) 5' -WG T G C T T W-3' ImHpImPyHpHp-y-PyPyImPyPyPy 2014) 5' -WG T G C T A W-3' ImHpImPyHpPy-y-HpPyImPyPyPy 2015) 5' -WG T G C T G W-3' ImHpImPyHpIm-y-PyPyImPyPyPy 2016) 5' -WG T G C T C W-3' ImHpImPyHpPy-y-ImPyImPyPyPy 2017) 5' -WG T G C A T W-3' ImHpImPyPyHp-y-PyHpImPyPyPy 2018) 5' -WG T G C A A W-3' ImHpImPyPyPy-y-HpHpImPyPyPy 2019) 5' -WG T G C A G W-3' ImHpImPyPyIm-y-PyHpImPyPyPy 2020) 5' -WG T G C A C W-3' ImHpImPyPyPy-y-ImHpImPyPyPy 2021) 5' -WG T G C G T W-3' ImHpImPyImHp-y-PyPyImPyPyPy 2022) 5' -WG T G C G A W-3' ImHpImPyImPy-y-HpPyImPyPyPy 2023) 5' -WG T G C C T W-3' ImHpImPyPyHp-y-PyImImPyPyPy 2024) 5' -WG T G C C A W-3' ImHpImPyPyPy-y-HpImImPyPyPy 2025) 5' -WG T G G G G W-3' ImHpImImImIm-y-PyPyPyPyPyPy 2026) 5' -WG T G G G C W-3' ImHpImImImPy-y-ImPyPyPyPyPy 2027) 5' -WG T G G C G W-3' ImHpImImPyIm-y-PyImPyPyPyPy 2028) 5' -WG T G G C C W-3' ImHpImImPyPy-y-ImImPyPyPyPy 2029) 5' -WG T G C G G W-3' ImHpImPyImIm-y-PyPyImPyPyPy 2030) 5' -WG T G C G C W-3' ImHpImPyImPy-y-ImPyImPyPyPy 2031) 5' -WG T G C C G W-3' ImHpImPyPyIm-y-PyImImPyPyPy 2032) 5' -WG T G C C C W-3' ImHpImPyPyPy-y-ImImImPyPyPy t-At3Ll;
110:
12-ring Hairpin Polyamides for recogmt~on of 8-by 5'-WGTTWNNW-3' DNA aromatic amino acid sequence sequence 2033) 5'-W G T T W-3' ImHpHpHpHpHp-y-pypypypypypy T
T
T
2034) 5''-W G T T T A W-3' ImHpHpHpHpPy-y-HpPyPyPypypy T
2035) 5'-W GT T T T G W-3' ImHpHpHpHpIm-y-Pypypypypypy 2036) 5'-W GT T T T C W-3' ImHpHpHpHpPy-y-ImPYPYPYPYP
y 2037) 5' GT T T A T W-3' ImHpHplipPyHp-y-PYHpPYPYPyPy -W
2038) 5'-W GT T T A A W-3' ImHpHpHpPypy-Y-HpHpPyPyPypy 2039) 5' GT T T A G W-3' ImHpHpHpPyIm-Y-PyHpPyPyPypy -W
2040) 5'-W GT T T A C W-3' ImHpHpHpPYPy-y-ImHppyPYpypy 2041) 5' GT T T G T W-3' ImHpHpHpImHp-Y-PypypypyPYPy -W
2042) 5'-W GT T T G A W-3' ImHpHpHpImPy-y-HpPyPypypypy 2043) 5' GT T T G G W-3' ImHpHpHpImIm-y-pypypypypypy -W
2044) 5'-W GT T T G C W-3' ImHpHpHpImPy-y-ImPYPYPYPyPy 2045) 5' GT T T C T W-3' ImHplipHpPyHp-y-pyImPYPyPyPy -W
2046) 5'-W GT T T C A W-3' ImHpHpHpPyPy-Y-HpImPyPyPyPy 2047) 5'-W GT T T C G W-3' ImHpHpHpPyIm-y-PyImPYPYPYPy 2048) 5' GT T T C C W-3' ImHpHpHpPyPy-y-ImImPyPyPyPy -W
2049) 5'-W GT T A T T W-3' ImHpHpPyHpHp-Y-pypyHpPyPyPy 2050) 5' GT T A T A W-3' ImHpHpPyHpPy-Y-HpPyHppyPYPy -W
2051) 5' GT T A T G W-3' ImHpHpPyHpIm-y-PypyHppypypY
-W
2052) 5' GT T A T C W-3' ImHpHpPyHpPy-y-ImPyHpPYPyPy -W
2053) 5' GT T A A T W-3' ImApHppyPyHp-y-pyHpHpPyPyPy -W
2054) 5'-W GT T A A A W-3' ImHpHpPyPypy-y-HpHpHpPyPyPy 2055) 5'-W GT T A A G W-3' ImHpHpPyPyIm-y-PyHpHppyPyPy 2056) 5'-W GT T A A C W-3' ImHpHpPYPYPy-Y-ImHpHpPYPypy 2057) 5'-W GT T A G T W-3' ImHpHpPyImHp-y-pypygpPyPyPy 2058) 5'-W GT T A G A W-3' ImHpHpPyImPy-y-HpPyHpPyPypy 2059) 5'-W GT T A G G W-3' ImHpHpPyImIm-y-pypyHppypypy 2060) 5'-W GT T A G C W-3' ImHpHpPyImPy-y-ImPyHppypyPy 2061) 5' GT T A C T W-3' ImHpHpPyPyHp-y-Pyl~ppypyp~, -W
2062) 5'-W GT T A C A W-3' ImHpHpPyPyPy-y-HpImHpPYPypy 2063) 5'-W GT T A C G W-3' ImHpHpPyPYIm-y-Pyl~ppypypY
2064) 5' GT T A C C W-3' ImHpHpPyPyPy-Y-ImImHpPYPYpy -W
TABLE
111:
12-ring-I-lairpin Polyamides for recognition of 8-by 5'-WGTTSNNW-3' DNA aromatic amino acid sequence sequence 2065) 5' -WG T T G T TW-3' ImHpHpImHpHp-y-PyPyPyPyPyPy 2066) 5' -WG T T G T AW-3' ImHpHpImHpPy-y-HpPyPyPyPyPy 2067) 5' -WG T T G T GW-3' ImHpHpImHpIm-y-PyPyPyPyPyPy 2068) 5' -WG T T G T CW-3' ImHpHpImHpPy-y-ImPyPyPyPyPy 2069) 5' -WG T T G A TW-3' ImHpHpImPyHp-y-PyHpPyPyPyPy 2070) 5' -WG T T G A AW-3' ImHpHpImPyPy-y-HpHpPyPyPyPy 2071) 5' -WG T T G A GW-3' ImHpHpImPyIm-y-PyHpPyPyPyPy 2072) 5' -WG T T G A CW-3' ImHpHpImPyPy-y-ImHpPyPyPyPy 2073) 5' -WG T T G G TW-3' ImHpHpImImHp-y-PyPyPyPypypy 2074) 5' -WG T T G G AW-3' ImHpHpImImPy-y-HpPyPyPyPyPy 2075) 5' -WG T T G C TW-3' ImHpHpImPyHp-y-PyImPyPyPyPy 2076) 5' -WG T T G C AW-3' ImHpHpImPyPy-y-HpImPyPyPyPy 2077) 5' -WG T T G G GW-3' ImHpHpImImIm-y-PyPyPyPyPypy 2078) 5' -WG T T G G CW-3' ImHpHpImImPy-y-ImPyPyPyPyPy 2079) 5' -WG T T G C GW-3' ImHpHpImPyIm-y-PyImPyPyPyPy 2080) 5' -WG T T G C CW-3' ImHpHpImPyPy-y-ImImPyPyPyPy 2081) 5' -WG T T C T TW-3' ImlipHpPyHpHp-y-PyPyImPyPyPy 2082) 5' -WG T T C T AW-3' ImHpHpPyHpPy-y-HpPyImPyPyPy 2083) 5' -WG T T C T GW-3' ImHpHpPyHpIm-y-PyPyImPyPyPy 2084) 5' -WG T T C T CW-3' ImHpHpPyHpPy-y-ImPyImPyPyPy 2085) 5' -WG T T C A TW-3' ImHpHpPyPyHp-y-PyHpImPyPyPy 2086) 5' -WG T T C A AW-3' ImHpHpPyPyPy-y-HpHpImPyPyPy 2087) 5' -WG T T C A GW-3' ImHpHpPyPyIm-y-PyHpImPyPyPy 2088) 5' -WG T T C A CW-3' ImHpHpPyPyPy-y-ImHpImPyPyPy 2089) 5' -WG T T C G TW-3' ImHpHpPyImHp-y-PyPyImPyPyPy 2090) 5' -WG T T C G AW-3' ImHpHpPyImPy-y-HpPyImPyPyPy 2091) 5' -WG T T C C TW-3' ImHpHpPyPyFip-y-PyImImPyPyPy 2092) 5' -WG T T C C AW-3' ImHpHpPyPyPy-y-HpImImPyPyPy 2093) 5' -WG T T C G GW-3' ImHpHpPyImIm-y-PyPyImPyPyPy 2094) 5' -WG T T C G CW-3' ImHpHpPyImPy-y-ImPyImPyPyPy 2095) 5' -WG T T C C GW-3' ImHpHpPyPyIm-y-PyImImPyPyPy 2096) 5' -WG T T C C CW-3' ImHpHpPyPyPy-y-ImImImPyPyPy TABLE
I 12:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTAWNNW-3' DNA aromatic amino acid sequence sequence 2097) 5' -WG T AT T T W-3' ImHpPyHpHpHp-y-pypypyHppypy 2098) 5' -WG T AT T A W-3' ImHpPyHpHpPy-y-HpPyPyHpPyPy 2099) 5' -WG T AT T G W-3' ImHpPyApHpIm-y-PyPypyHpPyPy 2100) 5' -WG T AT T C W-3' ImHpPyHpHpPy-y-ImPyPyHpPyPy 2101) 5' -WG T AT A T W-3' ImHpPyHpPyHp-y-PyHpPyHppyPy 2102) 5' -WG T AT A A W-3' ImHpPyHpPyPy-y-HpHpPyHpPyPy 2103) 5' -WG T AT A G W-3' ImHpPyHpPyIm-y-PyHpPyHpPyPy 2104) 5' -WG T AT A C W-3' ImHpPyHpPyPy-y-ImHpPyHpPyPy 2105) 5' -WG T AT G T W-3' ImHpPyHpImHp-y-pypypyHppypy 2106) 5' -WG T AT G A W-3' ImHpPyHpImPy-y-HpPyPyHpPyPy 2107 5' -WG T AT G G W-3 ImHpPyHpImIm-y-PyPypyI-Ippypy ) ' 2108) 5' -WG T AT G C W-3' ImHpPyHpImPy-y-ImPyPyHpPypy 2109) 5' -WG T AT C T W-3' ImHpPyHpPyHp-y-PyImPyHpPyPy 2110) 5' -WG T AT C A W-3' ImHpPyHpPyPy-y-HpImPyHpPyPy 2111) 5' -WG T AT C G W-3' ImHpPyHpPyIm-y-PyImPyHpPyPy 2112) 5' -WG T AT C C W-3' ImHpPyHpPyPy-y-ImImPyHpPyPy 2113) 5' -WG T AA T T W-3' ImHpPyPyHpHp-y-PyPyHpHpPyPy 2114) 5' -WG T AA T A W-3' ImHpPyPyHpPy-y-HpPyHpHpPyPy 2115) 5' -WG T AA T G W-3' ImHpPyPyHpIm-y-PyPyHpHpPyPy 2116) 5' -WG T AA T C W-3' ImHpPyPyHpPy-y-ImPyHpHpPyPy 2117) 5' -WG T AA A T W-3' ImHpPyPyPyHp-y-PyHpApHpPyPy 2118 5' -WG T AA A A W-3 ImHpPyPyPyPy-y-HpHpHpHpPyPy ) ' 2119 5' -WG T AA A G W-3 ImHpPyPyPyIm-y-PyHpHpHpPyPy ) ' 2120) 5' -WG T AA A C W-3' ImHpPyPyPyPy-y-ImHpHpHpPyPy 2121) 5' -WG T AA G T W-3' ImHpPyPyImHp-y-PypyHpgpPypy 2122) 5' -WG T AA G A W-3' ImHpPyPyImPy-y-HppyHpHpPyPy 2123 5' -WG T AA G G W-3' ImHppyPyImIm-y-PyPyHpHpPyPy ) 2124) 5' -WG T AA G C W-3' ImHpPyPyImPy-y-ImPyHpHpPyPy 2125) 5' -WG T AA C T W-3' ImApPyPyPyHp-y-pyImHpHpPyPy 2126) 5' -WG T AA C A W-3' ImHpPyPyPyPy-y-HpImHpHpPyPy 2127) 5' -WG T AA C G W-3' ImHppyPyPyIm-y-PyImHpHpPyPy 2128) 5' -WG T AA C C W-3' ImHpPyPypyPy-y-ImImHpHpPyPy TABLE
1 I3:
I2-ring-Hairpin Polyamides for recognition of 8-by S'-WGTASNNW-3' DNA aromatic amino acid scquence sequence 2129) 5' -W GT AG T T W-3' ImHpPyImHpHp-y-PyPyPyHpPyPy 2130) 5''-W GT AG T A W-3' ImHpPyImHpPy-y-HpPyPyHpPyPy 2131) 5' -W GT AG T G W-3' ImHpPyImHpIm-y-PyPyPyHpPyPy 2132) 5' -W GT AG T C W-3' ImHpPyImHpPy-y-ImPyPyHpPyPy 2133) 5' -W GT AG A T W-3' ImHpPyImPyHp-y-PyHpPyHpPyPy 2134) 5' -W GT AG A A W-3' ImHpPyImPyPy-y-HpHpPyHpPyPy 2135} 5' -W GT AG A G W-3' ImHpPyImPyIm-y-PyHpPyHpPyPy 213 6 5' -W GT AG A C W-3 ImHpPyImPypy-y- ImHpPyHpPyPy ) ' 2137) 5' -W GT AG G T W-3' ImHpPyImImHp-y-PyPyPyHpPyPy 213 8 5' -W GT AG G A W-3 ImHpPyImImPy-y-HpPyPyHpPyPy ) ' 213 9 5' -W GT AG C T W-3 ImHpPyImPyHp-y-PyImPyHpPyPy ) ' 2140) 5' -W GT AG C A W-3' ImHpPyImPyPy-y-HpImPyHpPyPy 2141) 5' -W GT AG G G W-3' ImHpPyImImIm-y-PyPyPyHppyPy 2142) 5' -W GT AG G C W-3' ImHpPyImImPy-y-ImPyPyHpPyPy 2143 ) 5' -W GT AG C G W-3 ImHpPyImPyIm-y-PyImPyHpPyPy ' 2144) 5' -W GT AG C C W-3' ImHpPyImPyPy-y-ImImPyHpPyPy 2145) 5' -W GT AC T T W-3' ImHpPyPyHpHp-y-PyPyImHpPyPy 2146) 5' -W GT AC T A W-3' ImHpPyPyHpPy-y-HppyImHpPyPy 2147} 5' -W GT AC T G W-3' ImHpPyPyHpIm-y-PyPyImHpPyPy 2148) 5' -W GT AC T C W-3' ImHpPyPyHpPy-y-ImPyImHpPyPy 2149) 5' -W GT AC A T W-3' ImHpPyPyPyHp-y-PyHpImHpPyPy 2150) 5' -W GT AC A A W-3' ImHpPyPyPyPy-y-HpHpImHpPyPy 2151) 5' -W GT AC A G W-3' ImHpPyPyPyIm-y-PyHpImHpPyPy 2152) 5' -W GT AC A C W-3' ImHpPyPypyPy-y-ImHpImHpPyPy 2153) 5' -W GT AC G T W-3' ImHpPyPyImHp-y-PyPyImHpPyPy 2154) 5' -W GT AC G A W-3' ImHpPyPyImPy-y-HpPyImHpPyPy 2155) 5' -W GT AC C T W-3' ImHpPyPyPyHp-y-PyImImHpPyPy 2156) 5' -W GT AC C A W-3' ImHpPypyPyPy-y-HpImImHpPyPy 2157) 5' -W GT AC G G W-3' ImHpPyPyImIm-y-PyPyImHpPyPy 2158) 5' -W GT AC G C W-3' ImHpPyPyImPy-y-ImPyImHpPyPy 2159) 5' -W GT AC C G W-3' ImHpPyPyPyIm-y-PyImImHpPyPy 2160) 5' -W GT AC C C W-3' ImHpPyPyPyPy-y-ImImImHpPyPy _~.,.,,... _ , , , , .,.
WO 98/37067 , PCT/US98/01714 I
Al3Lt~
I
14:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTCWNNW-3' DNA aromatic amino acid sequence sequence 2161) 5'-W GT C T T T W-3' ImHpPyHpHpHp-y-Pypypylmpypy 2162) 5' GT C T T A W-3' ImHpPyHpHpPy-y-HpPyPyImPyPy -~n1 2163 ) 5' GT C T T G W-3 ImHpPyHpHpIm-y-PyPypyImPyPy -W ' 2164) 5'-W GT C T T C W-3' ImHpPYHpHpPy-y-ImPypyImPyPy 2165) 5'-W GT C T A T W-3' ImHpPyHpPyHp-y-PyHpPyImPyPy 2166) 5'-W GT C T A A W-3' ImHpPyHpPyPy-y-HpHpPyImpyPy 2167) 5'-W GT C T A G W-3' ImHppyHppYIm_Y_pYHppyImPyPy 2168) 5'-W GT C T A C W-3' ImHpPyHpPypy-y-ImHpPyImPyPy 2169) 5'-W GT C T G T W-3' ImHpPYHpImHp-y-PypypyImPyPy 2170) 5'-W GT C T G A W-3' ImHpPyHpImPy-y-HpPyPyImPyPy 2171) 5' GT C T G G W-3' ImHpPyHpImIm-y-PypypyzmPyPy -W
2172) 5' GT C T G C W-3' ImHpPyHpImPy-y-ImPyPyImPyPy -W
2173 ) 5' GT C T C T W-3' ImHpPyHpPyHp-y-PyImPyImPyPy -W
2174) 5' GT C T C A W-3' ImHpPyHpPYPy-y-HpImPyImPyPy -W
2175) 5' GT C T C G W-3' ImHppyHpPyIm-y-pyImPYImPyPy -W
2176) 5' GT C T C C W-3' ImHpPyHpPyPy-y-ImImPyImPyPy -W
2177 ) 5' GT C A T T W-3' ImHpPyPyHpHp-y-pypyHpImPYPy -W
2178) 5' GT C A T A W-3' ImHpPYPyHpPy-y-HpPYHpImPyPy -W
2179) 5' GT C A T G W-3' ImHpPyPyHpIm-y-PyPyHpImPyPy -W
2180) 5'-W GT C A T C W-3' ImHppypYHPPY_Y-ImPyHpImPyPy 2181) 5' GT C A A T W-3' ImHpPyPyPYHp-y-PyHpHpImPypy -W
2182) 5' GT C A A A W-3' ImHpPYPyPypy-Y-HpHpHpImPyPy -W
2183 ) 5' GT C A A G W-3' ImHpPyPyPyIm-Y-PyHpHpImPyPy -W
2184) 5' GT C A A C W-3' ImHpPyPypypy-Y-I~pHpImPyPy -W
2185) 5' GT C A G T W-3' ImHpPyPyImHp-y-PypyHpImPyPy -W
2186) 5'-W GT C A G A W-3' ImHppypylmpY_Y_HpPyHpImPyPy 2187) 5'-W GT C A G G W-3' ImHpPyPyImIm-y-PypygpImPyPy 2188) 5' GT C A G C W-3' ImHpPyPyImPy--W y -ImPyHpImPyPy 2189) 5'-W GT C A C T W-3' ImHpPyPyPyHp-Y-PyImHpImPyPy 2190) 5' GT C A C A W-3' ImHppypypypY_Y-HpImHpImpyPy -W
2191) 5' GT C A C G W-3' ImHpPypypylm-y-PyImHpImPyPy -W
2192) 5'-W GT C A C C W-3' ImHpPyPyPypy_y-ImImHpImPyPy WO 98/37067 , PCT/US98/01714 TABLE
115:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTCSNNW-3' DNA aromatic amino acid sequence sequence 2193) 5' -WG T C G TT W-3' ImHpPyImHpHp-y-PyPyPyImPyPy 2194) 5' -WG T C G TA W-3' ImHpPyImHpPy-y-HpPyPyImPyPy 2195) 5' -WG T C G TG W-3' ImHpPyImHpIm-y-PyPyPyImPyPy 2196) 5' -WG T C G TC W-3' ImHpPyImHpPy-y-ImPyPyImPyPy 2197) 5' -WG T C G AT W-3' ImHpPyImPyHp-y-PyHpPyImPyPy 2198) 5' -WG T C G AA W-3' ImHpPyImPyPy-y-HpHpPyImPyPy 2199) 5' -WG T C G AG W-3' ImHpPyImPyIm-y-PyHpPyImPyPy 2200) 5' -WG T C G AC W-3' ImHpPyImPyPy-y-ImHpPyImPyPy 2201) 5' -WG T C G GT W-3' ImHpPyImImHp-y-PyPyPyImPyPy 2202) 5' -WG T C G GA W-3' ImHpPyImImPy-y-HpPyPyImPyPy 2203) 5' -WG T C G CT W-3' ImHpPyImPyHp-y-PyImPyImPyPy 2204) 5' -WG T C G CA W-3' ImHpPyImPyPy-y-HpImPyImPyPy 2205) 5' -WG T C C TT W-3' ImHpPyPyHpHp-y-PyPyImImPyPy 2206) 5' -WG T C C.TA W-3' ImHpPyPyHpPy-y-HpPyImImPyPy 2207) 5' -WG T C C TG W-3' ImHpPyPyHpIm-y-PyPyImImPyPy 2208) 5' -WG T C C TC W-3' ImHpPyPyHpPy-y-ImPyImImPyPy 2209) 5' -WG T C C AT W-3' ImHpPyPyPyHp-y-PyHpImImPyPy 2210) 5' -WG T C C AA W-3' ImHpPyPyPyPy-y-HpHpImImPyPy 2211) 5' -WG T C C AG W-3' ImHpPyPyPyIm-y-PyHpImImPyPy 2212) 5' -WG T C C AC W-3' ImHpPyPyPyPy-y-ImHpImImPyPy 2213) 5' -WG T C C GT W-3' ImHpPyPyImHp-y-PyPyImImPyPy 2214) 5' -WG T C C GA W-3' ImHpPyPyImPy-y-HpPyImImPyPy 2215) 5' -WG T C C CT W-3' ImHpPyPyPyHp-y-PyImImImPyPy 2216) 5' -WG T C C CA W-3' ImHpPyPyPyPy-y-HpImImImPyPy 2217) 5' -WG T C G GG W-3' ImHpPyImImIm-y-PyPyPyImPyPy 2218) 5' -WG T C G GC W-3' ImHpPyImImPy-y-ImPyPyImPyPy 2219) 5' -WG T C G CG W-3' ImHpPyImPyIm-y-PyImPyImPyPy 2220) 5' -WG T C G CC W-3' ImHpPyImPyPy-y-ImImPyImPyPy 2221) 5' -WG T C C GG W-3' ImHpPyPyImIm-y-PyPyImImPyPy 2222) 5' -WG T C C GC W-3' ImHpPyPyImPy-y-ImPyImImPyPy 2223) 5' -WG T C C CG W-3' ImHpPyPyPyIm-y-PyImImImPyPy 2224) 5' -WG T C C CC W-3' ImHpPyPyPyPy-y-ImImImImPyPy TABLE 116:
12-ring Hairpin Polyamides for recognition of 8-by 5'WCGGWNNW-3' ' DNA aromatic amino acid sequence sequence 2225) 5'W C G G TT T W-3' PyImImHpHpHp-y-PyPypypypylm 2226) 5'W C G G TT A W-3' PyImImHpHpPy-y-HpPyPyPyPyim 2227 5' C G G TT G W-3' PyImImHpHpIm-y-PyPyPyPyPyIm ) W
2228) 5'W C G G TT C W-3' PyImImHpHpPy-y-ImPyPyPyPyIm 2229) 5'W C G G TA T W-3' PyImImHpPyHp-y-PyHpPyPyPyIm 223 0 5' C G G TA A W-3 ' PyImImHpPyPy-y-HpHpPyPyPyIm ) W
2231) 5'W C G G TA G W-3' PyImImHpPyIm-y-PyHpPyPyPyIm 2232) 5'W C G G TA C W-3' PyImImHpPyPy-y-ImHpPyPyPyIm 2233) 5'W C G G TG T W-3' PyImImHpImHp-y-PyPyPyPyPyIm 2234 5' C G G TG A W-3 ' PyImImHpImPy-y-HpPyPyPyPyIm ) W
2235) 5'W C G G TG G W-3' PyImImHpImIm-y-PyPyPypypyIm 2236) 5'W C G G TG C W-3' PyImImHpImPy-y-ImPyPyPyPyIm 2237) 5'W C G G TC T W-3' PyImImHpPyHp-y-PyImPyPyPyIm 223 8 5' C G G TC A W-3 ' PyImImHpPyPy-y-HpImPyPyPyIm ) W
223 9 5' C G G TC G W-3 ' PyImImHpPyIm-y-PyImPyPyPyIm ) W
2240) 5'W C G G TC C W-3' PyImImHpPyPy-y-ImImPyPyPyIm 2241) 5'W C G G AT T W-3' PyImImPyHpHp-y-PyPyHpPyPyIm 2242) 5'W C G G AT A W-3' PyImImPyHpPy-y-HpPyHpPyPyIm 2243 5' C G G AT G W-3 ' PyImImPyHpIm-y-PyPyHpPyPyIm ) W
2244) 5'W C G G AT C W-3' PyImImpyHpPy-y-ImPyHpPyPyIm 2245) 5'W C G G AA T W-3' PyImImPyPyHp-y-PyHpHpPyPyIm 2246) 5'W C G G AA A W-3' PyImImPyPyPy-y-HpHpHpPyPyIm 2247 5' C G G AA G W-3 ' PyImImPyPyIm-y-PyHpHpPyPyIm ) W
2248) 5'W C G G AA C W-3' PyImImPyPyPy-y-ImHpHpPyPyIm 2249) 5'W C G G AG T W-3' PyImImPyImHp-y-PyPyHpPyPyIm 2250) 5'W C G G AG A W-3' PyImImPyImPy-y-HpPyHpPyPyIm 2251) 5' C G G AG G W-3' PyImImPyImIm-y-PypyHpPyPyIm W
2252) 5'W C G G AG C W-3' PyImImPyImPy-y-ImPyHpPyPyIm 2253 5' C G G AC T W-3 ' PyImImPyPyHp-y-PyImHpPyPyIm ) W
2254) 5'W C G G AC A W-3' PyImImPyPyPy-y-HpImHpPyPyIm 2255) 5'W C G G AC G W-3' PyImImPyPyIm-y-PyImHpPyPyIm 2256) 5'W C G G AC C W-3' PyImImPyPyPy-y-ImImHpPyPyIm TABLE
117:
12-ring Hairpin Polyamides for recognition of 8-by 5'WCGGSNNW-3' DNA aromatic amino acid sequence sequence 2257) 5' W C G G GT T W-3' PyImImImHpHp-y-PyPyPyPyPyIm 2258) 5' W C G G GT A W-3' PyImImImHpPy-y-HpPyPyPyPyIm 2259) 5' W C G G GT G W-3' PyImImImHpIm-y-PyPyPyPyPyIm 2260) 5' W C G G GT C W-3' PyImImImHpPy-y-ImPyPyPyPyIm 2261) 5' W C G G GA T W-3' PyImImImPyHp-y-PyHpPyPyPyIm 2262) 5' W C G G GA A W-3' PyImImImPyPy-y-HpHpPyPyPyIm 2263) 5' W C G G GA G W-3' PyImImImPyIm-y-PyHpPyPyPyIm 2264) 5' W C G G GA C W-3' PyImImImPyPy-y-ImHpPyPyPyIm 2265) 5' W C G G GG T W-3' PyImImImImHp-y-PyPyPyPyPyIm 2266) 5' W C G G GG A W-3' PyImImImImPy-y-HpPyPyPyPyIm 2267) 5' W C G G GC T W-3' PyImImImPyHp-y-PyIircPyPyPyIm 226$) 5' W C G G GC A W-3' PyImImImPyPy-y-HpImPyPyPyIm 2269) 5' W C G G CT T W-3' PyImImPyHpHp-y-PyPyImPyPyIm 2270) 5' W C G G CT A W-3' PyImImPyHpPy-y-HpPyImPyPyIm 2271) 5' W C G G CT G W-3' PyImImPyHpIm-y-PyPyImPyPyIm 2272) 5' W C G G CT C W-3' PyImImPyHpPy-y-ImPyImPyPyIm 2273) 5' W C G G CA T W-3' PyImImPyPyHp-y-PyHpImPyPyIm 2274) 5' W C G G CA A W-3' PyImImPyPyPy-y-HpHpImPyPyIm 2275) 5' W C G G CA G W-3' PyImImPyPyIm-y-PyHpImPyPyIm 2276) 5' W C G G CA C W-3' PyImImPyPyPy-y-ImHpImPyPyIm 2277 5' W C G G CG T W-3 ' PyImImPyImHp-y-PyPyImPyPyIm ) 2278) 5' W C G G CG A W-3' PyImImPyImPy-y-HpPyImPyPyIm 227 9 5' W C G G CC T W-3 ' PyImImPyPyHp-y-PyImImPyPyIm ) 2280) 5' W C G G CC A W-3' PyImImPyPyPy-y-HpImImPyPyim G83) 5' W C G G GG G W-3' PyImImImImIm-y-PyPyPyPyPyIm G84) 5' W C G G GG C W-3' PyImImImImPy-y-ImPyPyPyPyIm G85) 5' W C G G GC G W-3' PyImImImPyIm-y-PyImPyPyPyIm G86 ) 5' W C G G GC C W-3 ' PyImImImPyPy-y-ImImPyPyPyIm G87 ) 5' W C G G CG G W-3 ' PyImImPyImIm-y-PyPyImPyPyIm G88) 5' W C G G CG C W-3' PyImImPyImPy-y-ImPyImPyPyIm G89) 5' W C G G CC G W-3' PyImImPyPyIm-y-PyImImPyPyIm G90) 5' W C G G CC C W-3' PyImImPyPyPy-y-ImImImPyPyIm WO 98/37067 . PCT/US98/01714 TABLE 12-ring 118: Hairpin Polyamides for recognition of 8-by 5'-WCGTWNNW-3' DNA aromatic amino acid sequence sequence 2281) 5'W C G T T T TW-3' PyImHpHpHpHp-y-PyPyPyPyPyIm 2282) 5'W C G T T T AW-3' PyImHpHpHpPy-y-HpPyPyPyPyIm 2283 ) 5' C G T T T GW-3 ' PyImHpHpHpIm-y-PyPyPyPyPyIm W
2284) 5'W C G T T T CW-3' PyImHpHpHpPy-y-ImPyPyPyPyIm 2285) 5'W C G T T A TW-3' PyImHpHpPyHp-y-PyHpPyPyPyIm 2286) 5'W C G T T A AW-3' PyImHpHpPyPy-y-HpHpPyPyPyIm 2287) 5'W C G T T A GW-3' PyImHpHpPyIm-y-PyHpPyPypyIm 2288) 5'W C G T T A CW-3' PyImHpHpPyPy-y-ImHpPyPyPyIm 2289) 5'W C G T T G TW-3' PyImHpHpImHp-y-PyPyPyPyPyIm 2290) 5'W C G T T G AW-3' PyImHpHpImPy-y-HpPypyPypylm 2291) 5'W C G T T G GW-3' PyImHpHpImIm-y-PyPyPyPyPyIm 2292) 5'W C G T T G CW-3' PyImHpHpImPy-y-ImPyPyPyPyIm 2293) 5'W C G T T C TW-3' PyImHpHpPyHp-y-PyTmPyPyPyIm 2294} 5'W C G T T C AW-3' PyImHpHpPyPy-y-HpImPyPyPyIm 2295) 5'W C G T T C GW-3' PyImHpHpPyIm-y-PyImPyPyPyIm 2296) 5'W C G T T C CW-3' PyImHpHpPyPy-y-ImImPyPyPyIm 2297) 5'W C G T A T TW-3' PyImHpPyHpHp-y-PyPyHpPyPyIm 2298) 5'W C G T A T AW-3' PyImHpPyHpPy-y-HpPyHpPyPyIm 2299) 5'W C G T A T GW-3' PyImHpPyHpIm-y-PyPyHpPyPyIm 2300} 5'W C G T A T CW-3' PyImHpPyHpPy-y-ImPyHpPyPyIm 2301) 5'W C G T A A TW-3' PyImHpPyPyHp-y-PyHpHpPyPyIm 2302) 5'W C G T A A AW-3' PyImHpPyPyPy-y-HpHpHpPyPyIm 2303) 5'W C G T A A GW-3' PyImHpPyPyim-y-PyHpHpPyPyim 2304) 5'W C G T A A CW-3' PyImHpPyPyPy-y-ImHpHpPyPyIm 2305) 5'W C G T A G TW-3' PyImHpPyImHp-y-PyPyHpPyPyIm 2306) 5'W C G T A G AW-3' PyImHpPyImPy-y-HpPyHpPyPyIm 2307) 5'W C G T A G GW-3' PyImHpPyImIm-y-PyPyHpPyPyIm 2308) 5'W C G T A G CW-3' PyImHpPyImPy-y-ImPyHpPyPyIm 2309) 5'W C G T A C TW-3' PyImHpPyPyHp-y-PyImHpPyPyIm 2310) 5'W C G T A C AW-3' PyImHpPyPyPy-y-HpImHpPyPyIm 2311) 5'W C G T A C GW-3' PyImHpPyPyIm-y-PyImHpPyPyIm 2312 ) 5' C G T A C CW-3 ' PyImHpPyPypy-y- ImImHpPyPyIm W
TABLE I 19: 12-ring-Hairpin Polyamides far recognition of 8-by 5'-WCGTSNNW-3' DNA sequence aromatic amino acid sequence 2313 ) 5' W C G T G T T W-3 ' PyImHpImHpHp-Y-PypypypypyIm 2314 ) 5' W C G T G T A W-3 ' PyImHpImHpPy-y-Hppypypypylm 2315) 5'W C G T G T G W-3' PyImHpImHpIm-y-PyPyPyPypyIm 2316 ) 5' W C G T G T C W-3 ' PyImHpImHpPy-y- ImPyPyPyPyIm 2317 ) 5' W C G T G A T W-3 ' PyImHpImPyHp-y-PyHpPyPyPyIm 2318) 5'W C G T G A A W-3' PyImHpImPyPy-y-HpHpPyPyPyIm 2319) 5'W C G T G A G W-3' PyImHpImPyIm-Y-PyHpPyPypyIm 2320) 5'W C G T G A C W-3' PyImHpImPyPy-y-ImHpPyPyPyIm 2321) 5'W C G T G G T W-3' PyImHpImImHp-y-pypypypypyim 2322) 5'W C G T G G A W-3' PyImHpImImPy-y-HPPyPyPyPyIm 2323) 5'W C G T G C T W-3' PyImHpImPyHp-y-pyImPyPyPyIm 2324) 5'W C G T G C A W-3' PyImHpImPyPy-y-HpImPyPyPyIm 2325) 5'W C G T G G G W-3' PyImHpImImIm-y-PyPyPyPyPyIm 2326) 5'W C G T G G C W-3' PyImApImImPy-y-ImPyPyPyPyIm 2327) 5'W C G T G C G W-3' PyImHpImPyIm-y-PyImPyPyPyIm 2328) 5'W C G T G C C W-3' PyImHpImPyPy-y-ImImPyPyPyIm 2329) 5'W C G T CT T W-3' PyImHpPyHpHp-y-PypyImPyPyIm 2330) 5' C G T CT A W-3' PyImHpPyHpPy-y-HpPyImPyPyIm W
2331) 5'W C G T CT G W-3' PyImHpPyI3pIm-y-PyPyImPyPyIm 2332) 5'W C G T CT C W-3' PyImHpPyHpPy-y-ImpyImPyPyIm 2333 ) 5' C G T CA T W-3' PyImHpPyPyHp-y-PyHpImPyPyIm W
2334 ) 5' C G T CA A W-3 ' PyImHpPyPyPy-y-HpHpImPyPyIm W
2335) 5'W C G T CA G W-3' PyImHppypylm-y-PyHpImPyPyIm 2336) 5'W C G T CA C W-3' PyImHpPyPyPy-y-ImHpImPyPyIm 2337 ) 5' C G T CG T W-3 ' PyImHpPyImHp-y-pypyImPyPyim W
2338) 5'W C G T CG A W-3' PyImHpPyImPy-y-HpPyImPyPyIm 2339) 5'W C G T CC T W-3' PyImHpPyPyHp-y-PyImImPyPyIm 2340) 5'W C G T CC A W-3' PyImHpPyPyPy-y-HpImImPyPyIm 2341) 5'W C G T CG G W-3' PyImHpPyImIm-y-pypyImPyPyIm 2342) 5'W C G T CG C W-3' PyImHpPyImPy-y-ImpyImPyPyIm 2343 ) 5' C G T CC G W-3 ' PyImHpPyPyIm-y-PyImImPyPyIm W
2 3 44 ) 5' C G T CC C W- 3 PyImHpPyPyPy-y- ImImImPyPyIm W ' 1A13LIr 120:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGAWNNW-3' DNA aromatic amino acid sequence sequence 2345) 5'W C GA T T T W-3' PyImPyHpHpHp-y-pypypyHppylm 2346) 5'W C GA T T A W-3' PyImPyHpHpPy-y-HpPyPyHpPyIm 2347) 5'W C GA T T G W-3' PyImpyHpHpIm-y-pyPypyHpPyIm 2348) 5'W C GA T T C W-3' PyImPyHpHpPy-y-ImPyPyHpPyIm 2349) 5'W C GA T A T W-3' PyImPyHpPyHp-y-PyHpPyHpPyIm 2350) 5'W C GA T A A W-3' pyImPyHpPyPy-y-HpHpPyHpPyIm 2351) 5'W C GA T A G W-3' PyImPyApPyIm-y-PyHpPyHpPyIm 2352) 5'W C GA T A C W-3' PyImPyHpPyPy-y-ImHpPyHpPyIm 2353) 5'W C GA T G T W-3' PyImPyHpImHp-y-Pypypygppylm 2354 ) 5' C GA T G A W-3 ' PyImPyHpImPy-y-HpPyPyHpPyIm W
2355) 5'W C GA T G G W-3' PyImPyHpImIm-y-PyPyPyHpPyIm 2356) 5'W C GA T G C W-3' PyImPyHpImPy-y-ImPyPyHpPyIm 2357) 5'W C GA T C T W-3' PyImPyHpPyHp-y-PyImPyHpPyIm 2358) 5'W C GA T C A W-3' PyImPyHpPyPy-y-HpImPyHpPyIm 2359) 5'W C GA T C G W-3' PyImPyHpPyIm-y-PyImPyHpPyIm 2360) 5'W C GA T C C W-3' PyImPyHpPyPy-y-ImImPyHpPyIm 2361) 5'W C GA A T T W-3' PyImPyPyHpHp-y-PypyHpHpPyIm 2362) 5'W C GA A T A W-3' PyImPyPyHpPy-y-HpPyHpHpPyIm 2363) 5'W C GA A T G W-3' PyImPyPyHpIm-y-PypyHpHpPyIm 2364) 5'W C GA A T C W-3' PyImPyPyHpPy-y-ImPyHpHpPyIm 2365) 5'W C GA A A T W-3' PyImPyPyPyHp-y-PyHpHpHpPyIm 2366) 5'W C GA A A A W-3' PyImPyPyPyPy-y-HpHpHpHpPyIm 2367) 5'W C GA A A G W-3' PyImPyPypylm-y-PyHpHpHpPyIm 2368) 5'W C GA A A C W-3' PyImPyPyPyPy-y-ImHpHpHpPyIm 2369) 5'W C GA A G T W-3' PyImPyPyImHp-y-PyPyHpHpPyIm 2370) 5'W C GA A G A W-3' PyImPyPyImPy-y-HpPyHpHpPyIm 2371) 5'W C GA A G G W-3' PyImPyPyImIm-y-PyPyHpHpPyIm 2372) 5'W C GA A G C W-3' yImPypyImPy-y-ImPyHpHpPyIm P
. 2373 ) 5' C GA A C T W-3 ' PyImPyPypyHp-y-PyImHpHpPyIm W
2374 ) 5' C GA A C A W-3' PyImPyPyPyPy-y-HpImHpHpPyIm W
2375) 5'W C GA A C G W-3' PyImPyPyPyIm-y-PyImHpHpPyIm 2376) 5'W C GA A C C W-3' PyImPyPyPyPy-y-ImImHpIipPyIm TABLE
121:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGASNNW-3' DNA aromatic amino acid sequence sequence 2377) 5'W C G A GT T W-3' PyImPyImHpHp-y-PyPyPyHpPyIm 2378) 5'W C G A GT A W-3' PyImPyImHpPy-y-HpPyPyHppyIm 2379) 5'W C G A GT G W-3' PyImPyImHpIm-y-PyPyPyHpPyIm 2380) 5'W C G A GT C W-3' PyImPyImHpPy-y-ImPyPyHpPyIm 2381) 5'W C G A GA T W-3' PyImPyImPyHp-y-PyHpPyHpPyIm 2382) 5'W C G A GA A W-3' PyImPyImPyPy-y-HpHpPyHpPyIm 2383) 5'W C G A GA G W-3' PyImPyImPyIm-y-PyHpPyHpPyIm 2384) 5'W C G A GA C W-3' PyImPyImPyPy-y-ImHpPyHpPyIm 2385) 5'W C G A GG T W-3' PyImPyImImHp-y-PyPyPyHpPyIm 2386) 5'W C G A GG A W-3' PyImPyImImPy-y-HpPyPyHpPyIm 2387) 5'W C G A GC T W-3' PyImPyImPyHp-y-PyImPyHpPyIm 2388) 5'W C G A GC A W-3' PyImPyImPyPy-y-HpImPyHpPyIm 2389) 5'W C G A GG G W-3' PyImPyImImIm-y-PyPyPyHpPyIm 2390) 5'W C G A GG C W-3' PyImPyImImPy-y-ImPyPyHpPyIm 2391) 5'W C G A GC G W-3' PyImPyImPyIm-y-PyImPyHpPyIm 2392) 5'W C G A GC C W-3' PyImPyImPyPy-y-ImImPyHpPyim 2393) 5'W C G A CT T W-3' PyImPyPyHpHp-y-PyPyImHpPyIm 2394) 5'W C G A CT A W-3' PyImPyPyHpPy-y-HpPyImHpPyIm 2395) 5'W C G A CT G W-3' PyImPyPyHpIm-y-PyPyImHpPyIm 2396) 5'W C G A CT C W-3' PyImPyPyHpPy-y-ImPyImHpPyIm 2397) 5'W C G A CA T W-3' PyImPyPyPyHp-y-PyHpImHpPyIm 2398) 5'W C G A CA A W-3' PyImPyPyPyPy-y-HpHpImHpPyIm 2399) 5'W C G A CA G W-3' PyImPyPyPyIm-y-PyHpImHpPyIm 2400) 5'W C G A CA C W-3' PyImPyPyPyPy-y-ImHpImHpPyIm 2401) 5'W C G A CG T W-3' PyImPyPyImHp-y-PyPyImHpPyIm 2402) 5'W C G A CG A W-3' PyImPyPyImPy-y-HpPyImHpPyIm 2403) 5'W C G A CC T W-3' PyImPyPyPyHp-y-PyImImHpPyIm 2404 5' C G A CC A W-3 PyImPyPyPyPy-y-HpImImHpPyIm ) W ' 2405) 5'W C G A CG G W-3' PyImPyPyImIm-y-PyPyImHpPyIm 2406) 5'W C G A CG C W-3' PyImPyPyImPy-y-ImPyImFFpPyIm 2407) 5'W C G A CC G W-3' PyImPyPyPyIm-y-PyImImHpPyIm 2408) 5'W C G A CC C W-3' PyImPyPyPyPy-y-ImImImHpPyIm TABLE 12-ring I22: Hairpin Polyamides for recognition of 8-by 5'-WCGCWNNW-3' DNA aromatic amino acid sequence sequence 2409) 5'W CG C T T T W-3' PyImPyHpHpHp-y-pypypyImPyIm 2410 ) 5' CG C T T A W-3 ' PyImPyHpHpPy-y-HpPyPyImPyIm TnT
2411) 5'W CG C T T G W-3' PyImPyHpHpIm-y-PypypyImPyIm 2412) 5'W CG C T T C W-3' PyImPyHpHpPy-y-ImPyPyImPyIm 2413 ) 5' CG C T A T W-3 ' PyImPyHpPyHp-y-PyHpPyImPyIm W
2414 ) 5' CG C T A A W-3 ' PyImPyHpPyPy-y-HpHpPyImPyIm W
2415 ) 5' CG C T A G W-3 T PyImPyHpPyIm-y-PyHpPyImPyIm W
2416) 5'W CG C T A C W-3' PyImPyHpPyPy-y-ImHpPyImPyIm 2417) 5'W CG C T G T W-3' PyImPyHpImHp-y-PyPypyImPyIm 2418 ) 5' CG C T G A W-3 ' PyImPyHpItttPy-y-HpPyPyImPyIm W
2419 ) 5' CG C T G G W-3' PyImPyHpImIm-y-PyPyPyImPyIm W
2420) 5'W CG C T G C W-3' PyImPyHpImPy-y-ImPyPyImPyIm 2421) 5'W CG C T C T W-3' PyImPyHpPyHp-y-PyImPyImPyIm 2422) 5'W CG C T C A W-3' PyImPyHpPyPy-y-HpImPyImPyIm 2423 ) 5' CG C T C G W-3' PyImPyHpPyIm-y-PyImPyImPyIm W
2424) 5'W CG C T C C W-3' PyImPyHpPyPy-y-ImImPyImPyIm 2425) 5'W CG C A T T W-3' PyImPyPyHpHp-y-pyPyHpimPyIm 2426 ) 5' CG C A T A W-3 ' PyImPyPyHppy-y-HpPyHpImPyIm W
2427 ) 5' CG C A T G W-3 ' PyImPypyHpIm-y-PyPyHpImPyIm W
2428) 5'W CG C A T C W-3' PyImPyPyHpPy-y-ImPyHpImPyIm 2429) 5'W CG C A A T W-3' PyImPyPyPyHp-y-PyHpHpImPyIm 2430) 5'W CG C A A A W-3' PyImPyPyPyPy-y-HpHpHpImPyIm 2431) 5'W CG C A A G W-3' PyImPyPyPyIm-y-PyHpHpImPyIm 2432) 5'W CG C A A C W-3' PyImPyPyPyPy-y-ImHpHpImPyIm 2433) 5'4JCG C A G T W-3' PyImPyPyImHp-y-PyPyHpImPyIm - 2434) 5'W CG C A G A W-3' PyImPyPyImPy-y-HpPyHpImPyIm 2435) 5'W CG C A G G W-3' PyImPyPyImIm-y-PyPyHpImPyIm 24 3 6 5' CG C A G C W-3 ' PyImPyPyImPy-y- ImPyHpImPyIm ) W
2437 ) 5' CG C A C T W-3' pyImPyPyPyHp-y-PyImHpImPyIm W
2438) 5'W CG C A C A W-3' PyImPyPyPyPy-y-HpImHpImPyIm _ 2439) 5'W CG C A C G W-3' PyImPyPyPyIm-y-PyImHpImPyIm 2440) 5'W CG C A C C W-3' PyImPyPyPyPy-y-ImImHpImPyim WO 9$/37067 PCT/US98/01714 TABLE 123:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGCSNNW-3' DNA aromatic amino acid sequence sequence 2441) 5' W C GC GT T W-3' PyImPyImApHp-y-PyPyPyImPyIm 2442) 5' W C GC GT A W-3' PyImPyImHpPy-y-HpPyPyImPyIm 2443) 5' W C GC GT G W-3' PyImPyImHpIm-y-PyPyPyImPyIm 2444) 5' W C GC GT C W-3' PyImPyImHpPy-y-ImPyPyImPyIm 2445) 5' W C GC GA T W-3' PyImPyImPyHp-y-PyHpPyImPyIm 2446) 5' W C GC GA A W-3' PyImPyImPyPy-y-HpHpPyImPyim 2447) 5' W C GC GA G W-3' PyImPyImPyIm-y-PyHpPyImPyIm 2448) 5' W C GC GA C W-3' PyImPyImPyPy-y-ImHpPyImPyIm 2449) 5' W C GC GG T W-3' PyImPyImImHp-y-PyPyPyImPyim 2450) 5' W C GC GG A W-3' PyImPyImImPy-y-HpPyPyImPyIm 2451) 5' W C GC GC T W-3' PyImPyImPyHp-y-PyImPyImPyIm IS 2452) 5' W C GC GC A W-3' PyImPyImPyPy-y-HpImPyImPyIm 2453) 5' W C GC CT T W-3' PyImPyPyHpHp-y-PyPyImImPyIm 2454 5' W C GC CT A W-3 ' PyImPyPyHpPy-y-HpPyImImPyIm ) 2455) 5' W C GC CT G W-3' PyImPyPyHpIm-y-PyPyImImPyIm 2456 5' W C GC CT C W-3' PyImPyPyHpPy-y-ImPyImImPyIm ) 2457 5' W C GC CA T W-3' PyImPyPyPyHp-y-PyHpImImPyIm ) 2458) 5' W C GC CA A W-3' PyImPyPyPyPy-y-HpHpImImPyIm 2459) 5' W C GC CA G W-3' PyImPyPyPyIm-y-PyHpImImPyIm 2460) 5' W C GC CA C W-3' PyImPyPyPyPy-y-ImHpImImPyIm 2461) 5' W C GC CG T W-3' PyImPyPyImHp-y-PyPyImImPyIm 2462 5' W C GC CG A W-3' PyImPyPyImPy-y-HpPyImImPyIm ) 2463) 5' W C GC CC T W-3' PyImPyPyPyHp-y-PyImImImPyIm 2464) 5' W C GC CC A W-3' Py3mPyPyPyPy-y-HpImImImPyIm G91) 5' W C GC GG G W-3' PyImPyImImIm-y-PyPyPyImPyIm G92 ) 5' W C GC GG C W-3' PyImPyImImPy-y-ImPyPyImPyIm G93 ) 5' W C GC GC G W-3' PyImPyImPyIm-y-PyImPyImPyIm G94) 5' W C GC GC C W-3' PyImPyImPyPy-y-ImImPyImPyIm G95) 5' W C GC CG G W-3' PyImPyPyImIm-y-PyPyImImPyIm G96) 5' W C GC CG C W-3 ' PyImPyPyImPy-y-ImPyImImPyIm G97 ) 5' W C GC CC G W- 3 PyImPyPyPyIm-y-PyImImImPyIm ' G98) 5' W C GC CC C W-3' PyImPyPyPyPy-y-ImImImImPyIm TABLE
124:
12-ring Hairpin Polyamides for recognition of 8-by S'-WCCGWNNW-3' DNA aromatic amino acid sequence sequence 2465) 5'W C C G T T TW-3' PyPyImHpHpHp-y-PypypypyImIm S 2466) 5'W C C G T T AW-3' PyPyImHpHpPy-y-HpPyPypyImlm 2467) 5'W C C G T T GW-3' PyPyImHpHpIm-y-pyPypypylmlm 2468) 5'W C C G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyImIm 2469) 5'W C C G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyImIm 247 0 5' C C G T A AW-3 ' PyPyImHppyPy-y-HpHpPyPyImIm ) W
2471) 5'W C C G T A GW-3' PyPyImHpPyIm-y-PyHpPyPyImIm 2472) 5' C C G T A CW-3' PyPyImHpPyPy-y-ImHpPyPyImIm W
2473) 5'W C C G T G TW-3' PyPyImHpImHp_y-PyPypypylmlm 2474) 5'W C C G T G AW-3' PyPyImHpImPy-y-HpPyPyPyImIm 2475) 5'W C C G T G GW-3' PyPyImHpImIm-y-pyPypypylmlm 1S 2476) 5'W C C G T G CW-3' PyPyImHpImPy-y-ImpyPyPyImIm 2477 5' C C G T C TW-3 ' PyPyImHpPyHp-y-PyImPyPyImIm ) W
2478) 5'W C C G T C AW-3' PyPyImHpPyPy-y-HpImPyPyImIm 247 9 5' C C G T C GW-3 ' PyPyImHpPyIm-y-PyImPypyImlm ) W
2480) 5'W C C G T C CW-3' PyPyImHpPypy-y-ImImPyPyImIm 2481) 5'W C C G A T TW-3' PyPyImPyHpHp-y-PyPyHpPyImIm 2482) 5'W C C G A T AW-3' PyPyImPyHpPy-y-HpPyHppyImIm 2483) 5'W C C G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyImIm 2484) 5'W C C G A T CW-3' PyPyImPyHpPy-y-ImPyHpPyImIm 2485) 5'W C C G A A TW-3' PyPyImPyPyHp-y-PyHpHppyImlm 2S 2486) 5'W C C G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyImIm 2487) 5'W C C G A A GW-3' PyPyImPyPyIm-y-PyHpHpPyImIm 2488) 5'W C C G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyImIm 2489) 5'W C C G A G TW-3' PyPyImPyImHp-y-PyPyHpPyImIm 2490) 5'W C C G A G AW-3' PyPyImPyImPy-y-HppyHpPyImIm 2491) 5'W C C G A G GW-3' PyPyImPyImIm-y-PypyHpPyImIm 2492) 5'W C C G A G CW-3' PyPyImPyImPy-y-ImPyHpPyImIm 2493 5' C C G A C TW-3 ' PyPyImPypyHp-y-PyImHppyImIm ) W
24 94 5' C C G A C AW-3 ' PyPyImPyPyPy-y-HpImHpPyImIm ) W
_ 2495) 5'W C C G A C GW-3' PyPyImPyPyIm-y-PyImHpPyImIm 3S 2496) 5'W C C G A C CW-3' PyPyImPyPyPy-y-ImImHpPyImIm WO 98137067 , PCT/US98/01714 TABLE
125:
12-ring-Hairpin Polyamides for recognition of 8-by 5'-WCCGSNNW-3' DNA aromatic amino acid sequence sequence 2497) 5'W C C G G T TW-3' PyPyImImHpHp-y-PyPyPyPyImIm 2498} 5''W C C G G T AW-3' PyPyImImHpPy-y-HpPyPyPyImIm 2499) 5'W C C G G T GW-3' PyPyImImHpIm-y-PyPyPyPyImIm 2500) 5'W C C G G T CW-3' PyPyImImHpPy-y-ImPyPyPyImIm 2501) 5'W C C G G A TW-3' PyPyImImPyHp-y-PyHpPyPyImIm 2502) 5'W C C G G A AW-3' PyPyImImPyPy-y-HpHpPyPyImIm 2503 5' C C G G A GW-3 ' PyPyImImPyIm-y-PyHpPyPyImIm ) W
2504 5' C C G G A CW-3 ' PyPyImImPyPy-y-ImHpPyPyImIm ) W
2505) 5'W C C G G G TW-3' PyPyImImImHp-y-PyPyPyPyImIm 2506) 5'W C C G G G AW-3' PyPyImImImPy-y-HpPyPyPyImIm 2507) 5'W C C G G C TW-3' PyPyImImPyHp-y-PyImPyPyImIm 2508) 5'W C C G G C AW-3' PyPyImImPyPy-y-HpImPyPyImIm 2509) 5'W C C G C T TW-3' PyPyImPyHpHp-y-PyPyImPyImIm 2510 5' C C G C T AW-3' PyPyImPyHpPy-y-HpPyImPyImIm ) W
2511) 5'W C C G C T GW-3' PyPyImPyHpIm-y-PyPyImPyImIm 2512 5' C C G C T CW-3 ' PyPyImPyHpPy-y-ImPyImPyImIm ) W
2513 5' C C G C A TW-3' PyPyImPyPyHp-y-PyHpImPyImIm ) W
2514 5' C C G C A AW-3 ' PyPyImPyPyPy-y-HpHpImPyImIm ) W
2515 5' C C G C A GW-3 ' PyPyImPyPyIm-y-PyHpImPyImIm } W
2516) 5'W C C G C A CW-3' PyPyImPyPyPy-y-ImHpImPyImIm 2517 5' C C G C G TW-3 ' PyPyImPyImHp-y-PyPyImPyImIm ) W
2 518 5' C C G C G AW-3 ' PyPyImPyImPy-y-HpPyImPyImIm ) W
2519 5' C C G C C TW-3 ' PyPyImPyPyHp-y-PyImImPyImIm ) W
2520) 5'W C C G C C AW-3' PyPyImPyPyPy-y-HpImImPyImIm G99) 5'W C C G G G GW-3' PyPyImImImIm-y-PyPyPyPyImIm 6100) 5'W C C G G G CW-3' PyPyImImImPy-y-ImPyPyPyImIm 6101) 5'W C C G G C GW-3' PyPyImImPyIm-y-PyImPyPyImIm 6102) 5'W C C G G C CW-3' PyPyImImPyPy-y-ImImPyPyImIm 6103 5' C C G C G GW-3 ' PyPyImPyImIm-y-PyPyImPyImIm ) W
6104) 5'W C C G C G CW-3' PyPyImPyImPy-y-ImPyImPyImIm 6105) 5'W C C G C C GW-3' PyPyImPyPyIm-y-PyImImPyImIm 6106) 5'W C C G C C CW-3' PyPyImPyPyPy-y-ImImImPyImIm ~w_ ...~,.. . . , 1'A13LE
I26:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCTWNNW-3' DNA aromatic amino acid sequence sequence 2521) 5'W C C TT T T W-3' PyPyHpHpHpHp-y-PyPyPypyImIm 2522) 5'W C C TT T A W-3' PyPyHpHpHpPy-y-HpPyPyPyImIm 2523) 5'W C C TT T G W-3' PyPyHpHpHpIm-y-PyPyPyPyImIm 2524) 5'W C C TT T C W-3' PyPyHpHpHpPy-y-ImPyPypyImlm 2525) 5'W C C TT A T W-3' PyPyHpHpPyHp-y-PyHpPyPyImIm 2526) 5'W C C TT A A W-3' PyPyHpHpPyPy-y-HpHpPypyImIm 2527 ) 5' C C TT A G W-3' PyPyHpHpPyIm-y-PyHpPyPyImIm W
2528) 5'W C C TT A C W-3' PyPyHpHpPyPy-y-ImHppyPyImIm 2529) 5'W C C TT G T W-3' PyPyHpHpImHp-y-PyPyPyPyImIm 2530) 5'W C C TT G A W-3' PyPyHpHpImPy-y-HpPyPyPyImIm 2531) 5'W C C TT G G W-3' PyPyHpHpImIm-y-pypypypyImlm 2532) 5'W C C TT G C W-3' PyPyHpHpImPy-y-ImPyPyPyImIm 2533) 5'W C C TT C T W-3' PyPyHpHpPyHp-y-PyImPyPyImIm 2534 ) 5' C C TT C A W-3' PyPyHpHpPyPy-y-HpImPyPyImIm W
2535) 5'W C C TT C G W-3' PyPyHpI-ipPyIm-y-PyImPyPyImIm 2536) 5'W C C TT C C W-3' PypyHpHpPyPy-y-ImImPyPyImIm 2537) 5'W C C TA T T W-3' PyPyIipPyHpHp-y-PyPyHpPyImIm 2538) 5'W C C TA T A W-3' PyPyHpPyHpPy-y-HpPyHpPyImIm 2539) 5'W C C TA T G W-3' PyPyHpPyHpIm-y-PyPyHppyImlm 2540 ) 5' C C TA T C W-3 PyPyHpPyHpPy-y-ImPyHpPyImIm W ' 2541) 5'W C C TA A T W-3' PyPyHpPyPyHp-y-PyHpHpPyImIm 2542) 5'W C C TA A A W-3' PyPyHpPyPyPy-y-HpHplipPyImIm 2543) 5'W C C TA A G W-3' PyPyHpPyPyIm-y-PyHpHpPyImIm 2544) 5'W C C TA A C W-3' PyPyHpPyPyPy-y-ImHpHpPyImIm 2545) 5'W C C TA G T W-3' PyPyHpPyImHp-y-PyPyHpPyImIm 2546) 5'W C C TA G A W-3' PyPyHpPyImPy-y-HpPyHpPyImIm 2547 ) 5' C C TA G G W-3 PyPyHpPyImIm-y-PyPyHpPyImIm W ' 2548) 5'W C C TA G C W-3' PyPyHpPyImPy-y-ImPyFipPyImIm 2549) 5'W C C TA C T W-3' PypyHpPyPyHp-y-PyImHpPyImIm 2550) 5'W C C TA C A W-3' PyPyHpPyPyPy-y-HpImHpPyImIm 2551) 5'W C C TA C G W-3' PyPyHpPypyIm-y-PyImHpPyImIm 2552) 5'W C C TA C C W-3' PyPyHpPyPyPy-y-ImImHpPyImIm WO 98137067 , PCTIUS98/01714 TABLE
127:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCTSNNW-3' DNA aromatic amino acid sequence sequence 2553 5' C C T GT T W-3 ' PyPyHpImHpHp-y-PyPyPyPyImIm ) W
2554) 5'W C C T GT A W-3' PyPyHpImHpPy-y-HpPyPyPyImIm 2555) 5'W C C T GT G W-3' PyPyHpImFipIm-y-PyPyPyPyImIm 2556) 5'W C C T GT C W-3' PyPyHpImHpPy-y-ImPyPyPyImIm 2557 5' C C T GA T W-3 ' PyPyHpImPyHp-y-PyHpPyPyImIm ) W
2558) 5'W C C T GA A W-3' PyPyHpImPyPy-y-HpHpPyPyImIm 2559) 5'W C C T GA G W-3' PyPyHpImPyIm-y-PyHpPyPyImIm 2560) 5'W C C T GA C W-3' PyPyHpImPyPy-y-ImHpPyPyImIm 2561} 5'W C C T GG T W-3' PyPyHpImImHp-y-PyPyPypyImlm 2562) 5'W C C T GG A W-3' PyPyHpImImPy-y-HpPyPyPyImIm 2563) 5'W C C T GC T W-3' PyPyHpImPyHp-y-PyImPyPyImIm 2564) 5'W C C T GC A W-3' PyPyHpImPyPy-y-HpImPyPyImIm 2565) 5'W C C T GG G W-3' PypyHpImImIm-y-PyPyPyPyImIm 2566) 5'W C C T GG C W-3' PyPyHpImImPy-y-ImPyPyPyImIm 2567 5' C C T GC G W-3 ' PyPyHpImPyIm-y-PyImPyPyImIm ) W
2568) 5'W C C T GC C W-3' PyPyHpImPyPy-y-ImImPyPyImIm 2569) 5'W C C T CT T W-3' PyPyHpPyHpHp-y-PyPyImpyImlm 2570) 5'W C C T CT A W-3' PyPyHpPyHpPy-y-HpPyImPyImIm 2571) 5'W C C T CT G W-3' PyPyHpPyHpIm-y-PyPyImPyImIm 2572) 5'W C C T CT C W-3' PyPyHpPyHpPy-y-ImPyImPyImIm 2573) 5'W C C T CA T W-3' PyPyHpPyPyHp-y-PyHpImPyImIm 2574) 5'W C C T CA A W-3' PyPyHpPyPyPy-y-HpHpImPyImIm 2575) 5'W C C T CA G W-3' PyPyHpPyPyIm-y-PyHpImPyImIm 2 57 5' C C T CA C W-3 ' PyPyHpPyPyPy-y- ImHp ImPyImIm 6 } W
2577) 5'W C C T CG T W-3' PyPyHpPyImHp-y-PyPyImpyImIm 2578) 5'W C C T CG A W-3' PyPyHpPyImPy-y-HpPyImPyImIm 2579) 5'W C C T CC T W-3' PyPyHpPyPyF-Ip-y-PyImImPyImIm 2580) 5'W C C T CC A W-3' PypyHpPyPyPy-y-HpImImPyImIm 2581) 5'W C C T CG G W-3' PyPyHpPyImIm-y-PyPyImPyImIm 2582) 5'W C C T CG C W-3' PyPyHpPyImPy-y-ImPyImPyImIm 2583) 5'W C C T CC G W-3' PyPyHpPyPyIm-y-PyImImPyImIm 2584) 5'W C C T CC C W-3' PyPyHpPyPyPy-y-ImImImPyImIm 128:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCAWNNW-3' DNA aromatic amino acid sequence sequence 2585) 5'W CC A T T T W-3' PyPyPyHpHpHp-y-PyPypygpImIm 2586) 5'W CC A T T A W-3' PyPyPyHpHpPy-y-HpPyPyHpImIm 2587) 5'W CC A T T G W-3' PyPypyHpHpIm-y-PyPypyHpImIm 2588) 5'W CC A T T C W-3' PyPyPyHpHpPy-y-ImPyPyHpImIm 2589 ) 5' CC A T A T W-3' PyPyPyHpPyHp-y-PyHpPyHpImIm W
2590) 5'W CC A T A A W-3' PyPyPyHpPyPy-y-HpHpPyHpImIm 2591) 5'W CC A T A G W-3' PyPyPyHpPyIm-y-PyHpPyHpImIm 2592) 5'W CC A T A C W-3' PyPyPyHpPyPy-y-ImHpPyHpImIm 2593) 5'W C C A T G T W-3' PyPyPyHpImHp-y-PyPyPyHpImIm 2594) 5'W C C A T G A W-3' PyPyPyHpImPy-y-HpPyPyHpImIm 2595) 5'W C C A T G G W-3' PyPyPyHpImIm-y-PypypyHpImIm 2596) 5'W C C A T G C W-3' PyPyPyHpImPy-y-ImPyPyHpImIm 2597) 5'W C C A T C T W-3' PyPyPyHpPyHp-y-pyImPyHpImIm 2598) 5'W C C A T C A W-3' PyPyPyHpPypy-y-HpImPyHpImIm 2599) 5'W C C A T C G W-3' PyPyPyHpPyIm-y-PyImPyHpImIm 2600) 5'W C CA T C C W-3' PyPyPyHpPyPy-y-ImImPyHpImIm 2601) 5'W C CA A T T W-3' PyPyPyPyHpHp-y-PyPyHpHpImIm 2602) 5'W C CA A T A W-3' PyPyPyPyHpPy-y-HpPyHpHpImIm 2603) 5'W C CA A T G W-3' PyPyPyPyHpIm-y-PypyHpHpImIm 2604) 5'W C CA A T C W-3' PyPyPyPyHpPy-y-ImPyHpHpImIm 2605) 5'W C CA A A T W-3' PyPyPyPypyHp-y-pyHpHpHpImIm 2606) 5'W C CA A A A W-3' PyPyPyPyPyPy-y-HpHpHpHpImIm 2607) 5'W C CA A A G W-3' PyPyPypypyIm-y-PyHpHpHpImIm 2608) 5'W C CA A A C W-3' PyPyPyPyPyPy-y-ImHpHpHpImIm 2609) 5'W C CA A G T W-3' PyPyPyPyImHp-y-PyPyHpHpImIm 2610 ) 5' C CA A G A W-3 PyPyPyPyImPy-y-HpPyHpHpImIm W ' 2611) 5'W C CA A G G W-3' PyPyPyPyImIm-y-PyPyHpHpImIm 2 612 ) 5' C CA A G C W-3 yPyPyPyImPy-y- ImPyHpHpImIm W P ' 2613) 5'W C CA A C T W-3' PyPyPyPypyHp-y-PyImHpHpImIm 2 614 ) 5' C CA A C A W-3 PyPyPyPypypy-y-HpI~pHpImIm W ' _ 2615) 5'W C CA A C G W-3' pyPypypypylm-y-pyi~pHpimim 2616) 5'W C CA A C C W-3' PypyPypypypy-y-ImImHpHpImIm TABLE
129:
12-ring Hairpin Polyamides for recognition of 8-by S'-WCCASNNW-3' DNA aromatic amino acid sequence sequence 2617 ) 5' C CA GT T W-3 PyPyPyImHpHp-y-PyPyPyHpImIm W ' 2618) 5'~W C CA GT A W-3' PyPyPyImHpPy-y-HpPyPyHpImIm 2619) 5'W C CA GT G W-3' PyPyPyImHpIm-y-PyPyPyHpImIm 2620) 5'W C CA GT C W-3' PyPyPyImHpPy-y-ImPyPyHpImIm 2621) 5'W C CA GA T W-3' PyPypyImPyHp-y-PyHpPyHpImIm 2622) 5'W C CA GA A W-3' PyPypyImPyPy-y-HpHpPyHpImIm 2623) 5'W C CA GA G W-3' PyPyPyImPyIm-y-PyHpPyHpImIm 2624) 5'W C CA GA C W-3' PyPyPyImPyPy-y-ImHpPyHpImIm 2625) 5'W C CA GG T W-3' PyPyPyImImHp-y-PyPyPyHpImIm 2626) 5'W C CA GG A W-3' PyPyPyImImPy-y-HpPyPyHpImIm 2627) 5'W C CA GC T W-3' PyPyPyImPyHp-y-PyImPyHpImIm 2628) 5'W C CA GC A W-3' PyPyPyImPyPy-y-HpImPyHpImIm 2629) 5'W C CA GG G W-3' PyPyPyImImIm-y-PyPyPyHpImIm 2630) 5'W C CA GG C W-3' PyPyPyImImPy-y-ImPyPyHpImIm 2631) 5'W C CA GC G W-3' PyPyPyImPyIm-y-PyImPyHpImIm 2632) 5'W C CA GC C W-3' PyPyPyImPyPy-y-ImImPyHpImIm 2633) 5'W C CA CT T W-3' PyPyPyPyHpHp-y-PyPyImHpImIm 2634) 5'W C CA CT A W-3' PyPyPyPyHpPy-y-HpPyImHpImIm 2635) 5' C CA CT G W-3' PyPyPyPyHpIm-y-PyPyImHpImIm W
2636) 5'W C CA CT C W-3' PyPyPyPyHpPy-y-ImPyImHpImIm 2637) 5'W C CA CA T W-3' PyPyPyPyPyHp-y-PyHpImHpImIm 2638) 5'W C CA CA A W-3' PyPyPyPyPyPy-y-HpHpImHpImIm 2639) 5'W C CA CA G W-3' PyPyPyPyPyIm-y-PyHpImHpImIm 2640) 5'W C CA CA C W-3' PyPyPyPyPyPy-y-ImHpImHpImIm 2641) 5'W C CA CG T W-3' PyPyPyPyImHp-y-PyPyImHpImIm 2642) 5'W C CA CG A W-3' PyPyPyPyImPy-y-HpPyImHpImIm 2643) 5'W C CA CC T W-3' PyPyPyPyPyHp-y-PyImImHpImIm 2644) 5'W C CA CC A W-3' PyPyPyPyPyPy-y-HpImImHpImIm 2645) 5'W C CA CG G W-3' PyPyPyPyImIm-y-PyPyImHpImIm 2646) 5'W C CA CG C W-3' PyPyPyPyImPy-y-ImPyImHpImIm 2647) 5'W C CA CC G W-3' PyPyPyPyPyIm-y-PyImImHpImIm 2648) 5'W C CA CC C W-3' pypypyPyPyPy-y-ImImImHpImIm WO 98/37067 . PCT/US98/01714 'TABLE 130: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCCWNNW-3' DNA sequence aromatic amino acid sequence 2649) 5'W C C C T T T W-3' PyPyPyHpHpHp-y-PyPypyImImIm 2650) 5'W C C C T T A W-3' PyPyPyHpHpPy-y-HpPyPyImImIm 2651) 5'W C C C T T G W-3' PyPyPyHpHpIm-y-PyPyPyImImIm 2652) 5'W C C C T T C W-3' PyPyPyHpHpPy-y-ImPyPyImImIm 2653) 5'W C C C T A T W-3' PyPyPyHpPyHp-y-PyHpPyImImIm 2654} 5'W C C C T A A W-3' PyPyPyHpPyPy-y-HgHpPyImImIm 2655) 5'W C C C T A G W-3' PyPyPyHpPyIm-y-PyHpPyImImIm 2656) 5'W C C C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImImIm 2657) 5'W C C C T G T W-3' PyPyPyHpImHp-y-PyPypyImImIm 2658) 5'W C C C T G A W-3' PyPyPyHpImPy-y-HpPyPyImImIm 2659) 5'W C C C TG G W-3' PyPypyHpImIm-y-PyPyPyImImIm 2660) 5'W C C C TG C W-3' PyPyPyHpImPy-y-ImPyPyImImIm 2661} 5'W C C C TC T W-3' PyPyPyHpPyHp-y-PyImPyImImIm 2662) 5'W C C C TC A W-3' PyPyPyHpPyPy-y-HpImPyImImIm 2663) 5'W C C C TC G W-3' PyPyPyHpPyIm-y-PyImPyImImIm 2664) 5'W C C C TC C W-3 T PyPyPyHpPyPy-y-ImImPyImImIm 2665) 5'W C C C AT T W-3' PyPyPyPyHpHp-y-PyPyHpImImIm 2666) 5'W C C C AT A W-3' PyPyPyPyHpPy-y-HpPyHpImImIm 2667} 5'W C C C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImImIm 2668) 5'W C C C AT C W-3' PyPyPyPyHpPy-y-ImPyHpImImIm 2669) 5'W C C C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImImIm 2670) 5'W C C C AA A W-3' PyPyPyPyPyPy-y-HpHpHpImImIm 2671) 5'W C C C AA G W-3' PyPyPyPyPyIm-y-PyHpHpImImIm 2 672 ) 5' W C C C A A C W-3 ' PyPyPyPyPyPy-y- ImHpHpImImIm 2673) 5'W C C C A G T W-3' PyPyPyPyImHp-y-PyPyHpImImim 2674) 5'W C C C A G A W-3' PyPyPyPyImPy-y-HpPyHpImImIm 2675) 5'W C C C A G G W-3' PyPyPyPyImIm-y-pyPyHpImImIm 2676) 5'W C C C A G C W-3' PyPypypylmpy-y-ImPyHpImImIm 2677) 5'W C C C A C T W-3' PyPyPyPyPyHp-y-PyImHpImImIm 2678) 5'W C C C A C A W-3' Pypypypypypy-y-HpImFipImImIm 2679) 5'W C C C A C G W-3' Pypypypypylm-y-pyImHpImImIm 2680) 5'W C C C A C C W-3' PyPyPyPyPyPy-y-ImImHpImImIm TABLE 131: 12-ring Hairpin Polyamides far recognition of 8-by 5'-WCCCSNNW-3' DNA sequence aromatic amino acid sequence 2681) 5'W C C C G T T W-3' PyPyPyImApHp-y-PyPyPyImImIm 2 6 82 ) 5' C C C G TA W-3 ' PyPypyImHppy-y-HpPyPyImImIm W' 2683) 5'W C C C G TG W-3' PyPyPyImHpIm-y-PyPyPyImImIm 2684) 5'W C C C G TC W-3' PyPyPyImHpPy-y-ImPyPyImImIm 2685) 5'W C C C G AT W-3' pyPyPyImPyHp-y-PyHpPyImImIm 2686) 5'W C C C G AA W-3' PyPyPyImPyPy-y-HpHpPyImImIm 2687) 5'W C C C G AG W-3' PyPyPyImPyIm-y-PyHpPyImImIm 2688) 5'W C C C G AC W-3' PyPyPyImPyPy-y-ImHpPyImImIm 2689) 5'W C C C G GT W-3' PyPyPyImImHp-y-PypypyzmImIm 2690) 5'W C C C G GA W-3' PyPypyImImPy-y-HpPyPyImImIm 2691) 5'W C C C G CT W-3' PyPyPyImPyHp-y-PyImPyImImIm 2692) 5'W C C C G CA W-3' PyPyPyImpypy_y-HpImPyImImIm 2693) 5'W C C C C TT W-3' PyPyPyPyHpHp-y-PyPyImIm3mIm 2694) 5'W C C C C TA W-3' PyPyPyPyFipPy-y-HpPyImImImIm 2695) 5'W C C C C TG W-3' PyPyPyPyHpIm-y-PyPyImImImIm 2696) 5'W C C C C TC W-3' pyPyPyPyIipPy-y-ImPyImImImIm 2697) 5'W C C C C AT W-3' PyPyPyPyPyHp-y-PyHpImImImIm 2698) 5' C C C C AA W-3' PyPyPyPyPyPy-y-HpHpImImImIm W
2699) 5'W C C C C AG W-3' PyPyPyPyPyIm-y-PyHpImImImIm 2690) 5'W C C C C AC W-3' PypypyPyPyPy-y-ImHpImImImIm 2701) 5'W C C C C GT W-3' PyPyPyPyImHp-y-PyPyImImImIm 2702) 5'W C C C C GA W-3' PyPyPyPyImPy-y-HpPyImImImIm 2703) 5'W C C C C C T W-3' PyPyPyPyPyHp-y-PyImImImImIm 2704) 5'W C C C C C A W-3' PyPyPyPyPypy-y-HpImImImImIm 6107 ) 5' W C C C G G G W-3' PyPyPyImImIm-y-PyPyPyImImIm 6108) 5'W C C C G G C W-3' PyPyPyImImPy-y-ImPyPyImImIm 6109) 5'W C C C G C G W-3' PyPyPyImPyIm-y-PyImPyImImIm 6110) 5'W C C C G C C W-3' PyPyPyImPyPy-y-ImImPyImImIm 6111) 5' W C C C C G G W-3' PypyPyPyImIm-y-PyPyImImImIm 6112 ) 5' W C C C C G C W-3 ' PyPyPyPyImPy-y- ImPyImImImIm 6113 ) 5' W C C C C C G W-3 ' PyPypypypylm-y-pyImImImImIm 6114) 5'W C C C C C C W-3' pypypypypypy-y-ImImImImImIm ,. , 1-Al3Lt; 132:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAGWNNW-3' DNA aromatic amino acid sequencc sequence ' 2705) 5'W C A G T T TW-3' PyPyImHpHpHp-y-pypypypyHplm ' 5 2706) 5'W C A G T T AW-3' PypyImHpHpPy-y-HpPyPyPyHpIm 270?) 5'W C A G T T GW-3' PyPyImHpHpIm-y-pypypypyHpIm 2708) 5'W C A G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyHpIm 2709} 5'W C A G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyHpIm 2700) 5'W C A G T A AW-3' PyPyImHpPyPy-y-HpHpPyPyFipIm 2711) 5' C A G T A GW-3 ' PyPyImHpPyIm-y-PyHpPyPyHpIm W
2712) 5'W C A G T A CW-3' PyPyImHpPyPy-y-ImHppyPyHpIm 2713) 5'W C A G T G TW-3' PyPyImHpImHp-y-PyPyPyPyHpIm 2714 5' C A G T G AW-3 ' PyPyImHpImPy-y-HpPyPyPyHpIm ) W
2715) 5'W C A G T G GW-3' PyPyImHpImIm-y-PypypypyHplm 2716) 5'W C A G T G CW-3' PyPyImHpImPy-y-ImPyPyPyHpIm 2717) 5'W C A G T C TW-3' PyPyImHpPyHp-y-PyImPyPyHpIm 2718) 5'W C A G T C AW-3' PyPyImHpPyPy-y-HpImPyPyHpIm 2719) 5'W C A G T C GW-3' PyPyImHpPyIm-y-PyImPyPyHpIm 2720) 5'W C A G T C CW-3' PyPyImHpPyPy-y-ImImPyPyHpIm 2721) 5'W C A G A T TW-3' PyPyImPyHpHp-y-PyPyHppyHplm 2722) 5'W C A G A T AW-3' PypyImPyHpPy-y-HpPyHpPyHpIm 2723) 5'W C A G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyHpIm 2724) 5'W C A G A T CW-3' PyPyImPyHpPy-y- ImPyFipPyHpIm 2725) 5'W C A G A A TW-3' PyPyImPyPyHp-y-PyHpHpPyHpIm 2726) 5'W C A G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyHpIm 2727) 5'W C A G A A GW-3' 'PyPyImPyPyIm-y-PyHpHpPyHpIm 2728) 5'W C A G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyHpIm 2729) 5'W C A G A G TW-3' PyPyImPyImHp-y-pypyHpPyHpIm 2730) 5'W C A G A G AW-3' ' PyPyImPyImPy-y-HpPyHpPyHpIm 2731) 5'W C A G A G GW-3' PyPyImPyImIm-y-PyPyHpPyHpIm 2732) 5'W C A G A G CW-3' PyPyImPyImPy-y-ImPyHpPyHpIm 2733) 5'W C A G A C TW-3' PyPyImPyPyHp-y-PyImHpPyHpIm 2734) 5'W C A G A C AW-3' PyPyImPyPyPy-y-HpImHpPyHpIm 2735) 5'W C A G A C GW-3' PyPyImPyPyIm-y-pyImHpPyHpIm 2736) 5'W C A G A C CW-3' PyPyImPyPyPy-y-ImImHpPyHpIm TABLE 133: 12-ring Hairpin Polyamides for recognition of 8-by S'-WCAGSNNW-3' DNA sequence aromatic amino acid sequence 2737) 5'W C A G G T T W-3' PyPyImImHpHp-y-PyPyPyPyHpIm 2738) 5~'W C A G G T A W-3' PyPyImImHpPy-y-HpPyPyPyHpIm 2739) 5'W C A G G T G W-3' PyPyImImHpIm-y-PyPyPyPyHpIm 2740) 5'W C A G G T C W-3' PyPyImImHpPy-y-ImPyPyPyHpIm 2741) 5'W C A G G A T W-3' PyPyImImPyHp-y-PyHpPyPyHpIm 2742) 5'W C A G G A A W-3' PyPyImImPyPy-y-HpHpPyPyHpIm 2743) 5'W C A G G A G W-3' PyPyImImPyIm-y-PyHpPyPyHpIm 2744) 5'W C A G G A C W-3' PyPyImImPyPy-y-ImHpPyPyHpIm 2745) 5'W C A G G G T W-3' PyPyImImImHp-y-PyPyPyPyHpim 2746) 5'W C A G G G A W-3' PyPyImImImPy-y-HpPyPyPyHpIm 2747) 5'W C A G G C T W-3' PyPyImImPyHp-y-PyImPyPyHpIm 2748) 5'W CA G G C A W-3' PyPyImImPyPy-y-HpImPyPyHpIm 2749) 5'W CA G C T T W-3' PyPyImPyHpHp-y-PyPyImPyHpIm 2750} 5'W CA G C T A W-3' PyPyImPyHpPy-y-HpPyImPyHpIm 2751) 5'W CA G C T G W-3' PyPyImPyHpIm-y-PyPyImPyHpIm 2752) 5'W CA G C T C W-3' PyPyImPyHpPy-y-ImPyImPyHpIm 2753) 5'W CA G C A T W-3' PyPyImPyPyHp-y-PyHpImPyHpIm 2754) 5'W C A G C A A W-3' PyPyImPyPyPy-y-HpHpImPyHpIm 2755) 5'W C A G C A G W-3' PyPyImPyPyIm-y-PylipImPyHpIm 2756) 5'W C A G C A C W-3' PyPyImPyPyPy-y-ImHpImPyHpIm 2757} 5'W C A G C G T W-3' PyPyImPyImHp-y-PyPyImPyHpIm 2758} 5'W CA G C G A W-3' PyPyImPyImPy-y-HpPyImPyHpIm 2759) 5'W CA G C C T W-3' PyPyImPyPyHp-y-PyImImPyHpIm 2760) 5'W CA G C C A W-3' PyPyImPyPyPy-y-HpImImPyHpIm 2761) 5'W CA G G G G W-3' PyPyImImImIm-y-PyPyPyPyHpIm 2762) 5'W CA G G G C W-3' PyPyImImImPy-y-ImPyPyPyHpIm 2763) 5'W CA G G C G W-3' PyPyImImPyIm-y-PyImPyPyHpIm 2764) 5'W CA G G C C W-3' PyPyImImPyPy-y-ImImPyPyHpIm 2765) 5'W CA G C G G W-3' PyPyImPyImIm-y-PyPyImPyHpIm 2766) 5'W CA G C G C W-3' PyPyImPyImPy-y-ImPyImPyHpIm 2767) 5'W CA G C C G W-3' PyPyImPyPyim-y-PyImImPyHpIm 2768} 5'W CA G C C C W-3' PyPyImPyPyPy-y-ImImImPyHpIm TABLE 134:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCATWNNW-3 DNA sequence aromatic amino acid sequence 2769) 5'W C A T PyPyHpHpHpHp-y-pypypypyHpIm T T T W-3' 2770) .5'W C A T A W-3' PyPyHpHpHpPy-y-HpPyPypyHplm T T
2771) 5'W C A T T G W-3' PyPyHpHpHpIm-y-PypypypyHpim T
2772) 5'W C A T T C W-3' PyPyHpHpHpPy-y-ImPyPyPyHpIm T
2773) 5'W C A T A T W-3' PyPyHpHpPyHp-y-pyHppypyHpIm T
2774) 5'W C A T A A W-3' PyPyHpHpPyPy-y-HpHpPyPyHpIm T
2775} 5'W C A T A G W-3' PyPyHpHpPyIm-y-pygppypyHplm T
2776) 5'W C A T A C W-3' PyPyHpHpPyPy-y-ImHpPypygpIm T
2777) 5'W C A T G T W-3' PyPyHpHpImHp-y-PypypypyHplm T
2778) 5'W C A T G A W-3' PyPyHpHpImPy-y-HpPyPyPyHpIm T
2779) 5'W C A T G G W-3' PyPyHpHpImIm-y-pypypypyHpIm T
2780) 5'W C A T G C W-3' PyPyHpHpImPy-y-ImPyPyPyHpIm T
2781) 5'W C A T C T W-3' PyPyHpHpPyHp-y-PyImPyPyHpIm T
2782) 5'W C A T C A W-3' PyPyHpHpPyPy-y-HpImPyPyHpIm T
2783) 5'W C A T C G W-3' PyPyHpHpPyIm-y-pyImPyPyHpIm T
2784) 5'W C A T C C W-3' PyPyHpHpPyPy-y-ImImPyPyHpIm T
2785) 5'W C A T T T W-3' PyPyHpPyHpHp-y-PyPyHppyHpIm A
2786) 5'W C A T T A W-3' PyPyI-ippygpp~,_y-HpPyHpPyHpIm A
2787) 5'W C A T T G W-3' PyPyHpPyHpIm-y-pypyHppyHpIm A
2788) 5'W C A T T C W-3' PyPyHpPyHpPy-y-ImPyHpPyHpIm A
2789) 5'W C A T A T W-3' yPyHpPyPyHp-y-PyHpHpPyHpIm A P
2790) 5'W C A T A A W-3' PypyHpPyPypy-y-HpHpHpPyHpIm A
2791) 5'W C A T A G W-3' PypyHppypylm-y-PyHpHpPyHpIm A
2792) 5'W C A T A C W-3' PyPyHpPyPyPy-y-ImHpHpPyHpim A
2793) 5'W C A T G T W-3' pyPyHpPyImHp-y-pypygppyHpIm A
2794) 5'W C A T G A W-3' PyPyHpPyImPy-y-HpPyHpPyHpIm A
2795) 5'W C A T G G W-3' PyPyHpPyImIm-y-pypygppyHPIm A
2796) 5'W C A T G C W-3' PyPyHpPyImPy-y-ImPyHpPyHpIm A
2797) 5'W C A T C T W-3' PyPyHpPyPyHp-y-PyImHpPyHpIm A
2798) 5'W C A T C A W-3' PyPyHpPyPyPy-y-HpImHpPyHpIm A
2799) 5'W C A T C G W-3' PyPyHpPyPyIm-y-PyImHpPyHpIm A
2800) 5'W C A T C C W-3' PyPyHpPyPyPy-y-ImImHpPyHpIm A
TABLE 135: 12-ring Hanpm Polyamides for recogmt~on of 8-by 5'-WCATSNNW-3' DNA sequence aromatic amino acid sequence 2801) 5'W C PyPyHpImHpHp-y-pypypypyHprm A T G T T PyPyHpImHpPy-y-HpPyPyPyHpIm W-3' PyPyHpImHpIm-y-pypypypyHplm 2802) 5'W C PyPyHpImHppy-y-ImPyPypyHplm A T G T A PyPyHpImPyHp-y-pygppypyHplm W-3' PyPyHpImPyPy-y-HpHppypyHpIm 2803) 5'W C PyPyHpImPyIm-y-pyHppypyHpIm A T G T G PyPyHpImPyPy-y-ImHppypyHplm W-3' PypyHpImImHp_y-pypypypyHplm 2804) 5'W C PyPyHpImImPy-y-HppypypyHpIm A T G T C PypyHpImPyHp-y-pyImPyPyHpIm W-3' PyPyHpImpypy_y-HpImPyPyHpIm 2805) 5'W C PyPyHpImImIm-y-pypypypyHpim A T G A T PyPyHpImImPy-y-ImpypypyHpIm W-3' PyPyHpImPyIm-y-pylmpypyHpIm 2806) 5'W C PypyHpImPyPy-y-ImImPyPyHpIm A T G A A PyPyHppyHpHp-y-pypyimPyHpIm W-3' PyPyHpPyHpPy-y-HppyImPyHpIm 2807) 5'W PypyHpPyHpIm-y-PypyImPyHpIm C A T G A pyPyHpPyHpPy-y-ImPyImPyHpIm G W-3' PypyHpPypygp-y_pyHpImPyHpIm 2808) 5'W C PyPyHpPyPypy-y-HpHpImPyHpIm A T G A C PyPygppypylm-y_pyHpImPyHpIm W-3' PyPyHpPypypy-y-ImHpImPyHpIm 2809) 5'W C PypyHppyl~p-y-pypyImPyHpIm A T G G T PyPyHpPyImPy-y-HpPyImPyHpIm W-3' PyPyHpPypyHp-y-pyImImPyHpIm 2810) 5'W C PyPyHpPyPypy-y-HpImImPyHpIm A T G G A pypyHppyImIm-y-pypyImPyHpIm W-3' PyPyHppylmpy_y_ImpyImPyHpIm 2811) 5'W C PyPyHpPyPyIm-y-pyImImPyHpIm A T G C T PyPyHpPyPyPy-y-ImImImPyHpIm W-3' 2812) 5'W
C A T G C
A W-3' 2813) 5'W C
A T G G G
W-3' 2814) 5'W C
A T G G C
W-3' 2815) 5'W C
A T G C G
W-3' 2816) 5'W C
A T G C C
W-3' 2817) 5'W
C A T C T
T W-3' 2818) 5'W C
A T C T A
W-3' 2819) 5'W C
A T C T G
W-3' 2820) 5'W C
A T C T C
W-3' 2821) 5'W C
A T C A T
W-3' 2822) 5'W
C A T C A
A W-3' 2823) 5'W C
A T C A G
W-3' 2824) 5'W C
A T C A C
W-3' 2825) 5'W C
A T C G T
W-3' 2826) 5'W C
A T C G A
W-3' 2827) 5'W
C A T C C
T W-3' 2828) 5'W C
A T C C A
W-3' 2829) 5'W C
A T C G G
W-3' 2830) 5'W C
A T C G C
W-3' 2831) 5'W C
A T C C G
W-3' 2832) 5'W
C A T C C
C W-3' PCT1US98/Ol ? 14 TABLE
136:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAAWNNW-3' DNA aromatic amino acid sequence sequence ' 2833) 5'W C PyPYpyHpHpHp-y-pypypyHpHpim A
A
T
T
T
W-3' ' S 2834) 5'W C T A W-3' pypypyHpHppy_y_HppypyHpHpIm A
A
T
2835) 5'W C A T T G W-3' PyPyPyHpHpIm-y-PypypygpHplm A
2836) 5'W C A AT T C W-3' PYPypyHpHpPy-y-ImPyPyHpHpIm 2837) 5'W C A AT A T W-3' PyPyPyHppyHp-Y_pyHppyHpHpIm 2838) 5'W C A AT A A W-3' PYPyPyHpPYPy-y-HpHpPyHpHpIm 2839) 5'W C A AT A G W-3' PyPyPyHpPyIm-y-PyHpPYHpHpIm 2840) 5'W C A AT A C W-3' PyPyPYHpPYPy-Y-ImHppyHpHpIm 2841) 5'W C A AT G T W-3' PyPypyHpImHp-y-pypypygpHpIm 2842) 5'W C A AT G A W-3' PyPypyHpImPy-Y-HpPyPyHpHpIm 2843) 5'W C A AT G G W-3' PYPyPyHpImIm-Y-PypypYHpHpIm 1S 2844) 5'W C A AT G C W-3' PYPyPyHpImPy-y-ImPyPyHpHpIm 2845) 5'W C A AT C T W-3' PyPypyHpPYHp-y-PyImPyHpHpIm 2846) 5'W C A AT C A W-3' PyPyPyHpPyPy-y-HpImPyHpHpIm 2847) 5'W C A AT C G W-3' PyPypyHppYIm-y-PYImPyHpHpIm 2848) 5'W C A AT C C W-3' Pypypygppypy_Y_ImImPyHpHpIm 2849) 5'W C A AA T T W-3' PyPypypygpHp-y-PYPYHpHpHpIm 2850) 5'W C A AA T A W-3' PyPyPyPYHpPy-Y-HpPyHpHpHpim 2851) 5'W C A AA T G W-3' PyPyPypyHpIm-y-PYpyHpHpHpIm 2852) 5'W C A AA T C W-3' PyPyPyPyHpPy-y-ImPyHpHpHpIm 2853) 5'W C A AA A T W-3' PypypypypYHp_Y_pYHpHpHpHpIm 2854) 5'W C A AA A A W-3' PyPyPYPyPyPy-Y-HpHpHpHpHpIm 2855) 5'W C A AA A G W-3' PYPyPyPyPyIm-y-PyHpHpHpHpIm 2856) 5'W C A AA A C W-3' PYPypypypypy-y_ImHpHpHpHpIm 2857) 5'W C A AA G T W-3' PyPyPYPyImHp-Y-PypyHpHpHpIm 2858) 5'W C A AA G A W-3' Pypypypylmpy_y-HpPYHpHpHpIm 2859) 5'W C A AA G G W-3' PyPyPypyImlm-y-PYPYHpHpHpIm 2860 ) 5' C A AA G C W-3 ' PyPyPypyImpY_y_ ImPYHpHpHpIm W
2861) 5'W C A AA C T W-3' PYPyPyPyPyHp-Y-PyImHpHpHpIm 2862) 5'W C A AA C A W-3' PyPyPYpypypy-y-HpImHpHpHpIm 2863) 5'W C A AA C G W-3' PyPypypypYlm_y_pyImHpHpHpIm 3S 2864 ) 5' C A AA C C W-3 ' pypypypypypy-y_ ImImHpHpHpIm W
TABLE
137:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAASNNW-3' DNA aromatic amino acid sequence sequence 2865) 5'W C A A GT T w-3' PyPyPyImHpHp-y-pypypyHpHpIm 2866) - C A A GT A W-3' PyPyPyImHpPy-y-HpPyPyHpHpIm 5' W
2867) 5'W C A A GT G W-3' PyPyPyImHpIm-y-PyPyPyHpHpIm 2868) 5'W C A A GT C W-3' PyPyPyImHpPy-y-ImPyPyHpHpIm 2869) 5'W C A A GA T W-3' PyPyPyImPyHp-y-PyHpPyHpHpIm 2870) 5'W C A A GA A W-3' PyPyPyImPyPy-y-HpHpPyHpHpIm 2871) 5'W C A A GA G W-3' PyPyPyImPyIm-y-PyHpPyHpHpIm 2872) 5'W C A A GA C W-3' PyPyPyImPyPy-y-ImHpPyHpHpIm 2873) 5'W C A A GG T W-3' PyPyPyImImHp-y-PyPyPyHpHpIm 2874) 5'W C A A GG A W-3' PyPyPyImImPy-y-HpPyPyHpHpIm 2875) 5'W C A A GC T W-3' PyPyPyImPyHp-y-PyImPyHpF3pIm 2876) 5'W C A A GC A W-3' PyPyPyImPyPy-y-HpImPyHpHpIm 2877) 5'W C A A GG G W-3' PyPyPyImImIm-y-PyPyPyHpHpIm 2878) 5'W C A A GG C W-3' PyPyPyImImPy-y-ImPyPyHpHpIm 2879) 5'W C A A GC G W-3' PyPyPyImPyIm-y-PyImPyHpHpIm 2880) 5'W C A A GC C W-3' PyPyPyImPyPy-y-ImImPyHpHpIm 2881) 5' C A A CT T W-3' PyPyPyPyHpllp-y-PyPyImHpHpIm W
2882) 5'W C A A CT A W-3' PyPyPyPyHpPy-y-HpPyImHpHpIm 2883) 5'W C A A CT G W-3' PyPyPyPyHpIm-y-PypyImHpHpIm 2884) 5'W C A A CT C W-3' PyPyPyPyHpPy-y-ImPyImHpHpIm 2885) 5'W C A A CA T W-3' PyPyPyPyPyHp-y-PyHpImHpHpIm 2886) 5'W C A A CA A W-3' PyPyPyPyPyPy-y-HpHpImHpHpIm 2887) 5'W C A A CA G W-3' PyPyPyPyPyIm-y-PyHpImHpHpIm 2888) 5'W C A A CA C W-3' pyPypypypypy-y-I~pImHpHpIm 2889) 5'W C A A CG T W-3' PyPyPyPyImHp-y-PyPyImHpfIpIm 2890) 5'W C A A CG A W-3' PyPyPyPyImPy-y-HpPyImHpHpIm 2891) 5'W C A A CC T W-3' PyPyPyPyPyHp-y-PyImImHpHpIm 2892) 5'W C A A CC A W-3' PyPyPyPyPyPy-y-HpImImHpHpIm 2893) 5'W C A A CG G W-3' PyPyPyPyImIm-y-PyPyImHpHpIm 2894) 5'W C A A CG C W-3' PypypypyImPy-y-ImPyImHpHpIm 2895) 5'W C A A CC G W-3' PyPyPyPyPyIm-y-PyImImHpHpIm 3$ 2896) 5'W C A A CC C W-3' PyPyPyPyPyPy-y-ImImImHpHpIm TABLE 138: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCACWNNW-3' DNA aromatic amino acid sequence sequence 2897) 5'W C A C TT T W-3' PyPyPyHpHpHp-y-PyPyPyImHpIm 2898) 5'W C A C TT A W-3' PYPYPYHPHPPY-y-HPPYPYI~PIm 2899) 5'W C A C TT G W-3' PyPyPyHpHpIm-y-PyPypyl~plm 2900) 5'W C A C TT C W-3' PYPYPyHpHppy_y-ImPYPyImHpIm 2901) 5'W C A C TA T W-3' PyPyPyHpPyHp-y-PyHpPyImHpIm 2902) 5'W C A C TA A W-3' PyPyPyHpPyPy-y-HpHpPyImHpIm 2903) 5'W C A C TA G W-3' PyPyPyHpPyIm-y-PyHpPyImHpIm 2904) 5'W C A C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImHpIm 2905) 5'W C A C T G T W-3' PYpypygpl~p-y_pypypyl~plm 2906) 5'W C A C T G A W-3' PyPyPyHpImPy-y-HpPyPyImHpIm 2907) 5'W C A C T G G W-3' PyPyPyHpImIm-y-PypypyImHpIm 2908) 5'W C A C T G C W-3' PyPyPyHpImPy-y-ImPyPyImHpIm 2909) 5'W C A C T C T W-3' PyPyPyHpPyHp-y-PyImPyImHpIm 2910) 5'W C A C T C A W-3' PyPyPyHpPyPy-y-HpImPyImHpIm 2911) 5'W C A C TC G W-3' PyPyPyHpPyIm-y-PyImPyImHpIm 2912) 5'W C A C TC C W-3' PyPyPyHpPypy-y-ImImPyImHpIm 2913} 5'W C A C AT T W-3' PyPyPyPyHpHp-y-PypyHpImHpIm 2914) 5'W C A C AT A W-3' PyPyPyPyHpPy-y-HpPyHPImHpIm 2915) 5'W C A C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImHpIm 2916) 5'W C A C AT C W-3' PyPyPypyHPPy-y-ImPyHpImHpIm 2917) 5'W C A C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImHpIm 2918) 5'W C A C AA A W-3' PyPyPyPyPypy-y-HpHpHPImHpIm 2919) 5'W C A C AA G W-3' ~PyPyPyPyPyIm-y-PyHpHpImHpIm 2920) 5'W C A C AA C W-3' PyPyPyPyPypy-y-ImHpHpImHpIm 2921) 5'W C A C AG T W-3' PyPyPyPyImHp-y-PyPyHpImHpIm 2922) 5'W C A C AG A W-3' PyPyPyPyImPy-y-HpPyHpImHpIm 2923) 5'W C A C AG G W-3' PyPyPyPyImIm-y-PyPyHpImHpIm 2924) 5'W C A C AG C W-3' PyPyPyPyImPy-y-ImPyHPImHpIm - 2925) 5'W C A C AC T W-3' PypypypypyHp-y_pyl~pImHpIm 2926) 5'W C A C AC A W-3' PyPyPyPyPyPy-y-HpImHpImHpIm - 2927) 5'W C A C AC G W-3' PyPyPyPyPyIm-y-PyImHpImHpIm 2928) 5'W C A C AC C W-3' PyPyPyPyPyPy-y-ImImHpImHpIm TABLE
139:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCACSNNW-3' DNA aromatic amino acid sequence sequence 2929) 5'W C A CG T T W-3' PyPyPyImHpHp-y-PyPyPyImHpIm 2930) 5~'WC A CG T A W-3' PyPyPyImHpPy-y-HpPyPyImHpIm 2931) 5'W C A CG T G W-3' PyPyPyImHpIm-y-PyPyPyImHpIm 2932) 5'W C A CG T C W-3' PyPyPyImHpPy-y-ImPyPyImHpIm 2933) 5'W C A CG A T W-3' PyPyPyImPyHp-y-PyHpPyImHpIm 2934) 5'W C A CG A A W-3' PyPyPyImPyPy-y-HpHpPyImHpIm 2935) 5'W C A CG A G W-3' PyPyPyImPyIm-y-PyHpPyImHpIm 2936) 5'W C A CG A C W-3' PyPyPyImPyPy-y-ImHpPyImHpIm 2937) 5'W C A CG G T W-3' PyPyPyImImHp-y-PyPyPyImHpIm 2938) 5'W C A CG G A W-3' PyPyPyImImPy-y-HpPyPyImHpIm 2939) 5'W C A CG C T W-3' PyPyPyImPyHp-y-PyImPyImHpIm 2940) 5'W C A CG C A W-3' PyPyPyImPyPy-y-HpImPyImHpIm 2941) 5'W C A CC T T W-3' PyPyPyPyHpHp-y-PyPyImImI~ipIm 2942) 5'W C A CC T A W-3' PyPyPyPyHpPy-y-HpPyImImHpIm 2943) 5'W C A CC T G W-3' PyPyPyPyHpIm-y-PyPyImImHpIm 2944) 5'W C A CC T C W-3' PyPyPyPyHpPy-y-ImPyImImHpIm 2945) 5'W C A CC A T W-3' PyPyPyPyPyHp-y-PyHpImImHpIm 2946) 5'W C A CC A A W-3' PyPyPyPyPyPy-y-HpHpImImHpIm 2947) 5'W C A CC A G W-3' PyPyPyPyPyIm-y-PyHpImImHpIm 2948) 5'W C A CC A C W-3' PyPyPyPyPyPy-y-ImApImImHpIm 2949) 5'W C A CC G T W-3' PyPyPyPyImHp-y-PyPyImImHpIm 2950) 5'W C A CC G A W-3' PyPyPyPyImPy-y-HpPyImImHpIm 2951) 5'W C A CC C T W-3' ~PyPyPyPyPyHp-y-PyImImImHpim 2952) 5'W C A CC C A W-3' PyPyPyPyPyPy-y-HpImImImHpIm 2953) 5'W C A CG G G W-3' PyPyPyImImIm-y-PyPyPyImHpIm 2954) 5'W C A CG G C W-3' PyPyPyImImPy-y-ImPyPyImHPIm 2955) 5'W C A CG C G W-3' PyPyPyImPyIm-y-PyImPyImHpIm 2956) 5'W C A CG C C W-3' PyPyPyImPyPy-y-ImImPyImHpIm 2957) 5'W C A CC G G W-3' PyPyPyPyImIm-y-PyPyImImHpIm 2958) 5'W C A CC G C W-3' PyPyPyPyImPy-y-ImPyImImHpIm 2959) 5'W C A CC C G W-3' PyPyPyPyPyIm-y-PyImImImHpIm 2960) 5'W C A CC C C W-3' PyPyPyPyPyPy-y-ImImImImHpIm 1A13Lt; I2-ring 140: Hairpin Polyamides for recognition of 8-by 5'-WCTGWNNW-3' DNA aromatic amino acid sequence sequence ' 2961) 5'W C TG T T T W-3' PyHpImHpHpHp-y-PyPyPyPyPyIm 2962) ~5'W C TG T T A W-3' PyHpImHpHpPy-y-HpPyPyPyPyIm 2963) 5'W C TG T T G W-3' PyHpImHpHpIm-y-Pypypypypylm 2964) 5'W C TG T T C W-3' PyHpImHpHpPy-y-ImPyPyPyPyIm 2965) 5'W C TG T A T W-3' PyHpImHpPyHp-y-pyHpPyPyPyIm 2966) 5'W C TG T A A W-3' PyHpImHpPyPy-y-HpHpPyPypyIm 2967) 5'W C TG T A G W-3' PyHpImHpPyIm-y-PyHpPyPyPyIm 296$) 5'W C TG T A C W-3' PyHpImHpPyPy-y-ImHpPyPYPyIm 2969) 5'W C TG T G T W-3' PyHpImHpImHp-Y-PypypypyPyIm 2970) 5'W C TG T G A W-3' PyHpImHpImPy-y-HpPyPyPyPyIm 2971) 5'W C TG T G G W-3' PyHpImHpImIm-y-PypypypypyIm I5 2972) 5'W C TG T G C W-3' PyHpImHpImPy-y-ImPyPyPyPyIm 2973) 5'W C TG T C T W-3' PyHpImHpPyHp-y-PyImPyPyPyIm 2974) 5'W C TG T C A W-3' PyHpImHpPyPy-y-HpImPyPyPyIm 2975) 5'W C TG T C G W-3' PyHpImHpPyIm-y-PyImPyPyPyIm 2976) 5'W C TG T C C W-3' PyHpImHpPyPy-y-ImImPyPyPyIm 2977) 5'W C TG A T T W-3' PyHpImPyHpHp-y-pypyHpPyPyIm 2978) 5'W C TG A T A W-3' PyHpImPyHpPy-y-HpPyHpPyPyIm 2979) 5'W C TG A T G W-3' PyHpImPyHpIm-y-PyPyHpPyPyIm 2980) 5' C TG A T C W-3' PyHpImPyHpPy-y-ImPyHpPyPyIm W
2981) 5'W C TG A A T W-3' PyHpImPyPyHp-y-PyHpHpPyPyIm 2982) 5'W C TG A A A W-3' PyHpImPyPyPy-y-HpHpHpPyPyIm 2983) 5'W C TG A A G W-3' PyHpImPyPyIm-y-PyHpHpPyPyim 2984) 5'W T GA A C W-3' PyHpImPyPyPy-y-ImHpHpPyPyIm C
2985) 5'W T GA G T W-3' PyHpImPyImHp-y-PyPyHpPyPyIm C
2986) 5'W T GA G A W-3' PyHpImPyImPy-y-HpPyHpPyPyIm C
2 9 87 5' T GA G G W-3 ' PyHpImPyImIm-y-Pypygppypylm ) W
C
2988) 5'W T GA G C W-3' PyHpImPyImPy-y-ImPyHpPyPyIm C
2989) 5'W T GA C T W-3' PyHpImPyPyHp-y-PyImHpPyPyIm C
2990) 5'W T GA C A W-3' PyHpImPyPyPy-y-HpImHpPyPyIm C
2991) 5'W T GA C G W-3' PyHpImPyPyIm-y-PyImHpPyPyIm C
2992) 5'W T GA C C W-3' PyHpImPyPyPy-y-ImImHpPyPyIm C
TABLE 141:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTGSNNW-3' DNA aromatic amino acid sequence sequence 2993) 5'W C TG G T T W-3' PyHpIrnImHpHp-~-PyPyPyPyPyIm 2994) 5.'WC TG G T A W-3' PyHpImImHpPy-y-HpPyPyPyPyIm 2995) 5'W C TG G T G W-3' PyHpImImHpIm-y-PyPyPyPyPyIm 2996) 5'W C TG G T C W-3' PyHpImImHpPy-y-ImPyPyPyPyIm 2997) 5'W C TG G A T W-3' PyHpImImPyHp-'y-PyHpPyPyPyIm 2998) 5'W C TG G A A W-3' PyHpImImPyPy-~y-HpHpPyPyPyIm 2999) 5'W C TG G A G W-3' PyHpImImPyIm-'y-PyHpPyPyPyIm 3000) 5'W C TG G A C W-3' PyHpImImPyPy-y-ImHpPyPyPyIm 3001) 5'W C TG G G T W-3' PyHpImImImHp-y-PyPyPyPyPyIm 3002) 5'W C TG G G A W-3' PyHpIrnImImPy-y-HpPyPyPyPyim 3003) 5'W C TG G C T W-3' PyHpImImPyHp-y-PyImPyPyPyIm 3004) 5'W C TG G C A W-3' PyHpImImPyPy-y-HpImPyPyPyIm 3005) 5'W C TG C T T W-3' PyHpImPyHpHp-y-PyPyImPyPyIm 3006) 5'W C TG C T A W-3' PyHpImPyHpPy-~y-HpPyImPyPyIm 3007 ) 5' C TG C T G W-3' PyHpImPyHpIm-y-PyPyImPyPyIm W
3008) 5'W C TG C T C W-3' PyHpImPyFipPy-y-ImPyImPyPyIm 3009) 5'W C TG C A T W-3' PyHpImPyPyHp-y-PyHpImPyPyim 3 O 10 5' C TG C A A W-3 PyHpImPyPyPy-y-HpHpImPyPyIm ) W ' 3011) 5'W C TG C A G W-3' PyHpImPyPyIm-~y-PyHpImPyPyim 3012) 5'W C TG C A C W-3' PyHpImPyPyPy-~y-ImHpImPyPyIm 3013) 5'W C TG C G T W-3' PyHpImPyImHp-y-PyPyImPyPyIm 3 014 5' C TG C G A W-3 PyHpImPyImPy-'y-HpPyImPyPyIm ) W ' 3015) 5'W C TG C C T W-3' 'PyHpImPyPyHp-y-PyImImPyPyIm 3016) 5'W C TG C C A W-3' PyHpImPyPyPy-y-HpImImPyPyIm 3017) 5'W C TG G G G W-3' PyHpImImImIm-y-PyPyPyPyPyIm 3018) 5'W C TG G G C W-3' PyHpImImImPy-y-ImPyPyPyPyIm 3019) 5'W C TG G C G W-3' PyHpImImPyIm-y-PyImPyPyPyIm 3020) 5'W C TG G C C W-3' PyHpImImPyPy-y-ImImPyPyPyIm 3021) 5'W C TG C G G W-3' PyHpImPyImIm-y-PyPyImPyPyIm 3022) 5'W C TG C G C W-3' PyHpImPyImPy-y-ImPyImPyPyIm 3023) 5'W C TG C C G W-3' PyHpImPyPyIm-y-PyImImPyPyIm 3024) 5'W C TG C C C W-3' PyHpImPyPyPy-y-ImImImPyPyIm TABLE 142: r recognition of 8-by 5'-WCTTWNNW-3' 12-ring Hairpin Polyamides fo DNA sequence aromatic amino acid sequence 3025) 5'W C T T PyHpHpHpHpHp-y-pypypypypylm T T T W-3' ' 5 3026) ~ 5'W C T PyHpHpHpHpPy-y-HpPyPyPypylm T T T A
W-3' 3027) 5'W C T T PyHpHpHpHpIm-y-PyPypypypylm T T G W-3' 3 028 5' W C T PyHpHpHpHpPy-y-ImPyPypypylm ) T T T C
W-3 ' 3029) 5'W C T T A PyHpHpHpPyHp-y-pyHpPypypylm T T
W-3' 3030) 5'W C T T A A W-3' PyHpHpHpPyPy-y-Hpgppypypylm T
3031) 5'W C T T A G W-3' PyHpHpHpPyIm-y-PyI-lppypypylm T
3032) 5'W C T T A C W-3' PyHpHpHpPyPy-y-ImHPPYPYPyIm T
3033) 5'W C T T G T W-3' PyHpHpHpImHp-y-Pypypypypylm T
3034) 5'W C T T G A W-3' PyHpHpHpImPy-y-HpPYPYPYPyIm T
3035) 5'W C T T G G W-3' PyHpHpHpImIm-y-pypypypypylm T
3036) 5'W C T T G C W-3' PyHpHpHpImPy-y-ImPyPyPyPyIm T
3037) 5'W C T T C T W-3' PyHpHpHpPyHp-y-Pylmpypypylm T
3038) 5'W C T T C A W-3' PyHpHpHpPyPy-y-HpImPyPypylm T
3 03 5' W C T C G W- 3 ' PyHPHpHpPyIm-y-PyImPyPyPyIm 9 ) T T
3 04 5' W C T C C W-3 ' PyHpHpHpPyPy-y- ImImPyPyPyIm 0 ) T T
3041) 5'W C T T T T W-3' PyHpHpPyHpHp-y-PypyHpPyPyim A
3 042 5' W C T T A W-3 ' PyHpHpPyHpPy-y-HpPyHpPYPyIm ) T A
3043) 5'W C T T T G W-3' PyHpHpPyHpIm-y-pypygppypylm A
3044) 5'W C T T T C W-3' PyFipI-IpPyHpPy-y-ImPyHpPyPyIm A
3045) 5'W C T T A T W-3' A pYHPHPPYPYHP-Y-pYHPHPPYPYIm 3046) 5'W C T T A A W-3' PyHpHpPyPyPy-y-HpgpHPPyPyIm A
3047) 5'W C T T A G W-3' ' PyHpHpPyPyIm-y-pyHpHpPyPyIm A
3 04 5' W C T A C W-3 ' PyHpHpPyPyPy-y- ImHpHpPyPyIm 8 ) T A
3049) 5'W C T T G T W-3' PyHpHpPyImHp-y-PypyHpPypyIm A
3 050 5' W C T G A W-3 ' PyHpHpPyImPy-y-HpPyHpPypyIm ) T A
3051) 5'W C T T G G W-3' PyHpHpPyImIm-y-PypyHppypylm A
3052) 5'W C T T G C W-3' PyHpHpPyImPy-y-ImPyHPPYPyIm A
' 3053) 5'W C T T C T W-3' PyHpHpPyPyHp-y-pylmgppypy=m A
3054) 5'W C T T C A W-3' PyHpHppypypy-Y-HpImHpPyPyIm A
3055) 5'W C T T C G W-3' PyHpHpPyPyIm-y-pylmI-ippypylm A
3056) 5'W C T T C C W-3' PyHpHpPyPyPy-y-ImImHpPyPyIm A
TABLE
143:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTTSNNW-3' DNA aromatic amino acid sequence sequence 3057) 5'W C T TG T T W-3' PyHpHpImHpHp-y-PyPyPyPyPyIm 3058) 5'W C T TG T A W-3' PyHpHpImHpPy-y-HpPyPyPyPyIm 3059) 5'W C T TG T G W-3' PyHpHpImHpIm-y-PyPyPyPyPyIm 3060) 5'W C T TG T C W-3' PyHpHpImHpPy-y-ImPyPyPyPyIm 3061) 5' C T TG A T W-3' PyHpHpImPyHp-y-PyHpPyPyPyIm W
3062) 5'W C T TG A A W-3' PyHpHpImPyPy-y-HpHpPyPyPyIm 3063) 5'W C T TG A G W-3' PyHpHpImPyIm-y-PyHpPyPyPyIm 3064) 5'W C T TG A C W-3' PyHpHpImPyPy-y-ImHpPyPyPyIm 3065) 5'W C T TG G T W-3' PyHpHpImImHp-y-PyPyPyPyPyIm 3066) 5'W C T TG G A W-3' PyHpHpImImPy-y-HpPyPyPyPyIm 3067) 5'W C T TG C T W-3' PyHpHpImPyHp-y-PyImPyPyPyIm 3068) 5'W C T TG C A W-3' PyHpHpImPyPy-y-HpImPyPyPyIm 3069) 5'W C T TG G G W-3' PyHpHpImImIm-y-PyPyPyPyPyIm 3 07 0 5' C T TG G C W-3 ' PyHpHpImImPy-y- ImPyPyPyPyIm ) W
3071) 5'W C T TG C G W-3' PyHpHpImPyIm-y-PyImPyPyPyIm 3072) 5'W C T TG C C W-3' PyHpHpImPyPy-y-ImImPyPyPyIm 3073) 5'W C T TC T T W-3' PyHpHpPyHpHp-y-PyPyImPyPyIm 3 074 5' C T TC T A W-3 ' PyHpHpPyHpPy-y-HpPyImPyPyIm ) W
3 07 5 5' C T TC T G W-3 ' PyHpHpPyHpIm-y-PyPyImPyPyIm ) W
3076) 5'W C T TC T C W-3' PyHpHpPyHpPy-y-ImPyImPyPyIm 3077) 5'W C T TC A T W-3' PyHpHpPyPyHp-y-PyHpImPyPyIm 3 07 8 5' C T TC A A W-3 ' PyHpHpPyPyPy-y-HpHpImPyPyIm ) W
3079) 5'W C T TC A G W-3' 'PyHpFIpPyPyIm-y-PyHpImPyPyIm 3080) 5'W C T TC A C W-3' PyHpHpPyPyPy-y-ImHpImPyPyIm 3081) 5'W C T TC G T W-3' PyHpHpPyImHp-y-PyPyImPyPyIm 3 082 5' C T TC G A W-3 ' PyHpHpPyImPy-y-HpPyImPyPyIm ) W
3083) 5'W C T TC C T W-3' PyHpHpPyPyHp-y-PyImImPyPyIm 3084) 5'W C T TC C A W-3' PyHpHpPyPyPy-y-HpImImPyPyIm 3085) 5'W C T TC G G W-3' PyHpHpPyImIm-y-PyPyImPyPyIm 3086) 5'W C T TC G C W-3' PyHpHpPyImPy-y-ImPyImPyPyIm 3087) 5'W C T TC C G W-3' PyHpHpPyPyIm-y-PyImImPyPyIm 3088) 5'W C T TC C C W-3' PyHpHpPyPyPy-y-ImImImPyPyIm TABLE
144:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTAWNNW-3' DNA aromatic amino acid sequence sequence 3089) 5'W C T A TT T W-3' PyHpPyHpHpHp-y-PyPypyHpPyIm S 3090) 5'W C T A TT A W-3' PyHpPyHpHpPy-y-HpPyPyHpPyIm 3091) 5'W C T A TT G W-3' PyHpPyHpHpIm-y-Pypypygppylm 3092) 5'W C T A TT C W-3' PyHpPyHpHpPy-y-ImPyPyHpPyIm 3093) 5'W C T A TA T W-3' PyHpPyHpPyHp-y-pyHpPyHpPyIm 3 0 94 5' C T A TA A W-3 ' PyHpPyHpPyPy-y-HpHpPyHpPyIm ) W
3 095 5' C T A TA G W-3 ' PyHpPyHpPyIm-y-PyHpPyHpPyIm ) W
3096) 5'W C T A TA C W-3' pYHPPYHPPYPY-Y-ImHppyHppyIm 3097) 5'W C T A TG T W-3' PYHPPYHPImHp-y-PyPyPyHpPyim 3 098 5' C T A TG A W-3 ' PyHppyHpImPy-y-HpPyPyHpPyIm ) W
3099) 5'W C T A TG G W-3' PyHpPyHpImIm-y-Pypypygppylm 3100) 5'W C T A TG C W-3' PyHpPyHpImPy-y-ImPyPyHpPyIm 3101) 5'W C T A TC T W-3' PyHpPyHpPyHp-y-PyImPyHpPyIm 3102 5' C T A TC A W-3 ' PyHpPyHpPyPy-y-HpImPyHpPyIm ) W
3103 5' C T A TC G W-3 ' PyHppyHppylm-y_pyImPYHpPyIm ) W
3104 5' C T A TC C W-3' PyHpPyHpPyPy-y-ImImPyHpPyIm ) W
3105) 5'W C T A AT T W-3' PyHpPyPyHpHp-y-PypyHpHpPyIm 3106) 5'W C T A AT A W-3' PyHpPyPyHpPy-y-HpPyHpHpPyIm 3107) 5'W C T A AT G W-3' PyHpPyPyHpIm-y-PyPyHpHpPyIm 3108) 5'W C T A AT C W-3' PyHpPyPyHpPy-y-ImPyHpHpPyIm 3109) 5'W C T A AA T W-3' PyHpPyPyPyHp-y-PyHpHpHpPyIm 3110 5' C T A AA A W-3 ' PyHpPyPyPyPy-y-HpHpHpHpPyIm ) W
3111) 5'W C T A AA G W-3' PyHpPyPyPyIm-y-PyHpHpHpPyIm 3112) 5'W C T A AA C W-3' PyHpPyPyPyPy-y-ImHPHpHppyIm 3113 5' C T A AG T W-3 ' PyHpPyPyImHp-y-PyPyHpHpPyIm ) W
3114 5' C T A AG A W-3' PyHpPyPyImPy-y-HpPyHpHpPyIm ) W
3115) 5'W C T A AG G W-3' PyHpPyPyImIm-y-pyPyHpHpPyIm 3116) 5'W C T A AG C W-3' PYHPPYPYImPy-y-ImPyHpHpPyIm 3117 5' C T A AC T W-3 ' PyHpPyPyPyHp-y-PyImHpHpPyIm ) W
3118 5' C T A AC A W-3 ' PyHpPyPyPyPy-y-HpImHpHpPyIm ) W
3119 5' C T A AC G W-3 ' PyHpPyPyPyIm-y-PyImHpHpPyIm ) W
3120) 5'W C T A AC C W-3' PyHpPyPyPyPy-y-ImImHpHpPyIm TABLE
145:
I2-ring Hairpin Yolyamides for recognition of 8-by 5'-WCTASNNW-3' DNA aromatic amino acid sequence sequence 3121) 5'W C T A GT T W-3' PyHpPyImHpHp-y-PyPyPyHpPyIm 3122 ) ~5' C T A GT A W-3 PyHpPyImHpPy-y-HpPyPyHpPyIm W ' 3123 ) 5' C T A GT G W-3 PyHpPyImHpIm-y-PyPyPyHpPyIm W ' 3124) 5'W C T A GT C W-3' PyHpPyImHpPy-y-ImPyPyHpPyIm 3125 ) 5' C T A GA T W-3 PyHpPyImPyHp-y-PyHpPyHpPyIm W ' 3126) 5'W C T A GA A W-3' PyHpPyImPyPy-y-HpHpPyHpPyIm 3127 ) 5' C T A GA G W-3 PyHpPyImPyIm-y-PyHpPyHpPyIm W ' 3128 ) 5' C T A GA C W-3 PyHpPyImPyPy-y-ImHpPyHpPyIm W ' 3129) 5'W C T A GG T W-3' PyHpPyImImHp-y-PyPyPyHpPyIm 313 0 5' C T A GG A W- 3 PyHpPyImImPy-y-HpPyPyHpPyIm ) W ' 3131) 5'W C T A GC T W-3' PyHpPyImPyHp-y-PyImPyHpPyIm 3132 ) 5' C T A GC A W-3 PyHpPyImPyPy-y-HpImPyHpPyIm W ' 3133) 5'W C T A GG G W-3' PyHpPyImImIm-y-PyPyPyHpPyIm 3134) 5'W C T A GG C W-3' PyHpPyImImPy-y-ImPyPyHpPyIm 33.35) 5'W C T A GC G W-3' PyHpPyImPyIm-y-PyImPyHpPyIm 3136) 5'W C T A GC C W-3' PyHpPyImPyPy-y-ImImPyHpPyIm 3137 ) 5' C T A CT T W-3 PyHpPyPyHpHp-y-PyPyImHpPyIm W ' 313 8 5' C T A CT A W-3 PyHpPyPyHpPy-y-HpPyImHpPyIm ) W ' 3139) 5'W C T A CT G W-3' PyHpPyPyHpIm-y-PyPyImHpPyIm 3140 ) 5' C T A CT C W-3 PyHpPyPyHpPy-y- ImPyImHpPyIm W ' 3141) 5'W C T A CA T W-3' PyHpPyPyPyHp-y-PyHpImHpPyIm 3142) 5'W C T A CA A W-3' PyHpPyPyPyPy-y-HpHpImHpPyIm 3143 ) 5' C T A CA G W-3' ~ PyHpPyPyPyIm-y-PyHpImHpPyIm W
3144) 5'W C T A CA C W-3' PyHpPyPyPyPy-y-ImHpImHpPyIm 3145) 5'W C T A CG T W-3' PyHpPyPyImHp-y-PyPyImHpPyIm 3146) 5'W C T A CG A W-3' PyHpPyPyImPy-y-HpPyImHpPyIm 3147 ) 5' C T A CC T W-3' PyHpPyPyPyHp-y-PyImImHpPyIm W
3148) 5'W C T A CC A W-3' PyHpPyPyPyPy-y-HpImImHpPyIm 3149) 5'W C T A CG G W-3' PyHpPyPyImIm-y-PyPyImHpPyIm 3150) 5'W C T A CG C W-3' PyHpPyPyImPy-y-ImPyImHpPyIm 3151) 5'W C T A CC G W-3' PyHpPyPyPyIm-y-PyImImHpPyIm 3152) 5'W C T A CC C W-3' PyHpPyPyPyPy-y-ImImImHpPyIm TABLE 14b: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTCWNNW-3' DNA sequence aromatic amino acid sequence 3153) 5'W C T C T T T W-3' PyHpPyHpHpHp-y-PyPyPyImPyIm 3154 ) 5~' W C T C T T A W- 3 ' PyHpPyHpHpPy-y-HpPyPyImPyIm 3155 ) 5' C T CT T G W-3 ' PyHpPyHpHpIm-y-PyPyPyImPyTm W
3156) 5'W C T CT T C W-3' PyHpPyHpHpPy-y-ImPyPyImPyIm 3157 ) 5' C T CT A T W-3' PyHpPyHpPyHp-y-PyHpPyImPyIm W
3158) 5'W C T CT A A W-3' PyHpPyHpPyPy-y-HpHpPyImPyIm 3159) 5'W C T CT A G W-3' PyHpPyHpPyIm-y-PyHpPyImPyIm 3160) 5'W C T CT A C W-3' PyHpPyHpPyPy-y-ImHpPyImPyIm 3161) 5'W C T CT G T W-3' PyHpPyHpImHp-y-PyPyPyImPyIm 3162) 5'W C T CT G A W-3' PyHpPyHpImPy-y-HpPyPyImPyIm 3163) 5'W C T CT G G W-3' PyHpPyHpImIm-y-PyPyPyImPyIm 3164) 5'W C T CT G C W-3' PyHpPyHpImPy-y-ImPyPyImPyIm 3165 ) 5' C T CT C T W-3 ' PyHpPyHpPyHp-y-PyImPyImPyIm W
3166 ) 5' W C T C T C A W-3 ' PyHpPyHpPyPy-y-HpImPyImPyIm 3167 ) 5' W C T C T C G W-3' PyHpPyHpPyIm-y-PyImPyImPyIm 3168) 5'W C T C T C C W-3' PyHpPyHpPyPy-y-ImImPyImPyIm 3169) 5'W C T C A T T W-3' PyHpPyPyHpHp-y-PyPyHpImPyIm 3170) 5'W C T C A T A W-3' PyHpPyPyHpPy-y-HpPyHpImPyIm 3171) 5' W C T C A T G W-3' PyHpPyPyHpIm-y-PyPyHpImPyIm 3172) 5'W C T C A T C W-3' PyHpPyPyHpPy-y-ImPyHpImPyIm 3173) 5'W C T C A A T W-3' PyHpPyPyPyHp-y-PyHpHpImPyIm 3174 ) 5'W C T C AA A W-3' PyHpPyPyPyPy-y-HpHpHpImPyIm 3175) 5'W C T C AA G W-3' 'PyHpPyPyPyIm-y-PyHpHpImPyIm 317 6 ) 5'W C T C AA C W-3 ' PyHpPyPyPypy-y- ImHpHpImPyIm 3177) 5'W C T C AG T W-3' PyHpPyPyImHp-y-PyPyHpImPyIm 317 8 ) 5'W C T C AG A W-3 ' PyHpPyPyImPy-y-HpPyHpImPyIm 317 9 ) 5'W C T C AG G W-3 ' PyHpPyPyImIm-y-PyPyHpImPyIm 3180) 5'W C T C AG C W-3' PyHpPyPyImPy-y-ImPyHpImPyIm 3181) 5'W C T C AC T W-3' PyHpPyPyPyHp-y-PyImHpImPyIm 3182 ) 5'W C T C AC A W-3 ' PyHpPyPyPyPy-y-HpImHpImPyIm 3183 ) 5'W C T C AC G W-3 ' PyHpPyPyPyIm-y-PyImHpImPyIm 3184) 5'W C T C AC C W-3' PyHpPyPyPyPy-y-ImImHpImPyIm TABLE
147:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTCSNNW-3' DNA aromatic amino acid sequence sequence 3185) 5'W C T C GT T W-3' PyHpPyImHpHp-y-PyPyPyImPyIm 3186) 5~'WC T C GT A W-3' PyHpPyImHpPy-y-HpPyPyImPyIm 3187 ) 5' C T C GT G W-3 ' PyHpPyImHpIm-y-PyPyPyImPyIm W
3188) 5'W C T C GT C W-3' PyHpPyImHpPy-y-ImPyPyImPyIm 3189 ) 5' C T C GA T W-3 ' PyHpPyImPyHp-y-PyHpPyImPyIm W
3190) 5'W C T C GA A W-3' PyHpPyImPyPy-y-HpHpPyImPyIm 3191) 5'W C T C GA G W-3' PyHpPyImPyIm-y-PyHpPyImPyIm 3192 ) 5' C T C GA C W-3 ' PyHpPyImPyPy-y- ImHpPyImPyIm W
3193 ) 5' C T C GG T W-3' PyHpPyImImHp-y-PyPyPyImPyIm W
3194 ) 5' C T C GG A W-3 ' PyHpPyImImPy-y-HpPyPyImPyIm W
3195) 5'W C T C GC T W-3' PyHpPyImPyHp-y-PyImPyImPyIm 3196) 5'W C T C GC A W-3' PyHpPyImPyPy-y-HpImPyImPyIm 3197 ) 5' C T C CT T W-3' PyHpPyPyHpHp-y-PyPyImImPyIm W
3198 ) 5' C T C CT A W-3' PyHpPyPyHpPy-y-HpPyImImPyIm W
3199 ) 5' C T C CT G W-3 ' PyHpPyPyHpIm-y-PyPyImImPyIm W
3200) 5'W C T C CT C W-3' PyHpPyPyHpPy-y-ImPyImImPyIm 3201) 5'W C T C CA T W-3' PyHpPyPyPyHp-y-PyHpImImPyIm 3202) 5'W C T C CA A W-3' PyHpPyPyPyPy-y-HpHpImImPyIm 3203 ) 5' C T C CA G W-3' PyHpPyPyPyIm-y-PyHpImImPyIm W
3204) 5'W C T C CA C W-3' PyHpPyPyPyPy-y-ImHpImImPyIm 3205) 5'W C T C CG T W-3' PyHpPyPyImHp-y-PyPyImImPyIm 3206 ) 5' C T C CG A W-3 ' PyHpPyPyImPy-y-HpPyImImPyIm W
3207) 5'W C T C CC T W-3' PyHpPyPyPyHp-y-PyImImImPy3m 3208) 5'W C T C CC A W-3' PyHpPyPyPyPy-y-HpImImImPyIm 3209) 5'W C T C GG G W-3' PyHpPyImImIm-y-PyPyPyImPyIm 3210) 5'W C T C GG C W-3' PyHpPyImImPy-y-ImPyPyImPyIm 3211) 5'W C T C GC G W-3' PyHpPyImPyIm-y-PyImPyImPyIm 3212) 5'W C T C GC C W-3' PyHpPyImPyPy-y-ImImPyImPyIm 3213 ) 5' C T C CG G W-3' PyHpPyPyImIm-y-PyPyImImPyIm W
3214) 5'W C T C CG C W-3' PyHpPyPyImPy-y-ImPyImImPyIm 3215) 5'W C T C CC G W-3' PyHpPyPyPyIm-y-PyImImImPyIm 3216) 5'W C T C CC C W-3' PyHpPyPyPyPy-y-ImImImImPyIm TABLE 148: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGGWNNW-3' -DNA aromatic amino acid sequence sequence ' 1233(3) 5' -W G G G T T T W-3' ImImIm-(3-HpHp-y-pypy-(3-pypypy S 1234(3) 5' -W G G G T T A W-3' ImImIm-(3-HpPy-Y-HpPy-(3-Pypypy 1235(3) 5' -W G G G T T G W-3' ImImIm-(3-HpIm-y-Pypy-~-pypypy ' 1236(3) 5' -W G G G T T C W-3' ImImIm-(3-HpPy-Y-ImPy-(3-Pypypy 1237(3) 5'-WG G G T AT W-3' ImImIm-J3-PyHp-Y-pyHp-(3-Pypypy 1238(3) 5'-WG G G T AA W-3' ImImIm-(3-PyPy-y-HpHp-(3-PyPypy 1239(3) 5'-WG G G T AG W-3' ImImIm-(3-Pylm-y-PyHp-(3-pypypy 12403) 5'-WG G G T AC W-3' ImImIm-(3-PyPy-y-ImHp-~3-pypypy 12413) 5'-WG G G T GT W-3' ImImIm-~-ImHp-y-pypy-~-pypypy 1242(3) 5'-WG G G T GA W-3' ImImIm-(3-ImPy-y-HpPy-~3-PyPypy 1243(3) 5'-WG G G T GG W-3' ImImIm-/3-Imlm-y-pypy-p-pypypy 12443) 5'-WG G G T GC W-3' ImImIm-~3-ImPy-Y-ImPy-[3-PyPyPy 1245(3) 5' -W G G G T C T W-3' ImImIm-~3-PyHp-Y-Pylm-~-Pypypy 12463) 5' -W G G G T C A W-3' ImImIm-(3-PyPy-y-Helm-~3-pypypy 12473) 5' -W G G G T C G W-3' ImImIm-~3-Pyim-Y-PyIm-(3-PyPyPy 12483) 5' -W G G G T C C W-3' ImImIm-(3-PyPy-y-ImIm-(3-PyPyPy 1249~i) 5' -WG G GA T T W-3' ImImIm-(3-HpHp-y-pypy-j3-pypypy 1250(3) 5' -WG G GA T A W-3' ImImIm-/3-HpPy-y-HpPy-p-pypypy 1251(3) 5' -WG G GA T G W-3' ImImIm-(3-HpIm-y-PyPy-~3-pypypy 1252(3) 5' -WG G GA T C W-3' ImImIm-(3-HpPy-y-ImPy-(3-Pypypy 12533) 5' -WG G GA A T W-3' ImImIm-(3-PyHp-y-PyHp-~3-Pypypy 1254(3) 5' -WG G GA A A W-3' ImImIm-~i-Pypy-y-HpHp-a_pypypy 1255(3) 5' -WG G GA A G W-3' ImImIm-(3-PyIm-y-pyHp-(3-PyPyPy 1256(3) 5' -WG G GA A C W-3' ImImIm-~3-PyPy-y-I~p_~_pypypy 1257(3) 5' -WG G GA G T W-3' ImImIm-(3-ImHp-Y-PyPY-~-pYPYPY
1258(3) 5' -WG G GA G A W-3' ImImIm-~3-ImPy-y-HpPy-(3-PyPyPy 1259(3) 5' -WG G GA G G W-3' ImImIm-(3-Im=m-y-pypy-~3-pypypy 1260~i) 5' -WG G GA G C W-3' ImImIm-(3-ImPy-y-ImPy-~3-PyPyPy 1261(3) 5' -WG G GA C T W-3' ImImIm-(3-PyHp-Y-pylm_~3_pypypy 12623) 5' -WG G GA C A W-3' ImImIm-(3-PyPy-y-Hplm-(3-PyPyPy 1263(3) 5' -WG G GA C G W-3' ImImIm-(3-P ylm-y-Pylm-p-Pypypy 1264(3) 5' -WG G GA C C W-3' ImImIm-(3-PyPy-y-Imlm-~3-Pypypy TABLE
149:
12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGGGSNNW-3' DNA aromatic amino acid sequence sequence 1265 (3)5' -WG G G G TT W-3' ImImImIm-(3-Hp-y-Py-~-PyPyPyPy 1266 (3)~ -WG G G G TA W-3' ImImImIm-~-Py-y-Hp-~i-PyPyPyPy 5' 1267 (3)5' -WG G G G TG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy 1268 (3)5' -WG G G G TC W-3' ImImImIm-(3-Py-y-Im-~i-PyPyPyPy 1269 ~3)5' -WG G G G AT W-3' ImImImIm-(3-Hp-y-Py-(3-PyPyPyPy 1270 (3)5' -WG G G G AA W-3' ImImImIm-(3-Py-y-Hp-~3-PyPyPyPy 1271 (3)5' -WG G G G AG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy 1272 ~)5' -WG G G G AC W-3' ImImImIm-(3-Py-y-Im-(3-PyPyPyPy 1275 (3)5' -WG G G G CT W-3' ImImImIm-(3-Hp-y-PyImPy-(3-PyPy 1276 (3)5' -WG G G G CA W-3' ImImImIm-(3-Py-y-HpImPy-~i-PyPy 1277 (3)5' -WG G G C TT W-3' ImImIm-(3-HpHp-y-PyPyIm-(3-PyPy 1278 ~3)5' -WG G G C TA W-3' ImImIm-~3-HpPy-y-HpPyIm-(3-PyPy 1279 (3)5' -WG G G C TG W-3' ImImIm-~3-HpIm-y-PyPyIm-~3-PyPy 1280 (3)5' -WG G G C TC W-3' ImImIm-(3-HpPy-y-ImPyIm-p-PyPy 1281 (3)5' -WG G G C AT W-3' ImImIm-(3-PyHp-y-PyHpIm-(3-PyPy 1282 (3)5' -WG G G C AA W-3' ImImIm-(3-PyPy-y-HpHpIm-p-PyPy 1283 (3)5' -WG G G C AG W-3' ImImIm-(3-PyIm-y-PyHpIm-(3-PyPy 1284 (3)5' -WG G G C AC W-3' ImImIm-(3-PyPy-y-ImHpIm-(3-PyPy 1285 (3)5' -WG G G C GT W-3' ImImIm-(3-ImHp-y-PyPyIm-(3-PyPy 1286 ~3)5' -WG G G C GA W-3' ImImIm-(3-ImPy-y-HpPyIm-(3-PyPy 1287 (3)5' -WG G G C CT W-3' ImImIm-(3-PyHp-y-PyImIm-~3-PyPy 2S 1288 (3)5' -WG G G C CA W-3' ImImIm-~i-PyPy-y-HpImIm-J3-PyPy G52 5' -WG G G G CC W-3' ImImImIm-~3-Py-y-ImImPy-~3-PyPy (3) G53 5' -WG G G C GG W-3' ImImIm-(3-ImIm-y-PyPyIm-(3-PyPy (3) G54 5' -WG G G C GC W-3' ImImIm-~3-ImPy-y-ImPyIm-(3-PyPy (3) G55 5' -WG G G C CG W-3' ImImIm--Pylm-y-Pylmim-~3-PyPy ~3) G56 5' -WG G G C CC W-3' ImImIm--PyPy-y-ImImIm-(3-PyPy (3) TABLE -Hairpin 150: Polyamides 12-ring for (3 recognition of 8-by S'-WGGTWNNW-3' .
DNA aromatic amino acid sequence sequence 1289(3) 5' -W G GT T T T W-3' ImIm-(3-HpHpHp-y-pypypy-~3-pypy 12903} 5' -W G GT T T A W-3' ImIm-(3-HpHpPy-y-HpPyPy-(3-PyPy S 1291} ~ -W G GT T T G W-3' ImIm-~3-HpHpIm-y-Pypypy-(3-pypy 5' 1292(3) 5' -W G GT T T C W-3' ImIm-(3-HpHpPy-y-ImPypy-~i-Pypy 1293(3) 5' -W G GT T A T W-3' ImIm-G3-HpPyHp-y-pyHpPy-~3-pyPy 12943} 5' -W G GT T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-~3-PyPy 1295(3) 5' -W G GT T A G W-3' Imlm-(3-HpPyIm-y-PyHpPy-(3-PyPy 12963) 5' -W G GT T A C W-3' ImIm-~I-HpPypy-y-ImHppy_~_pyp~, 12973) 5' -W G GT T G T W-3' Imam-~3-HpImHp-y-pypypy-(3-pypy 12983) 5' -W G GT T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-PyPy 12993) 5' -W G GT T G G W-3' ImIm-~-HpImIm-y-PyPyPy-~3-Pypy 1300) 5' -W G GT T G C W-3' ImIm-(3-HpImPy-y-ImPyPy-(3-PYPy 1301(3) 5' -W G GT T C T W-3' Imam-p-HpPyHp-y-PyImPy-p-pypy 1302(3) 5' -W G GT T C A W-3' ImIm-~-HpPyPy-y-HpImPy-(3-PYPy 1303(3) 5' -W G GT T C G W-3' ImIm-p-HpPyIm-y-PyImPy-~3-PyPy 1304(3) 5' -W G GT T C C W-3' ImIm-(3-HpPyPy-y-ImImPy-(3-PyPy 1305(3) 5' -W G GT A T T W-3' Imlm-(3-PYHpHp-y-PyPYHp-~3-PyPy 1306~i) 5' -W G GT A T A W-3' ImIm-~3-PyHpPy-y-HpPyHp-(3-PyPy 13073) 5' -W G GT A T G W-3' ImIm-~3-PyHpIm-y-PyPyHp-(3-PyPy 13083) 5' -W G GT A T C W-3' Imam-(3-PyHpPy-y-ImPyHp-p-pyPy 1309(3) 5' -W G GT A A T W-3' ImIm-p-PyPyHp-y-PyHpHp-(3-PyPy 1310(3) 5' -W G GT A A A W-3' ImIm-p-PyPyPy-y-HpHpHp-/3-PyPy 2S 1311(3) 5' -W G GT A A G W-3' ImIm-~i-PyPyIm-y-PyHpHp--Pypy 1312(3) 5' -W G GT A A C W-3' ImIm-(3-PyPYPy-y-ImHpHp-~3-PyPy 1313(3) 5' -W G GT A G T W-3' Imlm-[3-PyImHp-y-PypyHp-(3-PYPy 13143) 5' -W G GT A G A W-3' Imlm-~i-pyImPy-y-HpPyHp-(3-pypy 1315(3) 5' -W G GT A G G W-3' Imlm-(3-PyImIm-y-PyPYHp-(3-PyPy 1316(3} 5' -W G GT A G C W-3' Imlm-~i-PyImPy-y-ImPyHp-(3-PyPy 1317~i) 5' -W G GT A C T W-3' ImIm-(3-PyPyHp-y-PyImHp-p-pypy 1318(3) 5' -W G GT A C A W-3' ImIm-(3-PyPyPy-y-HpImHp-p-PyPy 1319~i) 5' -W G GT A C G W-3' ImIm-(3-PyPyIm-y-PyImHp-~3-Pypy 1320(3) 5' -W G GT A C C W-3' ImIm-(3-PyPYPy-y-ImImHp-p-PyPy TABLE 151: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGTSNNW-3' DNA sequence aromatic amino acid sequence 1321(3) 5' -W G G T G T T W-3' ImIm-(i-ImHpHp-y-PyPyPy-(3-PyPy 1322(3) 5' -W G G T G T A W-3' Imlm-J3-ImHpPy-y-HpPyPy-~3-PyPy 1323(3) 5' -W G G T G T G W-3' ImIm-(3-ImHpIm-y-PyPyPy-p-PyPy 1324(3) 5' -W G G T G T C W-3' ImIm-(3-ImHpPy-y-ImPyPy-(3-PyPy 1325(3) 5' -W G G T G A T W-3' Imlm-(3-ImPyHp-y-PyHpPy-~3-PyPy 1326(3) 5' -WG G T G AA W-3' ImIm-(3-ImPyPy-y-HpHpPy-(3-PyPy 1327(3) 5' -WG G T G AG W-3' ImIm-~i-ImPyIm-y-PyHpPy-(3-PyPy 1328(3) 5' -WG G T G AC W-3' ImIm-(3-ImPyPy-y-ImHpPy-J3-Pypy 1329(3) 5' -WG G T G GT W-3' ImIm-(3-ImImHp-y-PyPyPy-(3-PyPy 1330(3) 5' -WG G T G GA W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy 1331(3) 5' -WG G T G CT W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy 1332(3) 5' -WG G T G CA W-3' ImIm-(3-ImPyPy-y-HpImPy-~3-PyPy 1333(3) 5' -WG G T G GG W-3' Imlm-(3-ImImIm-y-PypyPy-(3-PyPy 1334(3) 5' -W G G T G G C W-3' Imam-(3-ImImPy-y-ImPyPy-~i-PyPy 13353) 5' -W G G T G C G W-3' ImIm-p-ImPyIm-y-PyImPy-(3-PyPy 1336(3) 5' -W G G T G C C W-3' ImIm-(3-ImPyPy-y-ImImPy-~-PyPy 1337) 5' -W G G T C T T W-3' ImIm-~3-PyHpHp-y-PyPyIm-(3-PyPy 13383) 5' -W G G T C T A W-3' ImIm-(3-PyHpPy-y-HpPyIm-(3-PyPy 1339(3) 5' -W G G T C T G W-3' ImIm-~i-PyHpIm-y-PyPyIm-(3-PyPy 13403) 5' -W G G T C T C W-3' ImIm-(3-PyHpPy-y-ImPyIm-~3-PyPy 13413) 5' -W G G T C A T W-3' ImIm-~i-PyPyHp-y-PyHpIm-(3-PyPy 13423) 5' -W G G T C A A W-3' Imlm-(3-PyPyPy-y-HpHpIm-(3-PyPy 1343(3) 5' -W G G T C A G W-3' ImIm-(3-PyPyIm-y-PyFipIm-(3-PyPy 13440 5' -W G G T C A C W-3' ImIm-~i-PyPyPy-y-imHpIm-(3-PyPy 1345(3) 5' -W G G T C G T W-3' ImIm-(3-PyImHp-y-PyPyIm-(3-PyPy 1346(3) 5' -W G G T C G A W-3' Imlm-(3-PyImPy-y-HpPyIm-(3-PyPy 13470 5' -W G G T C C T W-3' Imlm-(3-PyPyHp-y-PyImIm-~3-PyPy 1348(3) 5' -W G G T C C A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy 1349~i) 5' -W G G T C G G W-3' Imlm-(3-PyImIm-y-PyPyIm-~3-PyPy 1350(3) 5' -W G G T C G C W-3' Imlm-(3-PyImPy-y-ImPyIm-(3-PyPy 1351(3) 5' -W G G T C C G W-3' ImIm-(3-PyPyIm-y-PyImIm-(3-PyPy 1352ø) 5' -W G G T C C C W-3' Imlm-~3-PyPyPy-y-ImImIm-~i-PyPy TABLE 152: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGAVVNNW-3' -DNA sequence aromatic amino acid sequence 1353(3) 5' -W G T T T W-3' ImIm-~3-HpHpHp-y-pypypy-(3-pypy G A
1354(3) '5'-W G T T A W-3' ImIm-~3-HpHpPy-y-HpPyPy-(3-PyPy G A
1355(3) 5' -W G T T G W-3' ImIm-(3-HpHp3m-y-PypyPy-~3-PyPy G A
1356(3) 5' -W G T T C W-3' ImIm-~-HpHpPy-y-ImPyPy-[3-PyPy G A
1357(3) 5' -W G T A T W-3' ImIm-(3-HpPyHp-y-PyHpPy-~-pypy G A
13583) 5'-W G T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-(3-PyPy G A
13593) 5'-W G GA T A G W-3' ImIm-(3-HpPyIm-y-PyHpPy-(3-PyPy 1360(3) 5'-W G GA T A C W-3' ImIm-~3-HppyPy-y-ImHppy_~3_pypy 1361(3) 5'-W G GA T G T W-3' ImIm-~3-HpImHp-y-pypypy_~_pypy 1362(3) 5'-W G GA T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-pypy 1363(3) 5'-W G GA T G G W-3' Imlm-~3-HpImIm-y-PyPyPy-(3-PyPy 1364(3) 5'-W G GA T G C W-3' Imlm-~3-HpImPy-y-ImPyPy-(3-PyPy 1365(3) 5'-W G GA T C T W-3' ImIm-R-HpPyHp-y-PyImPy-(3-PyPy 13663) 5'-W G GA T C A W-3' ImIm-(3-HpPyPy-y-HpImPy-(3-PyPy 13673) 5'-W G GA T C G W-3' ImIm-(3-HpPyIm-y-PyIrr~Py-(3-PyPy 1368(3) 5'-W G GA T C C W-3' ImIm-(3-HpPyPy-y-ImImpy-(3-Pypy 1369(3) 5'-W G GA A T T W-3' Imlm-p-PyHpHp-y-PypyHp-(3-PyPy 1370(3) 5'-W G GA A T A W-3' ImIm-(3-PyHpPy-y-HpPyHp-/3-PyPy 1371(3) 5'-W G GA A T G W-3' ImIm-J3-PyHpIm-y-PyPyHp-(3-PyPy 1372(3) 5'-W G GA A T C W-3' Imlm-~3-pyHpPy-y-ImPyHp-j3-PyPy 13733) 5'-W G GA A A T W-3' ImIm-(3-PyPyHp-y-pyHpHp-~i-Pypy 1374(3) 5'-W G GA A A A w-3' ImIm-(3-PyPyPy-y-HpHpHp-(3-PyPy 13753) 5'-W G GA A A G W-3' Imlm-(3-PyPyIm-y-PyHpHp-~3-PyPy 1376(3) 5'-W G GA A A C W-3' ImIm-~i-Pypypy-y-I~pHp_(3_pyp~, 13773) 5'-W G GA A G T W-3' Imam-a-pyImHp-y-PypyHp-~3-PyPy 13783) 5'-W G GA A G A W-3' ImIm-~3-pyImPy-y-HpPyHp-~3-PyPy 1379(3) 5'-W G GA A G G W-3' Imlm-(3-PyImIm-y-PypyHp-~3-Pypy 1380(3) 5'-W G GA A G C W-3' Imlm-(3-PyImPy-y-ImPyHp-~3-PyPy 1381~i) 5'-W G GA A C T W-3' ImIm-~3-PyPyHp-y-PyImHp-(3-PyPy 1382~i) 5'-W G GA A C A W-3' Imlm_(3_pypypy_y_Hp=~p-(3-pypy 1383(3) 5'-W G GA A C G W-3' ImIm-(3-PyPyim-y-pyImHp-(3-PyPy 13843) 5'-W G GA A C C W-3' ImIm-(3-PypyPy-y-ImImHp-~3-Pypy WO 98/370b7 PCT/US98/01714 TABLE
153:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGASNNW-3' DNA aromatic amino acid sequence sequence 1385(3) 5' -WG G A GT T W-3' ImIm-~i-ImHpHp-y-PyPyPy-~3-PYPy 13863) ' -WG G A GT A W-3' ImIm-~i-ImHpPy-y-HpPyPy-~3-PyPy 5' 1387(3) 5' -WG G A GT G W-3' Imlm-~3-ImHpIm-y-PyPyPy-~3-PyPy 1388(3) 5' -WG G A GT C W-3' ImIm-~i-ImHpPy-y-ImPyPy-~3-PyPy 1389(3) 5' -WG G A GA T W-3' ImIm-~3-TmPyHp-y-PyHpPy-(3-PyPy 1390(3) 5' -WG G A GA A W-3' ImIm-~i-ImPyPy-y-HpHpPy-(3-PyPy 13913) 5' -WG G A GA G W-3' ImIm-~3-ImPyIm-y-PyHpPy-(3-PyPy 1392(3) 5' -WG G A GA C W-3' ImIm-(3-ImPyPy-y-ImHpPy-(3-PyPy 13933) 5' -WG G A GG T W-3' ImIm-(3-ImImHp-y-PyPyPy-[3-PyPy 13943) 5' -WG G A GG A W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy 1395(3) 5' -WG G A GC T W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy 13963) 5' -WG G A GC A W-3' Imlm-(3-ImPyPy-y-HpImPy-(3-PyPy 1397(3) 5' -WG G A GG G W-3' Imlm-(3-ImImIm-y-PyPyPy-(3-PyPy 1398(3) 5' -WG G A GG C W-3' ImIm-/3-ImImPy-y-ImPYPy-(3-PyPy 1399(3) 5' -WG G A GC G W-3' ImIm-(3-ImPyIm-y-PyImPy-(3-PyPy 1400(3) 5' -WG G A GC C W-3' ImIm-~-ImPyPy-y-ImImPy-(3-PyPy 1401~i) 5' -WG G A CT T W-3' Imlm-(3-PyHpHp-y-PYPyIm-/3-PyPy 1402(3) 5' -WG G A CT A W-3' ImIm-(3-PyHpPy-y-HpPyIm-R-PyPy 1403(3) 5' -WG G A CT G W-3' ImIm-(3-PyHpIm-y-PyPy3m-~3-PyPy 14043) 5' -WG G A CT C W-3' ImIm-~-PyHpPy-y-ImPyIm-(3-PyPy 14053) 5' -WG G A CA T W-3' ImIm-~3-PyPyHp-y-PyHpIm-(3-PyPy 1406~i) 5' -WG G A CA A W-3' ImIm-(3-PyPyPy-y-HpHpIm-p-PyPy 1407(3) 5' -WG G A CA G W-3' ~ImIm-(3-PyPyIm-y-PyHpIm--PyPy 1408(3) 5' -WG G A CA C W-3' ImIm-(i-PyPyPy-y-ImHpIm-(i-PyPy 1409~i) 5' -WG G A CG T W-3' ImIm-(i-PyImHp-y-PyPyIm-(3-PyPy 1410(3) 5' -WG G A CG A W-3' Imlm-(3-PyImPy-y-HpPyIm-~-PyPy 1411) 5' -WG G A CC T W-3' ImIm-~3-PyPyHp-y-PyImIm-(3-PyPy 1412(3) 5' -WG G A CC A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy 1413(3) 5' -WG G A CG G W-3' ImIm-~3-PyImIm-y-PyPYIm-~i-PyPy 1414(3) 5' -WG G A CG C W-3' Imam-~3-PyImPy-y-ImPyIm-p-PyPy 1415p) 5' -WG G A CC G W-3' ImIm-~i-PyPyIm-y-PyImIm-(3-PyPy 1416(3) 5' -WG G A CC C W-3' Imlm-(3-PyPyPy-y-ImImIm-~i-PyPy _~__... _.._ ? , . , TABLE 154:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGCWNNW-3' -DNA sequence aromatic amino acid sequence 1417(3) ImImPy-~3-HpHp-y-PyPy-(3-ImPyPy 5' -W
G G C
T T T
W-3' 1418(3) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-/3-ImPyPy C T
1419(3) 5' -W G G T G W-3' ImImPy-~3-HpIm-y-Pypy-(3-Impypy C T
14200 5' -W G G T C W-3' ImImPy-~-HpPy-y-ImPy-(3-ImPypy C T
14213) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pygp-~-ImPyPy C T
1422(3) 5' -W G G A A W-3' ImImPy-(3-Pypy-y-HpHp_~3-ImPyPy C T
1423(3) 5' -W G G A G W-3' ImImPy-(3-Pylm-y-pygp-~3-ImPyPy C T
1424(3) 5' -W G G A C W-3' C T ImImPy-(3-PyPy-y-ImHp-~i-ImPyPy 1425(3) 5' -W G G G T W-3' C T ImImPy-(3-ImHp-y-PyPy-(3-ImPyPy 1426) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-~-ImPyPy C T
1427(3) 5' -W G G G G W-3' ImImPy-(3-ImIm-y-Pypy-~-ImPyPy C T
1428(3) 5' -W G G G C W-3' ImImPy-(3-ImPy-y-ImPy-/3-ImPyPy C T
1429(3) 5' -W G G C T W-3' ImImPy-(3-PyHp-y-pyIm-(3-ImPyPy C T
1430(3) 5' -W G G C A W-3' ImImPy-~3-pypy-y-HpIm-J3-ImPyPy C T
1431(3) 5' -W G G C G W-3' ImImPy-~3-pylm-y-pylm_(~_ImPyPy C T
14323) 5' -W G G C C W-3' ImImPy-(3-pypy-y-Imlm-(3-ImPyPy C T
14330 5' -W G G T T W-3' ImImPy-(3-HpHp-y-Pypy-~3-ImPyPy C A
1434~i) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-(3-ImPyPy C A
14353) 5' -W G G T G W-3' ImImPy-(3-Hplm-y-Pypy-~3-ImPyPy C A
14363) 5' -W G G T C W-3' C A ImImPy-~i-HpPy-y-ImPy-(3-ImPyPy 1437(3) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pyHp-(3-ImPyPy C A
1438~i) 5' -W G G A A W-3' ImImPy-(3-PyPy-y-HpHp-(3-ImPyPy C A
1439(3) 5' -W G G A G W-3' Imlmpy-a-pyim-y-pyHp-(3-ImPyPy C A
1440(3) 5' -W G G A C W-3' C A ImImPy-(3-PyPy-y-ImHp-~3-ImPyPy 14413) 5' -W G G G T W-3' C A ImImPy-~3-ImHp-y-PyPy-(3-ImPyPy 14423) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-(3-ImPyPy C A
1443(3) 5' -W G G G G W-3' ImImPy-p-Imlm-y-PyPy-R-ImPyPy C A
1444(3) 5'-W G G G C W-3' ImImPy-~3-ImPy-y-Impy-(3-ImPyPy C A
1445(3) 5' -W G G C T W-3' ImImPy-(3-pyHp-y-pylm-~i-ImPyPy C A
1446(3) 5' -W G G C A W-3' ImImPy-(3-PyPy-y-Hplm-(3-ImPyPy C A
1447(3) 5' -W G G C G W-3' ImImPy-(3-Pylm-y-Pylm-/3-ImPyPy C A
14483) 5' -W G G C C W-3' ImImPy-(3-pypy-y-ImIm-/3-ImPypy C A
TABLE
155:
12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGGCSNNW-3' -DNA aromatic amino acid sequence sequence 1449R) 5'-W G GC G T T W-3' ImIm-(3-ImHpHp-y-PyPy-~3-ImPyPy 14503) ~5'-W G GC G T A W-3' Imlm-~3-ImHpPy-y-HpPy-(3-ImPyPy 1451(3) 5'-W G GC G T G W-3' ImIm-(3-ImHpIm-y-PyPy-(3-ImPyPy 1452(3) 5'-W G GC G T C W-3' Imlm-(3-ImHpPy-y-ImPy-(3-ImPyPy 14530 5'-W G GC G A T W-3' ImIm-(3-ImPyHp-y-PyHp-(3-ImPyPy 1454(3) 5'-W G GC G A A W-3' ImIm-(3-ImPyPy-y-HpHp-~3-ImPyPy 14553) 5'-W G GC G A G W-3' Imlm-~-ImPyIm-y-PyHp-(3-ImPyPy 1456(3) 5'-W G GC G A C W-3' ImIm-(3-ImPyPy-y-ImHp-(3-ImPyPy 1457~i) 5'-W G GC G G T W-3 Imlm-(3-ImImHp-y-PyPy-(3-ImPyPy 14583) 5'-W G GC G G A W-3' ImIm-~-ImImPy-y-HpPy-~-ImPyPy 1459(3) 5'-W G GC G C T W-3' ImIm-(3-ImPyHp-y-PyIm-(3-ImPyPy 1460(3) 5'-W G GC G C A W-3' Imlm-(3-ImPyPy-y-HpIm-(3-ImPyPy 14613) 5'-W G GC C T T W-3' Imlm-p-PyHpHp-y-Py-(3-ImImPyPy 1462(3) 5'-W G GC C T A W-3' ImIm-~3-PyHpPy-y-Hp-~-ImImPyPy 14633) 5'-W G GC C T G W-3' ImIm-/3-PyHpIm-y-Py-~i-ImImPyPy 1464(3) 5'-W G GC C T C W-3' Imlm-(3-PyHpPy-y-Im-(3-ImImPyPy 1465~i) 5'-W G GC C A T W-3' ImIm-(3-PyPyHp-y-Py-p-ImImPyPy .
1466(3) 5'-W G GC C A A W-3' ImIm-[3-PyPyPy-y-Hp-/3-ImImPyPy 1467(3) 5'-W G GC C A G W-3' ImIm-(3-PyPyIm-y-Py-(3-ImImPyPy 14683) 5'-W G GC C A C W-3' ImIm-p-PyPyPy-y-Im-(3-ImImPyPy 1469p) 5'-W G GC C G T W-3' Imlm-(3-PyImHp-y-Py-(3-ImImPyPy 1470(3) 5'-W G GC C G A W-3' Imlm-(3-PyImPy-y-Hp-~3-ImImPyPy 14713) 5'-W G GC C C T W-3' ' ImIm-J3-PyPyHp-y-PyImImIm-(3-Py 1472(3) 5'-W G GC C C A W-3' Imlm-~3-PyPyPy-y-HpImImIm-(3-Py G57(3) 5'-W G GC G G G W-3' Imlm-(3-ImImIm-y-PyPy-(3-ImPyPy G58(3) 5'-W G GC G G C W-3' Imlm-J3-ImImPy-y-ImPy-(3-ImPyPy G59~) 5'-W G GC G C G W-3' ImIm-~3-ImPyIm-y-PyIm-~3-ImPyPy G60(3) 5'-W G GC G C C W-3' ImIm-(3-ImPyPy-y-ImIm-(3-ImPyPy G6l~i) 5'-W G GC C G G W-3' ImIm-(3-PyImIm-y-Py-(3-ImImPyPy G62~3) 5'-W G GC C G C W-3' ImIm-(3-PyImPy-y-Im-(3-ImImPyPy G63(3) 5'-W G GC C C G W-3' ImIm-(3-PyPyIm-y-PyImImIm-(3-Py G64(3) 5'-W G GC C C C W-3' ImIm-(3-PyPyPy-y-ImImImIm-(3-Py TABLE 156:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCGWNNW-3' .
DNA aromatic amino acid sequence sequence 1473(3) 5'-WG C G T TT W-3' ImPyIm-(3-HpHp-y-PyPyPy-(3-ImPy 1474(3) ~5'-WG C G T TA W-3' ImPyIm-(3-HpPy-y-Hppypy-~3_Impy 1475(3) 5'-WG C G T TG W-3' ImPyIm-(3-Hplm-y-PyPyPy-~3-ImPy 1476(3) 5'-WG C G T TC W-3' ImPyIm-(3-HpPy-y-ImPyPy-(3-ImPy 1477(3) 5'-WG C G T AT W-3' ImPyIm-~-PyHp-y-pyHpPy-(3-ImPy 1478) 5'-WG C G T AA W-3' ImPyIm-~3-PyPy-y-HpHpPy-(3-ImPy 1479(3) 5'-WG C G T AG W-3' ImPyIm-(3-PyIm-y-pyHppy-(3-ImPy 14803) 5'-WG C G T AC W-3' ImPyIm-(3-PyPy-y-ImHpPy-(3-ImPy 1481(3) 5'-WG C G T GT W-3' ImPyIm-(3-ImHp-y-pypypy-~3-ImPy 14823) 5'-WG C G T GA W-3' ImPyIm-(3-ImPy-y-HpPyPy-p-ImPy 1483(3) 5'-WG C G T GG W-3' ImPyIm-(3-ImIm-y-Pypypy-(3-ImPy 14843) 5'-WG C G T GC W-3' ImPyIm-~3-ImPy-y-ImPyPy-j~-ImPy 1485(3) 5'-WG C G T CT W-3' ImPyIm-(3-PyHp-Y-PyImPy-(3-ImPy 1486(3) 5'-WG C G T CA W-3' ImPyIm-~3-PyPy-y-HpImPy-(3-ImPy 1487(3) 5'-WG C G T CG W-3' ImPyIm-(3-Pylm-y-PyImPy-~3-Irr~Py 1488(3) 5'-WG C G T CC W-3' ImPyIm-(3-PyPy-y-ImImPy-~i-ImPy 14893) 5'-WG C G A TT W-3' ImPyIm-~-HpHp-Y-PypyHp-/3-ImPy 1490(3) 5'-WG C G A TA W-3' ImPyIm-~-HpPy-y-HpPyHp-(3-ImPy 1491(3) 5'-WG C G A TG W-3' ImPyIm-(3-HpIm-y-PyPyHp-(3-ImPy 1492(3) 5'-WG C G A TC W-3' ImPyIm-(3-HpPy-y-ImPyHp-~-ImPy 1493(3) 5'-WG C G A AT W-3' ImPyIm-~3-PyHp-y-pyHpHp-(3-ImPy 14940 5'-WG C G A AA W-3' ImPyIm-(3-pyPy-y-HpHpHp-(3-ImPy 1495(3) 5'-WG C G A AG W-3' ImPyIm-(3-PyIm-y-PyHpHp-~3-ImPy 1496(3) 5'-WG C G A AC W-3' ImPyIm-(3-Pypy-y-ImHpHp-~3-ImPy 1497(3) 5'-WG C G A GT W-3' ImPyIm-~-ImHp-y-PyPyHp-(3-ImPy 1498(3) 5'-WG C G A GA W-3' ImPyIm-(3-ImPy-y-HpPyHp-(3-ImPy 1499(3) 5'-WG C G A GG W-3' ImPyIm-(3-Imlm-y-PyPyHp-p-ImPy 1490(3) 5'-WG C G A GC W-3' ImPyIm-/3-ImPy-y-ImPyHp-(3-ImPy 1501(3) 5'-WG C G A CT W-3' ImPyIm-(3-PyHp-y-PyImHp-(3-ImPy 1502(3) 5'-WG C G A CA W-3' ImPyIm-~3-PyPy-Y-HpImHp-p-ImPy 1503(3) 5'-WG C G A CG W-3' ImPyIm-(3-PyIm-y-pyImHp-a-ImPy 1504(3) 5'-WG C G A CC W-3' ImPyIm-p-PyPy-y-ImImHp-p-ImPy TABLE
157:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCGSNNW-3' -DNA aromatic amino acid sequence sequence 15053) 5'-W G C G GT T W-3' Im-(3-ImImHpHp-y-PyPyPy-(3-ImPy 1506(3) 5'-W G C G GT A W-3' Im-(3-ImImHpPy-y-HpPyPy-(3-ImPy 1507(3) 5'-W G C G GT G W-3' Im-(3-ImImHpIm-y-PyPyPy-(3-ImPy 1508(3) 5'-W G C G GT C W-3' Im-(3-ImImHpPy-y-ImPyPy-(3-ImPy 1509(3) 5'-W G C G GA T W-3' Im-(3-ImImPyHp-y-PyHpPy-(3-ImPy 1510(3) 5'-W G C G GA A W-3' Im-(3-ImImPyPy-y-HpHpPy-(3-Impy 1511~i) 5'-W G C G GA G W-3' Im-(3-ImImPyIm-y-PyHpPy-(3-ImPy 1512(3) 5'-W G C G GA C W-3' Im-(3-ImImPyPy-y-ImHpPy-(3-ImPy 1513(3) 5'-W G C G GG T W-3' Im-~3-ImImImHp-y-PyPyPy-p-ImPy 153-4(3) 5'-W G C G GG A W-3' Im-~3-ImImImPy-y-HpPyPy-(3-ImPy 1515(3) 5'-W G C G GC T W-3' Im-p-ImImPyHp-y-PyImPy-(3-ImPy 1516(3) 5'-W G C G GC A W-3' Im-~-ImImPyPy-y-HpImPy-~3-ImPy 1517(3) 5'-W G C G CT T W-3' ImPyIm-(3-HpHp-y-PyPyIm-~i-ImPy 1518(3) 5'-W G C G CT A W-3' ImPyIm-(3-HpPy-y-HpPyIm-~3-ImPy 1519(3) 5'-W G C G CT G W-3' ImPyIm-a-HpIm-y-PyPyIm-(3-ImPy 1520(3) 5'-W G C G CT C W-3' ImPyIm-(3-HpPy-y-ImPyIm-(3-ImPy 15213) 5'-W G C G CA T W-3' ImPyIm-(3-PyAp-y-PyHpIm-(3-ImPy 1522(3) 5'-W G C G CA A W-3' ImPyIm-(3-PyPy-y-HpHpIm-(3-ImPy 1523(3) 5'-W G C G CA G W-3' ImPyIm-(3-PyIm-y-PyHpIm-(3-ImPy 1524(3) 5'-W G C G CA C W-3' ImPyIm-~3-PyPy-y-ImHpIm-(3-ImPy 1525(3) 5'-W G C G CG T W-3' ImPyIm-(3-ImHp-y-PyPyIm-~3-ImPy 15263) 5'-W G C G CG A W-3' ImPyim-(3-ImPy-y-HpPyIm-(3-ImPy 1527) 5'-W G C G CC T W-3' ImPyIm-~i-PyHp-y-PyImIm-(3-ImPy 1528(3) 5'-W G C G CC A W-3' ImPyIm-~-PyPy-y-HpImIm-(3-ImPy G65~) 5'-W G C G GG G W-3' Im-~i-ImImImIm-y-PyPyPy-~i-ImPy G66~3) 5'-W G C G GG C W-3' Im-p-ImImImPy-y-ImPyPy-(3-ImPy G67(3) 5'-W G C G GC G W-3' Im-(3-ImImPyIm-y-PyImPy-/3-ImPy G68(3) 5'-W G C G GC C W-3' Im-(3-ImImPyPy-y-ImImPy-p-ImPy G69(3) 5'-W G C G CG G W-3' ImPyIm-(3-ImIm-y-PyPyIm-(3-ImPy G70~3) 5'-W G C G CG C W-3' ImPyIm-(3-ImPy-y-ImPyIm-~3-ImPy G71(3) 5'-W G C G CC G W-3' ImPyIm-~i-PyIm-y-PyImIm-p-ImPy G72(3) 5'-W G C G CC C W-3' ImPyIm-(3-PyPy-y-ImImIm-(3-ImPy ,, TABLE 158:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGCTWNNW-3' -DNA aromatic amino acid sequence sequence ' 1529(3) 5' G C T T T TW-3' ImPy-~3-HpHpHp-y-Pypypy_~3-ImPy -W
15303) - G C T T T AW-3' ImPy-~i-HpHpPy-y-HpPyPy-~3-ImPy 5' -W
1531(3) 5' G C T T T GW-3' ImPy-(3-HpHpIm-y-Pypypy-a-ImPy -W
15323) 5' G C T T T CW-3' ImPy-(3-HpHpPy-y-ImPyPy-(3-ImPy -W
15333) 5' G C T T A TW-3' ImPy-~3-HpPyHp-y-pyHpPy-~i-ImPy -W
1534(3) 5' G C T T A AW-3' ImPy-~3-HpPyPy-y-HpHpPy-(3-ImPy -W
15353) 5' G C T T A GW-3' ImPy-(3-HpPyIm-y-PyHpPy-(3-ImPy -W
1536~i) 5'-W G C T T A CW-3' ImPy-~;-Hppypy_y_I~ppy-~_Impy 15373) 5' G C T T G TW-3' ImPy-(1-HpImHp-y-PyPypy-(3-ImPy -W
1538(3) 5' G C T T G AW-3' ImPy-/3-HpImPy-y-HpPyPy-~i-ImPy -W
1539(3) 5' G C T T G GW-3' ImPy-~-HpImIm-y-Pypypy-(3-Impy -W
1540p) 5' G C T T G CW-3' ImPy-a-HpImPy-y-ImPyPy-~3-ImPy -W
1541(3) 5' G C T T C TW-3' ImPy-(3-HppyHp-y-pyImPy-~3-ImPy -W
1542~i) 5' G C T T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-~-ImPy -W
15433) 5' G C T T C GW-3' ImPy-~3-HpPyIm-y-pyImPy-p-ImPy -W
15443) 5' G C T T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-(3-ImPy -W
1545(3) 5' G C T A T TW-3' ImPy-(1-pyHpHp-y-pypyHp-(3-ImPy -W
15463) 5' G C T A T AW-3' Impy-(3-PyHppy-y-HppyHp-~i-ImPy -W
1547(3) 5' G C T A T GW-3' ImPy-(3-PyHpIm-y-pypyHp-~3-ImPy -W
1548(3) 5' G C T A T CW-3' ImPy-(3-PyHpPy-y-ImPyHp-p-ImPy -W
1549~i) 5' G C T A A TW-3' ImPy-(3-PyPyHp-y-pyHpHp-~i-ImPy -W
1550p) 5' G C T A A AW-3' ImPy-(3-PyPyPy-y-HpHpHp_~3-ImPy -W
1551(3) 5' G C T A A GW-3' ImPy-~-Pypylm-y_pyHpHp-(3-ImPy -W
1552(3) 5' G C T A A CW-3' ImPy-p-Pypypy-y-I~pHp-(3-ImPy -W
1553(3) 5' G C T A G TW-3' ImPy-~-PyImHp-y-PypyHp-(3-ImPy -W
1554(3) 5' G C T A G AW-3' ImPy-p-PyImPy-y-HpPyHp-/3-ImPy -W
1555(3) 5' G C T A G GW-3' Impy-(3-PyImIm-y-pypyHp-(3-ImPy -W
1556(3) 5' G C T A G CW-3' ImPy-~3-PyImPy-y-ImPyHp-(3-ImPy -W
I557(3) 5' G C T A C TW-3' ImPy-(3-PyPyHp-y-PyImHp-p-ImPy -W
15583) 5' G C T A C AW-3' ImPy-(3-Pypypy-Y_Hpl~p_~3_ImPy -W
1559(3) 5' G C T A C GW-3' ImPy-R-Pypylm-Y-PyImHp-/3-ImPy -W
1560~i) 5' G C T A C CW-3' Impy-~i-pypypy-y-ImImHp-(3-ImPy -W
TABLE
159:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCTSNNW-3' DNA aromatic amino acid sequence sequence 15613) 5'-W G C TG T T W-3' ImPy-j3-ImHpHp-y-PyPyPy-(3-ImPy 1562(3) 5'-W G C TG T A W-3' ImPy-~3-ImHpPy-y-HpPyPy-(3-ImPy 1563(3) 5'-W G C TG T G W-3' ImPy-(3-ImHpIm-y-PyPyPy-(3-ImPy 1564(3) 5'-W G C TG T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy 1565(3) 5'-W G C TG A T W-3' ImPy-(3-ImPyHp-y-PyHppy-(3-ImPy 1566(3) 5'-W G C TG A A W-3' Impy-(3-ImPyPy-y-HpHpPy-(3-ImPy 1567(3) 5'-W G C TG A G W-3' ImPy-p-ImPyIm-y-PyHpPy-p-ImPy 1568(3) 5'-W G C TG A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-(3-ImPy 1569(3) 5'-W G C TG G T W-3' ImPy-~3-ImImHp-y-PyPyPy-(3-ImPy 1570(3) 5'-W G C TG G A W-3' ImPy-(3-ImImPy-y-HpPyPy-(3-ImPy 15713) 5'-W G C TG C T W-3' ImPy-(3-ImPyHp-y-PyImPy-(3-ImPy 1572(3) 5'-W G C TG C A W-3' ImPy-~-ImPyPy-y-HpImPy-(3-ImPy 1573~i) 5'-W G C TG G G W-3' ImPy~-(3-ImImIm-y-PyPyPy-(3-ImPy 1574(3) 5'-W G C TG G C W-3' ImPy-[3-ImImPy-y-ImPyPy-p-ImPy 1575(3) 5'-W G C TG C G W-3' ImPy-(3-ImPyIm-y-PyImPy-(3-ImPy 15760 5'-W G C TG C C W-3' ImPy-(3-ImPyPy-y-ImImPy-(3-ImPy 1577(3) 5'-W G C TC T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-ImPy 1578(3) 5'-W G C TC T A W-3' ImPy-(3-PyHpPy-y-HpPyIm-(3-ImPy 1579(3) 5'-W G C TC T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-/3-ImPy 1580(3) 5'-W G C TC T C W-3' ImPy-(3-PyHpPy-y-ImPyIm-(3-ImPy 1581(3) 5'-W G C TC A T W-3' ImPy-(3-PyPyHp-y-PyHpIm-/3-ImPy 1582(3) 5'-W G C TC A A W-3 ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy T
1583(3) 5'-W G C TC A G W-3' 'Impy-J3-Pypylm-y-PyHpIm-(3-ImPy 1584(3) 5'-W G C TC A C W-3' ImPy-~3-PyPyPy-y-ImHpIm-(3-ImPy 15853) 5'-W G C TC G T W-3' ImPy-(3-PyImHp-y-PypyIm-~-ImPy 1586(3) 5'-W G C TC G A W-3' ImPy-(3-PyImPy-y-HpPyIm-~i-ImPy 1587(3) 5'-W G C TC C T W-3' ImPy-(3-PyPyHp-y-PyImIm-(3-ImPy 1588(3) 5'-W G C TC C A W-3' ImPy-~3-PyPyPy-y-HpImIm-(3-ImPy 1589~i) 5'-W G C TC G G W-3' ImPy-(3-PyImIm-y-PyPyIm-(3-ImPy 1590~i) 5'-W G C TC G C W-3' ImPy-~3-PyImPy-y-ImPyIm-(3-ImPy 15913) 5'-W G C TC C G W-3' ImPy-p-PyPyIm-y-PyImIm-(3-ImPy 1592(3) 5'-W G C TC C C W-3' ImPy-p-PyPyPy-y-ImImIm-p-ImPy ,..
TABLE 160: 12-ring ~i-Hairpin Polyamides for recognition of 8-by 5'-WGCAWNNW-3' DNA sequence aromatic amino acid sequence 1593(3) 5' -W G C A T T T W-3' ImPy-~-HpHpHp-y-Pypypy-(3-ImPy 1594(3) 5' -W G C A T T A W-3' ImPy-~3-HpHpPy-y-HpPyPy-p-ImPy 1595(3) 5' -W G C A T T G W-3' ImPy-~i-HpHpIm-y-pypypy-(3-ImPy 1596(3) 5' -W G C A T T C W-3' ImPy-~3-HpHpPy-y-ImPyPy-(3-ImPy 1597) 5'-WG C A T A TW-3' ImPy-(3-HpPyHp-y-PyHpPy-~3-ImPy 1598(3) 5'-WG C A T A AW-3' ImPy-(~-HpPyPy-y-HpHpPy-(3-ImPy 1599(3) 5'-WG C A T A GW-3' ImPy-~3-HpPyIm-y-PyHpPy-~3-ImPy 1600(3) 5'-WG C A T A CW-3' ImPy-~3-HpPyPy-y-ImHpPy-p-ImPy 1601(3) 5'-WG C A T G TW-3' ImPy-p-HpImHp-y-PyPyPy-(3-ImPy 1602~i) 5'-WG C A T G AW-3' ImPy-(3-HpImPy-y-HpPyPy-(3-ImPy 1603(3) 5'-WG C A T G GW-3' ImPy-~3-HpImIm-y-Pypypy-(3-ImPy IS 16043) 5'-WG C A T G CW-3' ImPy-~-HpImPy-y-ImPyPy-(3-ImPy 1605(3) 5'-WG C A T C TW-3' ImPy-~i-HpPyHp-y-pylmPy-(3-ImPy 1606(3) 5'-WG C A T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-(3-ImPy 16073) 5'-WG C A T C GW-3' ImPy-(3-HpPyIm-y-PyImPy-~-ImPy 1608(3) 5'-WG C A T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-~3-ImPy 1609~i) 5'-WG C A A T TW-3' ImPy-~-PyHpHp-y-PypyHp-(3-ImPy 16103) 5'-WG C A A T AW-3' ImPy-~3-pyHpPy-y-HpPyHp-~-ImPy 16113) 5'-WG C A A T GW-3' ImPy-(3-PyHpIm-y-PypyHp-p-ImPy 1612(3) 5'-WG C A A T CW-3' ImPy-~3-PyHpPy-y-ImPyHp-p-ImPy 1613(3) 5'-WG C A A A TW-3' ImPy-(3-PypyHp-y-pyHpHp-(3-ImPy 1614(3) 5'-WG C A A A AW-3' Impy-(3-PyPyPy-y-HpHpHp-(3-Impy 1615(3) 5'-WG C A A A GW-3' ~ImPy-~3-pypylm-y-PyHpHp-~3-ImPy 16163) 5'-WG C A A A CW-3' ImPy-R-PyPypy-y-I~pHp-~3-ImPy 1617(3) 5'-WG C A A G TW-3' ImPy-(3-pyl~p_y-pypyHp-~-ImPy 16183) 5'-WG C A A G AW-3' ImPy-(3-PyImPy-y-HpPyHp-(3-ImPy 1619(3) 5'-WG C A A G GW-3' ImPy-(3-PyImIm-y-PypyHp-~i-ImPy 1620(3) 5'-WG C A A G CW-3' ImPy-J3-PyImPy-y-ImPyHp-(3-ImPy 16213) 5'-WG C A A C TW-3' ImPy-(3-pypyHp-Y-pYI~Pv-ImPy 1622(3) 5'-WG C A A C AW-3' ImPy-~3-Pypypy-y-Hpl~p_~3_ImPy 1623(3) 5'-WG C A A C GW-3' ImPy-(3-PyPyIm-y-py=mt-tp_~3_ImPy 1624(3) 5'-WG C A A C CW-3' ImPy-~3-pypypy-y_ImImHp-~3-ImPy WO 98/37067 PCTIi1S98/01714 TABLE 161:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGCASNNW-3' -DNA aromatic amino acid sequence sequence 1625(3) 5' -WG C A G TT W-3' ImPy-(3-ImHpHp-y-PyPyPy-~3-ImPy 1626~i) ~ -WG C A G TA W-3' ImPy-[3-ImHpPy-y-HpPyPy-p-ImPy 5' 1627(3) 5' -WG C A G TG W-3' ImPy-(3-ImHpIm-y-PyPyPy-/3-ImPy 1628(3) 5' -WG C A G TC W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy 1629(3) 5' -WG C A G AT W-3' ImPy-p-ImPyHp-y-PyHpPy-~-ImPy 1630(3) 5' -WG C A G AA W-3' ImPy-(3-ImPyPy-y-HpHpPy-~i-ImPy 1631(3) 5' -WG C A G AG W-3' ImPy-~i-ImPyIm-y-PyHpPy-(i-ImPy 1632(3) 5' -WG C A G AC W-3' ImPy-[3-ImPyPy-y-ImHpPy-(3-ImPy 16333) 5' -WG C A G GT W-3' ImPy-(3-ImImHp-y-PyPyPy-(3-ImPy 16343) 5' -WG C A G GA W-3' ImPy-p-ImImPy-y-HpPyPy-(3-ImPy 1635(3) 5' -WG C A G CT W-3' ImPy-~3-ImPyHp-y-PyImPy-~3-ImPy 1636(3) 5' -WG C A G CA W-3' ImPy-(3-ImPyPy-y-HpImPy-(3-ImPy 1637) 5' -WG C A G GG W-3' ImPy-(3-ImImIm-y-PyPyPy-~i-ImPy 1638(3) 5' -WG C A G GC W-3' ImPy-~3-ImImPy-y-ImPyPy-~3-ImPy 1639(3) 5' -WG C A G CG W-3' ImPy-J3-ImPyIm-y-PyImPy-~i-ImPy 1640(3) 5' -WG C A G CC W-3' ImPy-~i-ImPyPy-y-ImImPy-(3-ImPy 1641(3) 5' -WG C A C TT W-3' ImPy-(3-PyHpHp-y-PyPyIm-[3-ImPy 1642(3) 5' -WG C A C TA W-3' ImPy-(3-PyHpPy-y-HpPyIm-~3-ImPy 16433) 5' -WG C A C TG W-3' ImPy-(3-PyHpIm-y-PyPyIm-(3-ImPy 1644(3) 5' -WG C A C TC W-3' ImPy-~3-PyHpPy-y-ImPyIm-(3-ImPy 1645(3) 5' -WG C A C AT W-3' ImPy-~-PyPyHp-y-PyHpIm-(3-ImPy 16463) 5' -WG C A C AA W-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy 1647(3) 5' -WG C A C AG W-3' ImPy-(3-PyPyIm-y-PyHpIm-(3-ImPy 1648(3) 5' -WG C A C AC W-3' ImPy-(3-PyPyPy-y-ImHpIm-(3-ImPy 1649(3) 5' -WG C A C GT W-3' ImPy-(3-PyImHp-y-PyPyIm-~3-ImPy 1650~i) 5' -WG C A C GA W-3' ImPy-(3-PyImPy-y-HpPyIm-(3-ImPy 1651~i) 5' -WG C A C CT W-3' ImPy-~3-PyPyHp-y-PyImIm-(3-ImPy 1652(3) 5' -WG C A C CA W-3' ImPy-(3-PyPyPy-y-HpImIm-(3-ImPy 1653(3) 5' -WG C A C GG W-3' ImPy-(3-PyImIm-y-PyPyIm-p-ImPy 1654(3) 5' -WG C A C GC W-3' ImPy-f3-PyImPy-y-ImPyIm-(3-ImPy 1655(3) 5' -WG C A C CG W-3' ImPy-(3-PyPyIm-y-PyImIm-(3-ImPy 1656~i) 5' -WG C A C CC W-3' ImPy-p-PyPyPy-y-ImImIm-(3-ImPy TABLE 162: 12-ring ~3-Hairpin Polyamides for recognition of 8-by S'-WGCCWNNW-3' -DI'TA sequence aromatic amino acid sequence ' 1657R) 5' -W G T T T W-3' ImPyPy-~-HpHp-y-pypy-(3-ImImPy C C
1658(3) 5' -W G T T A W-3' ImPyPy-(3-HpPy-y-HpPy-~3-ImImPy C C
16593) 5' -W G T T G W-3' ImPyPy-(3-HpIm-y-PyPy-(3-ImImPy C C
1660~i) 5' -W G T T C W-3' ImPyPy-/~-HpPy-y-ImPy-(3-ImImPy C C
1661(3) 5' -W G T A T W-3' C C ImPyPy-(3-PyHp-y-PyHp-(3-ImImPy 1662(3) 5'-WG C C T A A W-3' ImPyPy-~3-pypy-y-HpHp-(3-ImImPy IO 1663(3) 5'-WG C C T A G W-3' ImPyPy-(3-pylm-y-pyHp-(3-ImImPy 1664(3) 5'-WG C C T A C W-3' ImPyPy-~-pypy-y-I~p-~3-ImImPy 16653) 5'-WG C C T G T W-3' ImpyPy-~-ImHp-y-pypy_~3_ImImPy 16663) 5'-WG C C T G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImImPy 1667(3) 5'-WG C C T G G W-3' ImPyPy-(3-Imlm-y-pypy-~3-ImImPy 1668(3) 5'-WG C C T G C W-3' ImPyPy-J3-Impy-y-Impy-(3-Imlmpy 1669(3) 5'-WG C C T C T W-3' ImPyPy-(3-PyHp-y-pyIm-(3-ImImPy 1670(3) 5'-WG C C T C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy 1671(3) 5'-WG C C T C G W-3' ImPyPy-~3-pylm-y-PyIm-(3-ImImPy 1672(3) 5'-WG C C T C C W-3' ImPypy-~-PyPy-y-Imlm-(3-ImImpy 16733) 5'-WG C C A T T W-3' ImPyPy-~3-HpHp-y-pypy_~-ImImPy 1674(3) 5'-WG C C A T A W-3' ImPyPy-(3-HpPy-y-HpPy-(i-ImImPy 1675(3) 5'-WG C C A T G W-3' ImPyPy-p-HpIm-y-pypy-~-ImImPy 1676(3) 5'-WG C C A T C W-3' ImPyPy-(3-HpPy-y-ImPy-~3-ImImPy 1677(3) 5'-WG C C A A T W-3' ImPyPy-~3-PyHp-y-PyHp-(3-ImImPy 1678(3) 5'-WG C C A A A W-3' ImPyPy-R-Pypy-y-HpHp-(3-ImImPy 16793) 5'-WG C C A A G W-3' ImPyPy-~3-PyIm-y-pyHp-~i-ImImPy 1680(3) 5'-WG C C A A C W-3' ImPyPy-(3-pypy-y-I~p-a-ImImPy 1681(3) 5'-WG C C A G T W-3' ImPyPy-~i-ImHp-y-PyPy-p-ImImPy 1682(3) 5'-WG C C A G A W-3' ImPyPy-(3-ImPy-y-HpPy-~3-ImImPy 1683~i) 5'-WG C C A G G W-3' ImPyPy-~3-Imim-y-Pypy-(3-ImImPy 1684(3) 5'-WG C C A G C W-3' ImPyPy-j3-ImPy-y-ImPy-~3-ImImPy 16853) 5'-WG C C A C T W-3' ImPyPy-(3-PyHp-y-Pylm-(3-ImImPy 1686(3) 5'-WG C C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy 1687(3) 5'-WG C C A C G W-3' ImPyPy-(3-Pylm-y-PyIm-~3-ImImPy 1688~i) 5'-WG C C A C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImImPy TABLE 163:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCCSNNW-3' DNA aromatic amino acid sequence sequence 1689(3) 5'-WG C C G T TW-3' ImPy-(3-ImHpHp-y-PyPy-~3-ImImPy 16903) ~5'-WG C C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImImPy 1691(3) 5'-WG C C G T GW-3' ImPy-(3-ImHpim-y-PyPy-(3-ImImPy 1692(3) 5'-WG C C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImImPy 1693(3) 5'-WG C C G A TW-3' ImPy-~3-ImPyHp-y-PyHp-(3-ImImPy 1694(3) 5'-WG C C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-(3-ImImPy 16953) 5'-WG C C G A GW-3' ImPy-(3-ImPyIm-y-PyHp-~3-ImImPy 16963) 5'-WG C C G A CW-3' ImPy-~-ImPyPy-y-ImHp-(3-ImImPy 16973) 5'-WG C C G G TW-3' ImPy-(3-ImImHp-y-PyPy-(3-ImImPy 16983) 5'-WG C C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImImPy 1699(3) 5'-WG C C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-~3-ImImPy 17003) 5'-WG C C G C AW-3' ImPy-~i-ImPyPy-y-Hplm-~3-ImImPy 170/(3) 5'-WG C C C T TW-3' ImPy-~3-PyHpHp-y-Py-/3-ImImImPy 1702(3) 5'-WG C C C T AW-3' ImPy-p-PyHpPy-y-Hp-J3-ImImImPy 1703(3) 5'-WG C C C T GW-3' ImPy-(~-PyHpIm-y-Py-(3-ImImImPy 1704(3) 5'-WG C C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImImPy 1705(3) 5'-WG C C C A TW-3' ImPy-(3-PyPyAp-y-Py-(3-ImImImPy 1706(3) 5'-WG C C C A AW-3' ImPy-(3-PyPyPy-y-Hp-(3-ImImImPy 1707(3) 5'-WG C C C A GW-3' ImPy-(3-PyPyIm-y-Py-~3-ImImImPy 1708(3) 5'-WG C C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImImPy 1709(3) 5'-WG C C C G TW-3' ImPy-(3-PyImHp-y-Py-(3-ImImImPy 17100 5'-WG C C C G AW-3' ImPy-(3-PyImPy-y-Hp-(3-ImImImPy G73~3) 5'-WG C C G G GW-3' 'ImPy-p-ImImIm-y-PyPy-~i-ImImPy G74(3) 5'-WG C C G G CW-3' ImPy-~3-ImImPy-y-ImPy-~i-ImImPy G75(3) 5'-WG C C G C GW-3' ImPy-(3-ImPyIm-y-PyIm-p-ImImPy G76(3) 5'-WG C C G C CW-3' ImPy-(3-ImPyPy-y-Imlm-~i-ImImPy G77~3) 5'-WG C C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImImPy G78(3) 5'-WG C C C G CW-3' ImPy-(3-PyImPy-y-Im-~3-ImImImPy ...~. , . , TABLE 164: 12-ring Hairpin (3- Polyamides for recognition of 8-by 5'-WGAGWNNW-3' .
DNA aromatic amino acid sequence sequence 1713(3) 5' G AG T T T W-3' Im-(3-ImHpHpHp-y-pypypypY-(3-PY
-W
1714(3) 5' G AG T T A W-3' Im-(3-ImHpHppy-y-HppypypY_~_pY
-W
1715(3) .5' G AG T T G W-3' Im-(3-ImHpHpIm-y-pypypypy_~_py -W
1716(3) 5'-W G AG T T C W-3' Im-(3-ImHpIipPy-y-ImPYPYPy-~-py 1717(3) 5' G AG T A T W-3' Im-(3-ImHpPyHp-y-PYHpPYPy-(3-pY
-W
1718(3) 5' G AG T A A W-3' Im-~3-ImHpPyPY-y-HpHpPyPy-(3-Py -W
1719(3) 5' G AG T A G W-3' Im-(3-ImHpPyIm-y-PyHpPyPy-(3-Py -W
1720(3) 5' G AG T A C W-3' Im-~3-ImHppypY_y_Iml.lppypY-(3-pY
-W
1721(3) 5' G AG T G T W-3' Im-~3-ImHpImHp-y-pypypypY-p-pY
-W
1722(3) 5' G AG T G A W-3' Im-(3-ImHpImPY-y-HpPypyPY-(3-py -W
1723(3) 5' G AG T G G W-3' Im-p-ImHpImIm-y-Pypypypy-~3-pY
-W
1724(3) 5' G AG T G C W-3' Im-~3-ImHpImPy-y-ImPyPYPy-(3-Py -W
1725~i) 5' G AG T C T W-3' Im-/3-ImHpPyHp-y-PyImPYPy-~3-Py -W
17263) 5' G AG T C A W-3' Im-~3-ImHpPyPy-y-HpImPYPy-(3-Py -W
1727(3) 5' G AG T C G W-3' Im-(3-ImHpPyIm-y-PYImPYPy-(3-Py -W
1728(3) 5' G AG T C C W-3' Im-(3-ImHpPypY-y-ImImPyPy-J3-py -W
1729) 5' G AG A T T W-3' Im-/3-ImPyHpHp-y-pypYHppy-(3-pY
-W
17300 5' G AG A T A W-3' Im-p-ImPyHpPy-y-HpPyHpPy-(3-py -W
1731(3) 5' G AG A T G W-3' Im-(3-ImPYHpIm-y-pypygppy-(3-Py -W
1732~i) 5' G AG A T C W-3' Im-(3-ImpyHppy-y-ImpyHpPy-(3-Py -W
1733(3) 5' G AG A A T W-3' Im-p-ImPyPyHp-y-PyHpHpPy-(3-Py -W
1734(3) 5' G AG A A A W-3' Im-~-ImPyPYPy-y-HpHpHpPy-(3-Py -W
1735~i) 5' G AG A A G W-3' Im-~i-ImPyPYIm-y-pyHpHpPy-~3-Py -W
1736(3) 5' G AG A A C W-3' 'Im-~3-ImPyPyPy-y-ImHpHpPy-~3-Py -W
1737(3) 5' G AG A G T W-3' Im-(3-ImPYImHp-y-pypygpPy-(3-Py -W
1738(3) 5' G AG A G A W-3' Im-~i-ImPYImPy-y-HpPyHpPy-(3-Py -W
17393) 5' G AG A G G W-3' Im-(3-ImPYImIm-y-PYPyHpPy-(3-py -W
17403) 5' G AG A G C W-3' Im-(3-ImPyImPy-y-ImPyHpPy-(3-Py -W
1741~i) 5' G AG A C T W-3' Im-~3-ImPyPyHp-y-PyImHpPy-(3-Py -W
1742(3) 5' G AG A C A W-3' Im-(3-ImPyPyPy-y-HpImHpPy-(3_pY
-W
1743(3) 5' G AG A C G W-3' Im-(3-ImPyPyIm-y-PyImHpPy-(3-Py -W
1744(3) 5' G AG A C C W-3' Im-(3-ImPyPyPy-y-ImImHpPy-(3-Py -W
TABLE 165: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGAGSNNW-3' DNA sequence aromatic amino acid sequence 1745(3) 5' -W G A G G T T W-3' Im-(3-ImImHpHp-y-PyPyPyPy-~3-Py 1746(3) 5' -W G A G G T A W-3' Im-(3-ImImHpPy-y-HpPyPyPy-(3-Py 1747(3) 5' -W G A G G T G W-3' Im-(3-ImImHpIm-y-PyPyPyPy-(3-Py 1748(3) 5' -W G A G G T C W-3' Im-(3-ImImHpPy-y-ImPyPyPy-(3-Py 1749(3) 5' -W G A G G A T W-3' Im-(3-ImImPyHp-y-PyHpPyPy-~3-Py 17503) 5' -W G A G G A A W-3' Im-(3-ImImPyPy-y-HpHpPyPy-/3-Py 17513) 5' -W G A G G A G W-3' Im-~3-ImImPyIm-y-PyHpPyPy-(3-Py 1752(3) 5' -W G A G G A C W-3' Im-(3-ImImPyPy-y-ImHpPyPy-~3-Py 1753(3) 5' -W G A G G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-(3-Py 1754(3) 5' -W G A G G G A W-3' Im-(3-ImImImPy-y-HpPyPyPy-~3-Py 1755(3) 5'-W G A G G C T W-3' Im-(3-ImImPyHp-y-PyImPyPy-(3-Py 1756(3) 5' -W G A G G C A W-3' Im-(3-ImImPyPy-y-HpImPyPy-~3-Py 17573) 5' -W G A G C T T W-3' Im-(3-ImPyHpHp-y-PyPyImPy-(3-Py 1758j3) 5' -W G A G C T A W-3' Im-~3-ImPyHpPy-y-HpPyImPy-~3-Py 1759(3) 5' -W G A G C T G W-3' Im-~-ImPyHpIm-y-PyPyImPy-J3-Py 17603) 5' -W G A G C T C W-3' Im-~3-ImPyHpPy-y-ImPyImPy-(3-Py 1761~i) 5' -W G A G C A T W-3' Im-/3-ImPyPyHp-y-PyHpImPy-(3-Py 1762(3) 5' -W G A G C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~3-Py 1763(3) 5' -W G A G C A G W-3' Im-(3-ImPyPyIm-y-PyHpImPy-(3-Py 1764(3) 5' -W G A G C A C W-3' Im-(3-ImPyPyPy-y-ImHpImPy-(3-Py 17653) 5' -W G A G C G T W-3' Im-~3-ImPyImHp-y-PyPyImPy-~3-Py 1766~i) 5'-WG A G C GA W-3' Im-(3-IrnPyImPy-y-HpPyImPy-(3-Py 1767(3) 5'-WG A G C CT W-3' 'Im-~3-ImPyPyHp-y-PyImImPy-/3-Py 1768(3) 5'-WG A G C CA W-3' Im-j3-ImPyPyPy-y-HpImImPy-(3-Py 1769(3) 5'-WG A G G GG W-3' Im-(3-ImImImIm-y-PyPyPyPy-[3-Py 1770(3) 5'-WG A G G GC W-3' Im-(3-ImImImPy-y-ImPyPyPy-~-Py 1771(3) 5'-WG A G G CG W-3' Im-(3-ImImPyIm-y-PyImPyPy-(3-Py 1772(3) 5'-WG A G G CC W-3' Im-p-ImImPyPy-y-ImImPyPy-~3-Py 17733) 5'-WG A G C GG W-3' Im-~i-ImPyImIm-y-PyPyImPy-(3-Py 1774(3) 5'-WG A G C GC W-3' Im-(3-ImPyImPy-y-ImPyImPy-~i-Py 1775(3) 5'-WG A G C CG W-3' Im-(3-ImPyPyIm-y-PyImimPy-p-Py 1776(3) 5'-WG A G C CC W-3' Im-~i-ImPyPyPy-y-ImImImPy-(i-Py W.. . ~.. , 166: 12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGATWNNW-3' DNA aromatic amino acid sequence sequence 1777(3) 5' GA T T T T W-3' ImPy-(3-HpHpHp-y-PYPyPy-(3-HpPy -W
1778(3) 5' GA T T T A W-3' ImPy-~3-HpHpPy-y-HpPYPy-~3-HpPy . -W
17793) 5' GA T T T G W-3' ImPy-(3-HpHpIm-y-PyPyPy-(3-HpPy -W
1780(3) 5' GA T T T C W-3' ImPy-(3-HpHpPy-y-ImPYPy-~3-HpPy -W
17810 5' GA T T A T W-3' ImPy-(3-HppyHp-y-PYHpPy-(3-HpPy -W
17823) 5' GA T T A A W-3' ImPy-/3-HpPyPy-y-HpHpPy-(3-HpPy -W
1783(3) 5' GA T T A G W-3' ImPy-(3-HpPYIm-y-PyHpPy-~3-HpPy -W
1784(3) 5' GA T T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-~-HpPy -W
17853) 5' GA T T G T W-3' -W ImPy-/3-HpImHp-y-PyPypY-(3 _HppY
1786(3) 5' GA T T G A W-3' -W ImPy-~3-HpImPy-y-HpPYpy-~3-Hppy 1787~i) 5' GA T T G G W-3' ImPy-(3-HpImIm-y-Pypypy-(3-Hppy -W
1788(3) 5' GA T T G C W-3' ImPy-(3-HpImPy-y-ImPyPy-(3-Hppy -W
17893) 5' GA T T C T W-3' ImPy-(3-HpPyHp-y-PyImPy-(3-HpPy -W
17903) 5' GA T T C A W-3' ImPy-~3-HppyPy-y-HpImPy-~i-HpPy -W
1791(3) 5' GA T T C G W-3' ImPy-(3-HpPyIm-y-pylmPy-~i-HpPy -W
17923) 5' GA T T C C W-3' ImPy-(3-HpPYPy-y-ImImPy-R-HpPy -W
17933) 5' GA T A T T W-3' ImPy-~-PyHpHp-y-PYPyHp-(3-HpPy -W
1794(3) 5' GA T A T A W-3' ImPy-(3-PyHpPy-y-HpPyHp-(3-HpPy -W
17953) 5' GA T A T G W-3' ImPy-(3-PYHpIm-y-pypyHp-(3-HpPy -W
1796~i) 5' GA T A T C W-3' ImPy-(3-PYHpPy-y-ImPYHp-~3-HpPy -W
1797(3) 5' GA T A A T W-3' ImPy-(3-PyPyHp-y-pyHpHp-(3-HpPy -W
1798(3) 5' GA T A A A W-3' Impy-(3-PyPyPY-y-HpHpHp-(3-HpPy -W
1799(3) 5' GA T A A G W-3' ImPy-(3-PyPyIm-y-pyHpHp-/3-HpPy -W
1800(3) 5' GA T A A C W-3' ImPy-~3-PyPyPy-y-ImHpHp-(3-HpPy -W
1801(3) 5' GA T A G T W-3' -W ImPy-(3-PyImHp-y-pypyHp-p-Hppy 18023) 5' GA T A G A W-3' ImPy-~i-pyImPy-y-HpPYHp-(3-HpPy -W
18033) 5' GA T A G G W-3' Impy-~3-pylmIm-y-pypygp-~3-HppY
-W
1804(3) 5' GA T A G C W-3' ImPy-(3-PyImPy-y-ImPyHp-(3-HpPy -W
1805(3) 5' GA T A C T W-3' ImPy-(3-pypyHp-y-PyImHp-~i-Hppy -W
1806(3) 5' GA T A C A W-3' ImPy-(3-PYPyPy-y-HpImHp-~3-HpPy -W
1807(3) 5' GA T A C G W-3' ImPy-~i-PyPyIm-y-PyImHp-(3-HpPy -W
1808(3) 5' GA T A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPY
-W
TABLE 167: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGATSNNW-3' -DNA sequence aromatic amino acid sequence 1809(3) 5' -W G A T G T T W-3' ImPy-~-ImHpHp-y-PyPyPy-p-HpPy 1810(3) 5' -W G A T G T A W-3' ImPy-(3-ImHpPy-y-HpPyPy-~3-HpPy 1811(3) 5' -W G A T G T G W-3' ImPy-~i-ImHpIm-y-PyPyPy-~3-HpPy 1812(3) 5' -W G A T G T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-J3-HpPy 1813(3) 5' -W G A T G A T W-3' ImPy-~3-ImPyHp-y-PyHpPy-(3-HpPy 1814(3) 5' -W G A T G A A W-3' ImPy-(3-ImPyPy-y-HpHpPy-(3-HpPy 1815(3) 5' -W G A T G A G W-3' ImPy-~-ImPyIm-y-PyHpPy-(3-HpPy 1816(3) 5' -W G A T G A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-~i-HpPy 18173) 5' -W G A T G G T W-3' ImPy-p-ImImHp-y-PyPyPy-(3-HpPy 1818(3) 5' -W G A T G G A W-3' ImPy-~3-ImImPy-y-HpPyPy-p-HpPy 1819(3) 5' -W G A T G C T W-3' ImPy-~i-ImPyHp-y-PyImPy-(3-HpPy 1820(3) 5' -W G A T G C A W-3' ImPy-(3-ImPyPy-y-HpImPy-~3-HpPy 1821(3) 5' -W G A T G G G W-3' ImPy-~3-ImImIm-y-PyPyPy-(3-HpPy 1822(3) 5' -W G A T G G C W-3' ImPy-(3-ImImPy-y-ImPyPy-(3-HpPy 1823~i) 5' -W G A T G C G W-3' ImPy-(3-ImPyIm-y-PyImPy-p-HpPy 18243) 5' -W G A T G C C W-3' ImPy-[3-ImPyPy-y-ImImPy-(3-HpPy 1825(3) 5' -W G A T C T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-HpPy 1826(3) 5' -W G A T C T A W-3' ImPy-~3-PyHpPy-y-HpPyIm-(3-HpPy 1827) 5' -W G A T C T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-~-HpPy 1828(3) 5'-WG A T C T CW-3' ImPy-(3-PyHpPy-y-ImPyIm-/3-HpPy 1829(3) 5'-WG A T C A TW-3' ImPy-~3-PyPyHp-y-PyHpIm-p-HpPy 18303) 5'-WG A T C A AW-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-HpPy 18313) 5'-WG A T C A GW-3' 'ImPy-(3-PyPyIm-y-PyHpIm-~i-HpPy 1832(3) 5'-WG A T C A CW-3' ImPy-(3-PyPyPy-y-ImHpIm-~3-HpPy 1833(3) 5'-WG A T C G TW-3' ImPy-(3-PyImHp-y-PyPyIm-(3-HpPy 18343) 5'-WG A T C G AW-3' ImPy-(3-PyImPy-y-HpPyIm-(3-HpPy 18353) 5'-WG A T C C TW-3' ImPy-p-PyPyHp-y-PyImIm-(3-HpPy 1836~i) 5'-WG A T C C AW-3' ImPy-(3-PyPyPy-y-HpImIm-~-HpPy 1837(3) 5'-WG A T C G GW-3' ImPy-~3-PyImIm-y-PyPyIm-~3-HpPy 1838(3) 5'-WG A T C G CW-3' ImPy-~3-PyImPy-y-ImPyIm-(3-HpPy 18393) 5'-WG A T C C GW-3' ImPy-(3-PyPyIm-y-PyImIm-(3-HpPy 18403) 5'-WG A T C C CW-3' ImPy-(3-PyPyPy-y-ImImIm-(3-HpPy f , , WO 98'37067 PCT/US98/01714 ~1'ABLE 168;
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGAAWNNW-3' -DNA aromatic amino acid sequence sequence 1841(3) 5' G A A TT T W-3' ImPy-(3-HpHpHp-y-pyPypy-(3-HpPy -W
1842(3) 5' G A A TT A W-3' ImPy-[3-HpHpPy-y-HpPyPy-~3-HpPy -W
18433) 5' G A A TT G W-3' ImPy-(3-HpHpIm-y-Pypypy-~3-HppY
-W
1844(3) 5' G A A TT C W-3' ImPy-~i-HpHpPy-y-ImPYPy-~3-HpPy -W
1845(3) 5' G A A TA T W-3' ImPy-(3-HpPyHp-y-PyHpPy-(3-HpPy -W
18463) 5' G A A TA A W-3' ImPy-(3-HppyPy-y-HpHppy-[3-HpPy -W
1847(3) 5' G A A TA G W-3' ImPy-~3-HpPYIm-y-PYHpPy-(3-HpPy -W
1848(3) 5' -W G A A T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-(3-HpPy 1849(3) 5' -W G A A T G T W-3' ImPy-~3-HpImHp-y-Pypypy-(3-HpPy 1850(3) 5' -W G A A T G A W-3' ImPy-~-HpImPy-y-HpPyPy-(3-HpPy 1851(3) 5' -W G A A T G G W-3' ImPy-(3-HpImIm-y-PyPyPy-(3-HpPy 1852(3) 5' -WG A A TG C W-3' ImPy-~3-HpImPy-y-ImPyPy-(3-HpPy 1853(3) 5' -WG A A TC T W-3' ImPy-(3-HpPyHp-y-PYImPy-(3-HpPy 1854(3) 5' -WG A A TC A W-3' ImPy-(3-HpPyPy-y-HpImPy-(3-HpPy 1855(3) 5' -WG A A TC G W-3' ImPy-(3-HpPyim-y-PyImPy-~-HpPy 1856(3) 5' -WG A A TC C W-3' ImPy-(3-HpPyPy-y-ImImPy-(3-HpPy 18573) 5' -WG A A AT T W-3' ImPy-~3-PyHpHp-y-PyPyHp-~3-HpPy 18583) 5' -WG A A AT A W-3' ImPy-~3-PYHpPy-y-HpPyHp-~3-HpPy 1869(3) 5' -W G A A A T G W-3' ImPy-(3-PyHpIm-y-PypyHp-~3-HpPy 1860(3) 5' -W G A A A T C W-3' ImPy-(3-PYHpPy-y-ImPyHp-(3-HpPy 18613) 5' -W G A A A A T W-3' ImPy-~-PYPyHp-y-PyHpHp-(3-HpPy 1862(3) 5'-WG A A A A A W-3' ImPy-(3-Pypypy-y-HpHpHp-(3-HpPy 1863(3) 5'-WG A A A A G W-3' ImPy-~i-PyPYIm-y-PyHpHp-(3-HpPy 1864~i} 5'-WG A A A A C W-3' ImPy-(3-PYPyPy-y-ImHpHp-~3-HpPy 1865(3) 5'-WG A A A G T W-3' ImPy-(3-PyImHp-y-PYPYHp-~3-HpPy 1866(3) 5'-WG A A A G A W-3' ImPy-(3-PyImPy-y-HppyHp-p-HpPy 1867(3) 5'-WG A A A G G W-3' ImPy-~3-PyImIm-y-PYPyHp-p-HpPy 1868(3) 5'-WG A A A G C W-3' ImPy-J3-PyImPy-y-ImPyHp-(3-Hppy 1869(3) 5'-WG A A A C T W-3' ImPy-/3-PyPyHp-y-PYImHp-~3-HpPy 1870(3) 5'-WG A A A C A W-3' ImPy-(3-PyPyPy-y-HpImHp-(3-HpPy 1871(3) 5'-WG A A A C G W-3' ImPy-~3-PyPYIm-y-PyImHp-p-HpPy 1872(3) 5'-WG A A A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPy TABLE 169:
12-ring -Hairpin Polyamides for recognition of 8-by 5'-WGAASN1VW-3' DNA aromatic amino acid sequence sequence 1873(3) 5' -WG A A G TT W-3' ImPy--ImHpHp-y-PyPyPy--HpPy 1874(3) . -WG A A G TA W-3' ImPy--ImHpPy-y-HpPyPy--HpPy 5' 1875(3) 5' -WG A A G TG W-3' ImPy--ImHpIm-y-PyPyPy--HpPy 1876(3) 5' -WG A A G TC W-3' ImPy--ImHpPy-y-ImPyPy--HpPy 1877 ) 5' -WG A A G AT W-3' ImPy--ImPyHp-y-PyHpPy--HpPy 18783) 5' -WG A A G AA W-3' ImPy--ImPyPy-y-HpHpPy--HpPy 1879) 5' -WG A A G AG W-3' ImPy--ImPyIm-y-PyHpPy--HpPy 1880) 5' -WG A A G AC W-3' ImPy--ImPyPy-y-ImHpPy--HpPy 18813) 5' -WG A A G GT W-3' ImPy--ImImHp-y-PyPyPy--HpPy 18823) 5' -WG A A G GA W-3' ImPy--ImImPy-y-HpPyPy--HpPy 1883(3) 5' -WG A A G CT W-3' ImPy--ImPyHp-y-PyImPy--HpPy 1884(3) 5' -WG A A G CA W-3' ImPy--ImPyPy-y-HpImPy--HpPy 1885) 5' -WG A A G GG W-3' ImPy--ImImIm-y-PyPyPy--HpPy 1886) 5' -WG A A G GC W-3' ImPy--ImImPy-y-ImPyPy--HpPy 1887) 5' -WG A A G CG W-3' ImPy--ImPyIm-y-PyImPy--HpPy 1888) 5' -WG A A G CC W-3' ImPy--ImPyPy-y-ImImPy--HpPy 1889~i) 5' -WG A A C TT W-3' ImPy--PyHpHp-y-PyPyIm-(3-HpPy 18903) 5' -WG A A C TA W-3' ImPy--PyHpPy-y-HpPyIm--HpPy 1891(3) 5' -WG A A C TG W-3' ImPy--PyHpIm-y-PyPyIm--HpPy 1892) 5' -WG A A C TC W-3' ImPy--PyHpPy-'y-ImPyIm--HpPy 1893(3) 5' -WG A A C AT W-3' ImPy--PyPyHp-y-PyHpIm--HpPy 1894(3) 5' -WG A A C AA W-3' ImPy--PyPyPy-y-HpHpIm--HpPy 18953) 5' -WG A A C AG W-3' ImPy--PyPyIm-y-PyHpIm--HpPy 1896(3) 5' -WG A A C AC W-3' ImPy--PyPyPy-y-ImHpIm--HpPy 1897p) 5' -WG A A C GT W-3' ImPy--PyImHp-y-PyPyIm--HpPy 1898(3) 5' -WG A A C GA W-3' ImPy--PyImPy-y-HpPyIm--HpPy 1899(3) 5' -WG A A C CT W-3' ImPy--PyPyHp-y-PyImIm--HpPy 1900) 5' -WG A A C CA W-3' ImPy--PyPyPy-y-HpImIm--HpPy 1901(3) 5' -WG A A C GG W-3' ImPy--PyImIm-y-PyPyIm--HpPy 1902) 5' -WG A A C GC W-3' ImPy--PyImPy-y-ImPyIm--HpPy 1903) 5' -WG A A C CG W-3' ImPy--PyPyIm-y-PyImIm--HpPy 1904~i) 5' -WG A A C CC W-3' ImPy--PyPyPy-y-ImImIm--HpPy r , , WO 9t1~370b7 PCT/US98/01714 'TABLE 170: 12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGACWNNW-3' -DNA sequence aromatic amino acid sequence - 1905~i) 5' -W G A C T T T W-3' ImPyPy-~3-HpHp-y-PyPy-(3-ImHpPy _ 1906(3) ~5' -W G A C T T A W-3' ImPyPy-(3-Hppy-y-Hppy_R-ImHpPy 1907~i) 5' -W G A C T T G W-3' ImPyPy-(3-Hplm-y-PyPy-(3-ImHpPy 1908(3) 5'-W G A CT T C W-3' ImPyPy-~-HpPy-y-ImPy-(3-ImHpPy 1909(3) 5'-W G A CT A T W-3' ImPyPy-~3-pyHp-y-PyHp-(3-ImHpPy 19103) 5'-W G A CT A A W-3' ImPyPy-~3-Pypy-y-HpFip-(3-ImHpPy 1911(3) 5'-W G A CT A G W-3' ImPyPy-(3-Pylm-y-PyHp-~i-ImHpPy 1912 5'-W G A CT A C W-3' ) ImPyPy-~i-PyPy-y-ImHp-p-ImHpPy 19133) 5'-W G A CT G T W-3' ImPyPy-p-ImHp-y-pypy-(3-I~ppy 19143) 5'-W G A CT G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy 1915(3) 5'-W G A CT G G W-3' ImPyPy-j3-ImIm-y-Pypy-p-ImHpPy 1916(3) 5'-W G A CT G C W-3' ImPyPy-(3-ImPy-y-ImPy-(3-ImHpPy 19173) 5'-W G A CT C T W-3' ImPyPy-(3-pygp-y-pyIm-~i-ImHpPy 19183) 5'-W G A CT C A W-3' ImPyPy-~-PyPy-y-HpIm-p-ImHpPy 1919(3) 5'-W G A CT C G W-3' ImPyPy-~3-PyIm-y-PyIm-(3-ImHpPy 1920~i) 5'-W G A CT C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImHpPy 1921(3) 5'-W G A CA T T W-3' ImPyPy-~i-HpHp-y-Pypy-(3-ImHpPy 1922(3) 5'-W G A CA T A W-3' ImPyPy-(3-HpPy-y-HpPy-(3-ImHpPy 1923(3) 5'-W G A CA T G W-3' ImPyPy-(3-HpIm-y-PyPy-p-ImHpPy 19243) 5'-W G A CA T C W-3' ImPyPy-(3-HpPy-y-ImPy-~-ImHpPy 1925(3) 5'-W G A CA A T W-3' ImPyPy-(3-PyHp-y-PyHp-(3-ImHpPy 1926(3) 5'-W G A CA A A W-3' ImPyPy-(3-pypy-y-HpHp-(3-ImHpPy 1927(3) 5'-W G A CA A G W-3' ImPypy-(3-pylm-y-pyHp-~i-ImHpPy 1928) 5'-W G A CA A C W-3' ImPyPy-p-PyPy-y-ImHp-p-ImHpPy 1929(3) 5'-W G A CA G T W-3' ImPyPy-(3-ImHp-y-PyPy-~3-ImHpPy 19303) 5'-W G A CA G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy 1931(3) 5'-W G A CA G G W-3' ImPyPy-(3-Imlm-y-PyPy-(3-ImHpPy 19323) 5' -W G A C A G C W-3' ImPyPy-(3-Impy-y-ImPy-(3-ImHpPy 19333) 5' -W G A C A C T W-3' ImPyPy-~3-PyHp-y-PyIm-(3-ImHpPy 19343) 5' -W G A C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-(3-ImHpPy 19350 5' -W G A C A C G W-3' ImPyPy-R-pylm-y_pylm_(3-ImHpPy 1936(3) 5' -W G A C A C C W-3' ImPyPy-p-Pypy-y-ImIm-(3-ImHpPy TABLE
171:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGACSNNW-3' -DNA aromatic amino acid sequence sequence 1937(3) 5'-W GA C G T TW-3 T ImPy-(3-ImHpHp-y-PyPy-(3-ImHpPy 1938(3) 5'-W GA C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImHpPy 1939(3) 5'-W GA C G T GW-3' ImPy-[3-ImHpIm-y-PyPy-(3-ImHpPy 1940(3) 5'-W GA C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImHpPy 1941(3) 5'-W GA C G A TW-3' ImPy-(3-ImPyHp-y-PyHp-(3-ImHpPy 1942~i) 5'-W GA C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-~3-ImHpPy 1943(3) 5'-W GA C G A GW-3' ImPy-~3-ImPyIm-y-PyHp-(3-ImHpPy 19443) 5'-W GA C G A CW-3' ImPy-(3-ImPyPy-y-ImHp-(3-ImHpPy 19453) 5'-W GA C G G TW-3' ImPy-(3-ImImHp-y-PyPy-p-ImHpPy 19463) 5'-W GA C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImHpPy 1947(3) 5'-W GA C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-(3-ImHpPy 1948(3) 5'-W GA C G C AW-3' ImPy-(3-ImPyPy-y-HpIm-J3-ImHpPy 19493) 5'-W GA C C T TW-3' ImPy-~3-PyHpHp-y-Py-~3-ImImHpPy 1950(3) 5'-W GA C C T AW-3' ImPy-(3-PyHpPy-y-Hp-(3-ImImHpPy 1951(3) 5'-W GA C C T GW-3' ImPy-(3-PyHpim-y-Py-(3-ImImHpPy 19523) 5'-W GA C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImHpPy 1953(3) 5'-W GA C C A TW-3' ImPy-(3-PyPyHp-y-Py-p-ImImHpPy 1954(3) 5'-W GA C C A AW-3' ImPy-(3-PyPyPy-y-Hp-p-ImImHpPy 1955(3) 5'-W GA C C A GW-3' ImPy-(3-PyPyIm-y-Py-(3-ImImHpPy 1956(3) 5'-W GA C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImHpPy 1957(3) 5'-W GA C C G TW-3' ImPy-/3-PyImHp-y-Py-p-ImImHpPy 1958(3) 5'-W GA C C G AW-3' ImPy-(3-PyImPy-y-Hp-~3-ImImHpPy 1959(3) 5'-W GA C C C TW-3' ImPy-p-PyPyHp-y-PyImImIm-(3-Py 1960(3) 5'-W GA C C C AW-3 T ImPy-(3-PyPyPy-y-HpImImIm-(3-Py 1961(3) 5'-W GA C G G GW-3' ImPy-(3-ImImIm-y-PyPy-~-ImHpPy 19623) 5'-W GA C G G CW-3' ImPy-(3-ImImPy-y-ImPy-p-ImHpPy 1963(3) 5'-W GA C G C GW-3' ImPy-~i-ImPyIm-y-Pylm-(3-ImHpPy 1964(3) 5'-W GA C G C CW-3' ImPy-(3-ImPyPy-y-ImIm-(3-ImHpPy 1965~i) 5'-W GA C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImHpPy 1966~i) 5'-W GA C C G CW-3' ImPy-~3-PyImPy-y-Im-~3-ImImHpPy 1967(3) 5'-W GA C C C GW-3' ImPy-(3-PyPyIm-y-PyImImIm-(3-Py 1968(3) 5'-W GA C C C CW-3' ImPy-(3-PyPyPy-y-ImImImIm--Py .~. , , , WO 98/?7067 PCT/US98101714 ~hABLE 2:
17 12-ring [3-Hairpin Polyamides for recognition of 8-by 5'-WGTGVVNIVW-3' -DNA aromatic amino acid sequence sequence 1969(3) 5' G TG T T T W-3' Im-(3-ImHpHpHp-y-pypypypy-(3-py -W
1970(3) 5' G TG T T A W-3' Im-(3-ImHpHpPy-y-HpPyPYPy-(3-py -W
19713) 5' G TG T T G W-3' Im-(3-ImHpHpIm-y-PypypypY-~j-py -W
1972(3) 5' G TG T T C W-3' Im-~3-ImHpHpPy-y-ImPyPYPy-(3-Py -W
19733) 5' G TG T A T W-3' Im-(3-ImHpPYHp-y-PYHpPyPy-(3-Py -W
1974(3) 5' G TG T A A W-3' Im-~-ImHpPyPy-y-HpHpPyPy-(3-Py -W
1975(3) 5' G TG T A G W-3' Im-(3-ImHpPyIm-y-pYHpPYPy-p-py -W
1976(3) 5' G TG T A C W-3' Im-(3-ImHpPyPy-y-ImHpPyPy-(3-Py -W
19773) 5' G TG T G T W-3' Im-p-ImHpImHp-y-PypypypY-~-py -W
1978(3) 5' G TG T G A W-3' Im-(3-ImHpImPy-y-HpPyPyPy-~3-Py -W
1979(3) 5' G TG T G G W-3' Im-~-ImHpImIm-y-PYPyPyPy-(3-Py -W
19803) 5' G TG T G C W-3' Im-(3-ImHpImPy-y-ImPyPYPy-~3-py -W
1981(3) 5' G TG T C T W-3' Im-(3-ImHppyHp-y-pyImPyPy-(3-Py -W
1982(3) 5' G TG T C A W-3' Im-~i-ImHpPYPy-y-HpImPyPy-(3-Py -W
19833) 5' G TG T C G W-3' Im-(3-ImHpPyIm-y-PyImPyPy-(3-Py -W
1984(3) 5' G TG T C C W-3' Im-p-ImHpPYPy-y-ImImPyPy-~3-Py -W
19853) 5' G TG A T T W-3' Im-(3-ImPyHpHp-y-PypyHpPy-(3-Py -W
1986(3) 5' G TG A T A W-3' Im-~3-ImPYHpPy-y-HpPYHpPy-~i-py -W
1987(3) 5' G TG A T G W-3' Im-(3-ImPYHpIm-y-PYPYHpPy-(3-Py -W
1988(3) 5' G TG A T C W-3' Im-p-ImPyHpPy-y-ImPYHpPy-p-Py -W
1989(3) 5' G TG A A T W-3' Im-~-ImPYPYHp-y-pyI-IpHppy-~i-py -W
1990(3) 5' G TG A A A W-3' Im-(3-ImPYPyPy-y-HpHpHpPy-(3-Py -W
1991(3) 5' G TG A A G W-3' Im-(3-ImPyPyIm-y-PYHpHpPy-(3-Py -W
1992(3) 5' G TG A A C W-3' Im-p-ImPyPYPy-y-ImHpI-IpPy-p-Py -W
19933) 5' G TG A G T W-3' Im-(3-ImPyImHp-y-PyPyHpPy-(3-Py -W
19943) 5' G TG A G A W-3' Im-~3-ImPyImPy-y-HpPyHpPy-~3-py -W
19950 5' G TG A G G W-3' Im-(3-ImPyImIm-y-PyPyHpPy-(3-Py -W
19963) 5' G TG A G C W-3' Im-p-ImPyImPy-y-ImPYHpPy-~3-py -W
1997(3) 5' G TG A C T W-3' Im-(3-ImPyPyHp-y-PyImHpPy-p-Py -W
1998(3) 5' G TG A C A W-3' Im-p-ImPyPyPy-y-HpImHpPy-p-Py -W
1999~i) 5' G TG A C G W-3' Im-(3-ImPyPyIm-y-PYImHpPy-(3-Py -W
20003) 5' G TG A C C W-3' Im-/3-ImpyPypy-y-ImImHpPy-(3-Py -W
TABLE
173:
I2-ring (3-Hairpin Poiyamides for recognition of 8-by 5'-WGTGSNNW-3' DNA aromatic amino acid sequence sequence 2001(3) 5'-W G TG G T T W-3' Im-~3-ImImHpHp-y-PyPyPyPy-(3-Py 2002(3) '5'-W G TG G T A W-3' Im-~3-ImImHpPy-y-HpPyPyPy-~-Py 20033) 5'-W G TG G T G W-3' Im-/3-ImImHpIm-y-PyPyPyPy-(3-Py 20043) 5'-W G TG G T C W-3' Im-p-ImImHpPy-y-ImPyPyPy-(3-Py 2005~i) 5'-W G TG G A T W-3' Im-p-ImImPyHp-y-PyHpPyPy-~3-Py 2006~i) 5'-W G TG G A A W-3' Im-p-ImImPyPy-y-HpHpPyPy-p-Py 20070 5'-W G TG G A G W-3' Im-p-ImImPyIm-y-PyHpPyPy-p-Py 20083) 5'-W G TG G A C W-3' Im-~3-ImImPyPy-y-ImHpPyPy-p-Py 2009(3) 5'-W G TG G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-p-Py 20103) 5'-W G TG G G A W-3' Im-~3-ImImImPy-y-HpPyPyPy-(3-Py 2011(3) 5'-W G TG G C T W-3' Im-~3-ImIrnPyHp-y-PyImPyPy-(3-Py 2012(3) 5'-W G TG G C A W-3' Im-~i-ImImPyPy-y-HpImPyPy-(3-Py 2013(3) 5'-W G TG C T T W-3' Im-p-ImPyHpHp-y-PyPyImPy-p-Py 20143) 5'-W G TG C T A W-3' Im-(3-ImPyHpPy-y-HpPyImPy-(3-Py 20153) 5'-W G TG C T G W-3' Im-(3-ImPyHpIm-y-PyPyImPy-~3-Py 20160 5'-W G TG C T C W-3' Im-(3-ImPyHpPy-y-ImPyImPy-(3-Py 2017(3) 5'-W G TG C A T W-3' Im-(3-ImPyPyHp-y-PyHpImPy-(3-Py 2018(3) 5'-W G TG C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~i-Py 2019) 5'-W G TG C A G W-3' Im-~-ImPyPyIm-y-PyHpImPy-(3-Py 2020(3) 5'-W G TG C A C W-3' Im-~i-ImPyPyPy-y-ImHpImPy-~3-Py 2021(3) 5'-W G TG C G T W-3' Im-(3-ImPyImHp-y-PyPyImPy-(3-Py 2022~i) 5'-W G TG C G A W-3' Im-(1-ImPyImPy-y-HpPyImPy-(3-Py 2023(3) 5'-W G TG C C T W-3' ~Im-(3-ImPyPyHp-y-PyImImPy-p-Py 2024) 5'-W G TG C C A W-3' Im-~i-ImPyPyPy-y-HpImImPy-(3-Py 2025R) 5'-W G TG G G G W-3' Im-(3-ImImImIm-y-PyPyPyPy-(3-Py 2026(3) 5'-W G TG G G C W-3' Im-R-ImImImPy-y-ImPyPyPy-(3-Py 2027(3) 5'-W G TG G C G W-3' Im-~3-ImImPyIm-y-PyImPyPy-(3-Py 20283) 5'-W G TG G C C W-3' Im-~i-ImImPyPy-y-ImImPyPy-p-Py 20293) 5'-W G TG C G G W-3' Im-(3-mPyImIm-y-PyPyImPy-~3-Py 2030(3) 5'-W G TG C G C W-3' Im-(3-ImPyImPy-y-ImPyImPy-(3-Py 2031(3) 5'-W G TG C C G W-3' Im-~3-ImPyPyIm-y-PyImImPy-~i-Py 2032(3) 5'-W G TG C C C W-3' Im-(3-ImPyPyPy-y-ImImImPy-(3-Py i_ PCT/US98l01714 TABLE 174:
12-ring (3-Hairpin Polyamides for recogmUon of 8-by S'-WGTTWNNW-3' DNA sequence aromatic amino acid sequence 2033(3) 5' -W G T ImHp-/3-HpApHp-y-pypypy_a_pypY
T T T T
W-3' 2034(3) ~ 5' -W G ImHp-(3-HpHpPy-y-HpPyPy-~3-pypy T T T T
A W-3' 20353) 5' -W G T ImHp-(3-HpHpIm-y-pypypy-R_pypy T T T G
W-3' 20363) 5' -W G T ImHp-(3-HpHpPy-y-ImPyPy-(3-PyPy T T T C
W-3' 2037(3) 5' -W G T ImHp-(3-HpPYHp-y-pyHpPy-(3-PYPy T T A T
W-3' 2038(3) 5' -W G T A A W-3' ImHp-J3-HpPYPy-y-HpHpPy-(3-Pypy T T
2039(3) 5' -W G T A G W-3' ImHp-~3-HpPYIm-y-PyHpPy-(3-PYPy T T
2040(3} 5' -W G T A C W-3' ImHp_~3_Hppypy_y_ImHppy-(3_pypy T T
20413) 5' -W G T G T W-3' ImHp-(3-HpImHp-y_PyPypy-(3-pypY
T T
2042(3) 5' -W G T G A W-3' ImHp-(3-Hplmpy_y_HpPyPy-(3-PyPy T T
20433) 5' -W G T G G W-3' ImHp-~i-HpImIm-y-PypypY-~3_pypy T T
2044(3} 5' -W G T G C W-3' _ _ T T Imp R HpImPy y ImPyPy-(3-PyPy 2045(3) 5' -W G T C T W-3 ImHp-(3-HpPyHp-y-PYImPy-~-PyPy T T T
20463) 5' -W G T C A W-3' ImHp-(3-Hppypy_y_HpImPy-~3-pypy T T
20473) 5' -W G T C G W-3' ImHp-(3-HpPyIm-y-PYImPy-J3-pypY
T T
2048(3) 5'-W G T C C W-3' ImHp-~3-Hppypy_y_ImImpy-(3-PYPy T T
20493) 5' -W G T T T W-3' T A ImHp-~-PyHpHp-y-PyPyHp-p-PyPy 20503) 5'-W G T T A W-3' ImHp-~3-PyHpPy-y-HpPYHp-(3-PyPy T A
2051(3) 5' -W G T T G W-3' ImHp-(3-PYHpIm-y-PypyHp-(3_pypy T A
20523) 5' -W G T T C W-3' ImHp-~i-PyHppy-y-ImPYHp-(3-Pypy T A
2053J3) 5' -W G T A T W-3' ImHp-~3-pypyHp_y_pyHpHp-~3-pypy T A
2054(3) 5' -W G T A A W-3' ImHp-(3-PYPYpy-y_HpHpHp-~i-pypY
T A
2055(3) 5' -W G T A G W-3' ImHp-~3-PyPYIm-y-PyHpHp-(3-PYPy T A
2056(3) 5' -W G T A C W-3' ImHp-(3-PyPYPy-y-ImHpHp-~3-pypY
T A
2057~i) 5' -W G T G T W-3' ImHp-(3-pylmHp_y_pypYHp_~3_PyPy T A
2058(3) 5' -W G T G A W-3' ImHp-(3-PyImPY-y-Hppygp-(3-PyPy T A
2059~i) 5' -W G T G G W-3' ImHp-~-PyImIm-y-pyPyHp-(3-pypy T A
20603) 5' -W G T G C W-3' ImHp-~3-PyImPy-y_ImPYHp-~3-Pypy T A
2061~i) 5' -W G T C T W-3' Imp-(3_pypyHp_y_pyl~p_a-pYpy T A
2062(3) 5' -W G T C A W-3' ImHp-(3-pypypy-y_HpImHp-/3-PyPy T A
20633) 5' -W G T C G W-3' ImHp-(3-PYPyIm-y-pylmHp-p_pypy T A
2064(3) 5' -W G T C C W-3' ImHp-/3-PyPYPY-y-ImImHp-(3-Pypy T A
TABLE
175:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGTTSNNW-3' -DNA aromatic amino acid sequence sequence 2065(3) 5'-W G TT G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~-PyPy 20663) ~5'-W G TT G T A W-3' ImHp-(3-ImHpPy-y-HpPYPy-(3-PYPy 20673) 5'-W G TT G T G W-3' ImHp-(3-ImHpIm-y-PYPYPy-~3-PYPy 2068(3) 5'-W G TT G T C W-3' ImHp-(3-ImHpPy-y-ImPYPy-(3-PyPy 2069(3) 5'-W G TT G A T W-3' ImHp-p-ImPYHp-y-PyHpPy-p-PyPy 2070(3) 5'-W G TT G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-(3-PyPy 2071(3) 5'-W G TT G A G W-3' ImHp-p-ImPyIm-y-PyHpPy-(3-PYPy 20723) 5'-W G TT G A C W-3' ImHp-(3-ImPYPy-y-ImHpPy-(3-PYPy 2073(3) 5'-W G TT G G T W-3' ImHp-a-ImImHp-y-PyPYPy-(3-PYPy 20743) 5'-W G TT G G A W-3' ImHp-p-ImImPy-y-HpPyPy-(3-PYPy 2075(3) 5'-W G TT G C T W-3' ImHp-p-ImPyHp-y-PyImPy-(3-PYPy 2076(3) 5'-W G TT G C A W-3' ImHp-p-ImPyPy-y-HpImPy-(3-PYPy 2077(3) 5'-W G TT G G G W-3' ImHp-~3-ImImIm-y-PyPYPy-(3-PyPy 2078(3) 5'-W G TT G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-(3-PYPy 2079R) 5'-W G TT G C G W-3' ImHp-(3-ImPYIm-y-PyImPy-~-PYPy 2080(3) 5'-W G TT G C C W-3' ImHp-(3-ImPyPy-y-ImImPy-(3-PYPy 2081(3) 5'-W G TT C T T W-3' ImHp-(3-PYHpHp-y-PYPYIm-(3-PYPy 2082(3) 5'-W G TT C T A W-3' ImHp-(3-PYHpPy-y-HpPyIm-(3-PYPy 2083(3) 5'-W G TT C T G W-3' ImHp-(3-PYHpIm-y-PyPYIm-~3-PyPy 2084(3) 5'-W G TT C T C W-3' ImHp-(3-PYHpPy-y-ImPyIm-p-PyPy 20853) 5'-W G TT C.A T W-3' ImHp-(3-PYPyHp-y-PYHpIm-(3-PyPy 2086(3) 5'-W G TT C A A W-3' ImHp-p-PYPYPy-y-HpHpIm-(3-PyPy 2087(3) 5'-W G TT C A G W-3' ' ImHp-p-PyPYIm-y-PyHpIm-(3-PyPy 20883) 5'-W G TT C A C W-3' ImHp-J3-PYPyPy-y-ImHpIm-(3-PYPy 2089(3) 5'-W G TT C G T W-3' ImHp-(3-PyImHp-y-PyPYIm-~3-PyPy 2090(3) 5'-W G TT C G A W-3' ImHp-~i-PYImPy-y-HpPYIm-~3-PYPy 2091(3) 5'-W G TT C C T W-3' ImHp-(3-PYPyHp-y-PyImIm-(3-PyPy 2092(3) 5'-W G TT C C A W-3' ImHp-p-PYPyPy-y-HpImIm-p-PyPy 2093~i) 5'-W G TT C G G W-3' ImHp-p-PYImIm-y-PYPyIm-(3-PyPy 2094(3) 5'-W G TT C G C W-3' ImHp-[3-PYImPy-y-ImPYIm-(3-PYPy 2095(3) 5'-W G TT C C G W-3' ImHp-(3-PYPyIm-y-PyImIm-p-PYPy 2096(3) 5'-W G TT C C C W-3' ImHp-(3-PYPyPy-y-ImImIm-~3-PyPy ......~_.......-.. n TABLE 176: r recognition of 8-by 5'-WGTAWNNW-3' 12-ring -~3-Hairpin Polyamides fo DNA aromatic amino acid sequence sequence 2097(3) 5' G A T T W-3' ImHp-/3-HpHpHp-y-pypypy_p_pypy -W T T
20983) 5' G A TT A W-3' ImHp-(3-HpHpPy-y-HpPYPy-(3-PYPy -W T
2099(3) 5' G A TT G W-3' ImHp-(3-HpHpIm-y-Pypypy-(3-pypY
-W T
' 2100(3) 5' G A TT C W-3' -W T ImHp-p-HpHpPy-y-ImPyPy-~3-PYPy 2101) 5' G A TA T W-3' ImHp-(3-HpPYHp-y-PYHpPy-~i-Pypy -W T
2102(3) 5' G A TA A W-3' ImHp-~3-HpPYPy-y-HpHpPy-~3-PYpY
-W T
2103(3) 5' G A TA G W-3' ImHp-(3-HpPyIm-Y-PYHpPy-~3-PYPy -W T
2104(3) 5' G A TA C W-3' I~p_~_HppypY-Y_I~ppy-~_PypY
-W T
2105(3) 5' G A TG T W-3' I~p_~_Hpl~p_Y_pypypy-a-pYpY
-W T
21063) 5' G A TG A W-3' Imi-Ip-~_Hplmpy_y_HpPYpy-(3-pypy -W T
21073) 5' G A TG G W-3' ImHp-(3-HpImIm-y-PypypY-(3-pypY
-W T
2108~i) 5' G A TG C W-3' ImHp-~-HpImPy-y-ImPyPy-(3-pypy -W T
2109(3) 5' G A TC T W-3' ImHp-(3-HpPyHp-y-PyImPy-(3-PYPy -W T
21103) 5' G A TC A W-3' ImHp-(3-HpPyPy-y-HpImPy-~3-Pypy -W T
2111(3) 5' G A TC G W-3' ImHp-(3-HpPyIm-y-PyImPy-(3-Pypy -W T
21123) 5' G A TC C W-3' ImHp-~3-HpPyPy-y-ImImPy-(3-PyPy -W T
2113(3) 5' G A AT T W-3' ImHp-(3-PyHpHp-y-pypygp-(~-pypy -W T
2114) 5' G A AT A W-3' ImHp-(3-PYHpPy-y-HpPyHp-(3-PyPy -W T
2115(3) 5' G A AT G W-3' ImHp-~3-pyHplm-y-PypyHp-(3-Pypy -W T
2116(3) 5' G A AT C W-3' ImHp-p-pygppY_y_ImPYHp-(3-PYPy -W T
2117(3) 5' G A AA T W-3' ImHp-(3-PyPyHp-y-pYHpHp-(3-PYPy -W T
2118(3} 5' G A AA A W-3' ImHp-(3-PyPyPy-Y-HpHpHp-/3-Pypy -W T
2119(3) 5' G A AA G W-3' 'ImHp-p-pypylm-y-PYHpHp-(3-PyPy -W T
21203) 5' G A AA C W-3' I~p_R_p~,p~,py_y_I~pHp-p-PyPY
-W T
21213) 5' G A AG T W-3' I~p_~_p~,I~p_y-pYpYHp-~-pYpY
-W T
2122(3) 5' G A AG A W-3' ImHp-~i-pylmpy_y_HppYHp-~-pypY
-W T
2123(3) 5' G A AG G W-3' ImHp-p-PYImIm-y-Pypygp-(3-pYPy -W T
2124(3) 5' G A AG C W-3' ImHp-R-PYImPY-y-ImPYHp-~3-Pypy -W T
2125(3) 5' G A AC T W-3' ImHpPyPYPyHp-Y-PyImHp-(3-PyPy -W T
2126(3) 5' G A AC A W-3' ImHpPyPYPYPy-y-Hpl~p_~3-pypy -W T
2127(3) 5' G A AC G W-3' ImHpPyPYPYIm-y-PYImHp-(3-PYpY
-W T
2128(3) 5' G A AC C W-3' ImHpPYPYPYPY-Y-ImImHp-(3-PyPY
-W T
TABLE 177: 1-Iairpin 12-ring Polyamides p- for recognition of 8-by 5'-WGTASNNW-3' -DNA aromatic amino acid sequence sequence 2129(3) 5' -WG T A G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~3-PyPy 21303) ~ -WG T A G T A W-3' ImHp-(3-ImHpPy-y-HpPyPy-~3-PyPy 5' 21313) 5' -WG T A G T G W-3' ImHp-(3-ImHpIm-y-PyPypy-p-PyPy 2132(3) 5' -WG T A G T C W-3' ImHp-(3-ImHpPy-y-ImPyPy-[3-PyPy 21333) 5' -WG T A G A T W-3' ImHp-(3-ImPyHp-y-PyHpPy-(3-Pypy 2134(3) 5' -WG T A G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-~3-PyPy 2135(3) 5' -WG T A G A G W-3' ImHp-(3-ImPyIm-y-PyHpPy-~3-PyPy 2136(3) 5' -WG T A G A C W-3' ImHp-(3-ImPyPy-y-ImHpPy-~3-PyPy 21373) 5' -WG T A G G T W-3' ImHp-(3-ImImHp-y-PypyPy-~3-PyPy 21383) 5' -WG T A G G A W-3' ImHp-(3-ImImPy-y-HpPyPy-~-PyPy 2139(3) 5' -WG T A G C T W-3' ImHp-/3-ImPyHp-y-PyImPy-(3-PyPy 2140(3) 5' -WG T A G C A W-3' ImHp-(3-ImpyPy-y-HpImPy-(3-PyPy 2141(3) 5' -WG T A G G G W-3' ImHp-(3-ImImIm-y-PyPyPy-p-PyPy 2142(3) 5' -WG T A G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-~i-PyPy 2143(3) 5' -WG T A G C G W-3' ImHp-(3-ImPyIm-y-PyImPy-(3-PyPy 2144(3) 5' -WG T A G C C W-3' ImHp-~3-ImPyPy-y-ImImPy-~i-PyPy 2145(3) 5' -WG T A C T T W-3' ImHp-(3-PyHpHp-y-PyPyIm-R-PyPy 2146(3) 5' -WG T A C T A W-3' ImHp-(3-PyHpPy-y-HpPyIm-(3-PyPy 2147(3) 5' -WG T A C T G W-3' ImHp-j3-PyHpIm-y-PyPyIm-(3-PyPy 2148(3) 5' -WG T A C T C W-3' ImHp-(3-PyHpPy-y-ImPyIm-p-PyPy 2149(3) 5' -WG T A C A T W-3' ImHp-R-PyPyHp-y-PyHpIm-(3-PyPy 2150(3) 5' -WG T A C A A W-3' ImHp-(3-PyPyPy-y-HpHpIm-(3-PyPy 2151(3) 5' -WG T A C A G W-3' ImHp-~3-PyPyIm-y-PyHpIm-(3-PyPy 2152(3) 5' -WG T A C A C W-3' ImHp-(3-PyPyPy-y-ImHpim-~3-PyPy 2153(3) 5' -WG T A C G T W-3' ImHp-(3-PyImHp-y-PyPyIm-(3-PyPy 2154) 5' -WG T A C G A W-3' ImHp-(3-PyImPy-y-HpPyIm-(3-PyPy 2155(3) 5' -WG T A C C T W-3' ImHp-~i-PyPyHp-y-PyImIm-p-PyPy 2156(3) 5' -WG T A C C A W-3' ImHp-(3-PyPyPy-y-HpImIm--PyPy 2157(3) 5' -WG T A C G G W-3' ImHp-(3-PyImIm-y-PyPyIm-(3-PyPy 2158(3) 5' -WG T A C G C W-3' ImHp--PyImPy-y-ImPyIm-(3-PyPy 21593) 5' -WG T A C C G W-3' ImHp-~3-PyPyIm-y-PyImIm-(3-PyPy 21603) 5' -WG T A C C C W-3' ImHp-(3-PyPyPy-y-ImImIm-p-PyPy ,. , .
1A13LE 178: 12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGTCWNNW-3' DNA aromatic amino acid sequence sequence 2161(3) 5'-W G TC T T T W-3' ImHppy_~3_HpHp_y_pypy_~3-ImPyPy 21623) ~5'-W G TC T T A W-3' ImHpPy-J3-Hppy_y_Hppy-(3-ImPyPy 2163~i) 5'-W G TC T T G W-3' ImHpPy-~3-HpIm-y-PyPy-~3-ImPyPy ' 2164(3) 5'-W G TC T T C W-3' ImHpPy-(3-HpPy-y-ImPy-~3-ImPyPy 2165~i) 5'-W G TC T A T W-3' ImHpPy-~3-PyHp-y_pyHp-(3-ImPyPy 21663) 5'-W G TC T A A W-3' ImHpPy-(3-Pypy-y-HpHp-(3-ImPyPy 2167(3) 5'-W G TC T A G W-3' ImHpPy-(3-Pylm-y-PyHp-a-ImPyPy 2168(3) 5'-W G TC T A C W-3' ImHpPy-~i-PyPy-y-ImHp-p-ImPyPy 2169(3) 5'-W G TC T G T W-3' ImHpPy-(3-ImHp-y-pypy_R-ImPyPy 2170(3) 5'-W G TC T G A W-3' ImHpPy-(3-ImPy-y-HpPy-~3-ImPyPy 2171(3) 5'-W G TC T G G W-3' ImHpPy-(3-Imlm_y_pypy_~3-ImpyPy 2172(3) 5'-W G TC T G C W-3' ImHppy_~_Impy_y_Imp~,_(3-ImPyPy 2173(3) 5'-W G TC T C T W-3' ImHpPy-~3-PyHp-y-Pylm-(3-ImPyPy 21743) 5'-W G TC T C A W-3' ImHpPy-~3-Pypy-y-HpIm-(3-ImPyPy 2175(3) 5'-W G TC T C G W-3' ImHpPy-p-pyIm-y-PyIm-(3-ImPyPy 2176~i) 5'-W G TC T C C W-3' ImHpPy-(3-PyPy-y-Imlm-~3-ImPyPy 2177(3) 5'-W G TC A T T W-3' ImHpPy-~3-HpHp-y-Pypy-(3-ImPyPy 2178(3) 5'-W G TC A T A W-3' ImHpPy-(3-HpPy-y-HpPy-(3-ImPyPy 2179(3) 5'-W G TC A T G W-3' ImHpPy-(3-HpIm-y-PyPy-~i-ImPyPy 2180J3) 5'-W G TC A T C W-3' ImHpPy-~3-HpPy-y-ImPy-p-ImPyPy 21813) 5'-W G TC A A T W-3' ImHppy_(~_pyHp_y_pyHp_R-ImPyPy 2182~i) 5'-W G TC A A A W-3' ImApPy-(1-Pypy-y-HpHp-(3-ImPyPy 2183(3) 5' -W G T C A A G W-3' ImHpPy-(3-PyIm-y-PyHp-(3-ImPyPy 2184(3) 5' -W G T C A A C W-3' ImHpPy-(3-PyPy-y-ImHp-(3-ImPyPy 2185(3) 5' -W G T C A G T W-3' ImFipPy-~3-ImHp-y_pyp~,_~_ImPyPy 2186(3) 5' -W G T C A G A W-3' ImHpPy-(3-ImPy-y-HpPy-p-ImPyPy 2187(3) 5'-W G TC A G G W-3' ImHpPy-(3-ImIm-y-PyPy-(3-ImPyPy 2188(3) 5'-W G TC A G C W-3' ImHpPy-(3-ImPy-y-ImPy-~3-ImPyPy 2189(3) 5'-W G TC A C T W-3' ImHpPy-~i-PyHp-y-PyIm-(3-ImPyPy 2190~i) 5'-W G TC A C A W-3' ImHpPy-(3-PyPy-y-HpIm-/3-ImPyPy 2191(3) 5'-W G TC A C G W-3' ImHpPy-(3-PyIm-y-PyIm-(3-ImPyPy 2192(3) 5'-W G TC A C C W-3' ImHpPy-(3-PyPy-y-Imlm-(3-ImPyPy WO 981370b7 PCT/US98/01714 TABLE 179:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGTCSNNW-3' DNA aromatic amino acid sequence sequence 2193(3) 5'-WG T C G T TW-3' ImHp-(3-ImHpHp-y-PyPy-J3-ImPyPy 2194~i) 5'-WG T C G T AW-3' ImHp-(3-ImHpPy-y-HpPy-(3-ImPyPy 21953) 5'-WG T C G T GW-3' ImHp-j3-ImHpIm-y-PyPy-(3-ImPyPy 2196(3) 5'-WG T C G T CW-3' ImHp-~-ImHpPy-y-ImPy-(3-ImpyPy 21973) 5'-WG T C G A TW-3' ImHp-~3-ImPyHp-y-PyFip-(3-ImPyPy 2198(3) 5'-WG T C G A AW-3' ImHp-(3-ImPyPy-y-HpHp-(3-ImPyPy 2199(3) 5'-WG T C G A GW-3' ImHp-J3-ImPyIm-y-PyHp-(3-ImPyPy 22003) 5'-WG T C G A CW-3' ImHp-~i-ImPyPy-y-ImHp-(3-ImpyPy 2201(3) 5'-WG T C G G TW-3' ImHp-(3-ImImHp-y-PyPy-~3-ImPyPy 2202(3) 5'-WG T C G G AW-3' ImHp-(3-ImImPy-y-HpPy-p-ImPyPy 2203) 5'-WG T C G C TW-3' ImHp-(3-ImPyHp-y-PyIm-p-ImPyPy 2204~i) 5'-WG T C G C AW-3' ImHp-p-ImPyPy-y-HpIm-[3-ImpyPy 22053) 5'-WG T C C T TW-3' ImHp-(3-PyHpHp-y-Py-p-ImImPyPy 2206(3) 5'-WG T C C T AW-3' ImHp-(3-PyHpPy-y-Hp-(3-ImImPyPy 2207(3) 5'-WG T C C T GW-3' ImHp-(3-PyHpim-y-Py-(3-ImImPyPy 2208(3) 5'-WG T C C T CW-3' ImHp-~i-PyHpPy-y-Im-(3-ImImPyPy 2209(3) 5'-WG T C C A TW-3' ImHp-(3-PyPyHp-y-Py-(3-ImImPyPy 2210(3) 5'-WG T C C A AW-3' ImHp-(3-PyPypy-y-Hp-~3-ImImPyPy 22113) 5'-WG T C C A GW-3' ImHp-~3-PyPyIm-y-Py-~i-ImImpyPy 2212(3) 5'-WG T C C A CW-3' ImHp-(3-PypyPy-y-Im-~3-ImImPyPy 2213(3) 5'-WG T C C G TW-3' ImHp-(3-PyImHp-y-py-(3-ImImpyPy 2214(3) 5'-WG T C C G AW-3' ImHp-(3-PyImPy-y-Hp-~i-ImImPyPy 2215(3) 5'-WG T C C C TW-3' 'ImHp-~i-PyPyHp-y-PyImImIm-(3-Py 2216(3) 5'-WG T C C C AW-3' ImHp-(i-PyPyPy-y-HpImImIm-(3-Py 2217(3) 5'-WG T C G G GW-3' ImHp-~i-ImImIm-y-PyPy-(3-ImPyPy 2218(3) 5'-WG T C G G CW-3' ImHp-p-ImImPy-y-ImPy-~3-ImPyPy 22193) 5'-WG T C G C GW-3' ImHp-~3-ImPyIm-y-PyIm-p-ImPyPy 2220(3) 5'-WG T C G C CW-3' ImHp-(3-ImPyPy-y-ImIm-~-ImPyPy 22210 5'-WG T C C G GW-3' ImHp-(3-PyImIm-y-Py-(3-ImImPyPy 2222(3) 5'-WG T C C G CW-3' ImHp-(3-PyImPy-y-Im-~i-ImImPyPy 2223(3) 5'-WG T C C C GW-3' ImHp-(3-PyPyIm-y-PyImImIm-p-Py 2224~i) 5'-WG T C C C CW-3' ImHp-(3-PyPyPy-y-ImImImIm-~i-Py
10-ring Hairpin Polyamides for recognition of ?-by 5'-WACWNNW-3' DNA aromatic amino acid sequence sequence 913 ) 5' -WA C T T T W-3' PyPyHpHpHp-y-PyPyPyImHp 914 ) '5' -WA C T T A W-3 PyPyHpHpPy-Y-HpPyPyImHp ' 915) 5' -WA C T T G W-3' PYPYHpgpIm-Y-PYPYPyImHp 916) 5' -WA C T T C W-3' PyPyHpHpPy-y-ImPyPyImHp 917) 5' -WA C T A T W-3' PyPyHpPyHp-Y-PyHpPyImHp 918) 5' -WA C T A A W-3' PyPyHpPyPy-y-HpHpPyImHp 919) 5' -WA C T A G W-3' PyPyHpPyIm-y-PyHpPyImHp 92 0 5' -WA C T A C W- 3 PyPyHpPyPy-Y- ImHppyImHp ) ' 921) 5' -WA C T G T W-3' pypygpl~p-Y-p~,pypyl~p 922) 5' -WA C T G A W-3' PyPyHpImPy-y-HpPyPyImHp 923) 5' -WA C T G G W-3' PypyHpImIm-y-PyPyPyImHp 924} 5' -WA C T G C W-3' PyPyHpImPy-y-ImPyPyImHp 925) 5' -WA C T C T W-3' PyPyHpPyHp-y-PyImPyImHp 926) 5' -WA C T C A W-3' PyPyHpPyPy-Y-HpImPyImHp 927 ) 5' -WA C T C G W-3' PyPyHpPyim-y-PyImPyImHp 928) 5' -WA C T C C W-3' PypyHppypy-y-ImImPyImHp 929) 5' -WA C A T T W-3' PyPyPyHpHp-y-PyPyHpImHp 930) 5' -WA C A T A W-3' PypyPyHpPy-y-HpPyHpImHp 931) 5' -WA C A T G W-3' PyPyPyHpIm-y-PyPyHpImHp 932) 5' -WA C A T C W-3' PyPyPyHpPy-y-ImPyHpImHp 933) 5' -WA C A A T W-3' PypypypyHp-y-PyHpHpImHp 934) 5' -WA C A A A W-3' PyPyPyPyPy-y-HpHpHpImHp 935) 5' -WA C A A G W-3' PyPyPyPyIm-y-PyHpHpImHp 93 6 5' -WA C A A C W-3 PyPyPyPyPy-y- ImHpHpImHp ) ' 937) 5' -WA C A G T W-3' PyPypyImHp-y-PyPYHpImHp 938} 5' -WA C A G A W-3' PyPyPyImPy-y-HpPyHpImHp 939) 5' -WA C A G G W-3' PyPyPyImIm-y-PyPyHpImHp 940) 5' -WA C A G C W-3' PyPypyImPy-y-ImPyHpImHp 941) 5' -WA C A C T W-3' PyPyPyPyHp-Y-PyImI3pImHp 942 ) 5' -WA C A C A W-3 PyPyPyPyPy-y-HpImHpImHp ' 943 ) 5' -WA C A C G W-3 PyPypypylm-y-pyImHpImHp ' 944) 5' -WA C A C C W-3' pypypypypy-Y-ImImHpImHp 'TABLE 10-ring 43: Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' DNA aromatic amino acid sequence sequence 945) 5' A C G TT W-3' PyPyImHpHp-y-pypypylmHp -W
946) ~5'-W A C G TA W-3' PyPyImHpPy-y-HpPyPyImHp 947) 5'-W A C G TG W-3' PyPyImHpIm-y-PyPyPyImHp 948) 5' A C G TC W-3' PyPyImHpPy-y-ImPyPyImHp -W
949) 5'-W A C G AT W-3' PyPyImPyHp-y-pyHpPyImHp 950) 5'-W A C G AA W-3' PyPyImPyPy-y-HpHpPyImHp 951) 5' A C G AG W-3' PyPyImPyIm-y-PyHpPyImHp -W
952) 5' A C G AC W-3' PyPyImPyPy-y-ImHpPyImHp -W
953) 5'-W A C G GT W-3' PyPyImImHp-y-PyPyPyImHp 954) 5' A C G GA W-3' PyPyImImPy-y-HpPyPyImHp -W
955) 5' A C G CT W-3' PyPyImPyHp-y-PyImPyImHp -W
956) 5' A C G CA W-3' PyPyImPyPy-y-HpImPyImHp -W
957) 5'-W A C ~CTT W-3' PyPyPyHpHp-y-PyPyImImHp 958) 5'-W A C C TA W-3' PyPyPyHpPy-y-HpPyImImHp 959) 5' A C C TG W-3' PyPyPyHpIm-y-PyPyImImHp -W
960) 5' A C C TC W-3' PyPyPyHpPy-y-ImPyImImHp -W
961) 5' A C C AT W-3' PyPyPyPyHp-y-PyHpImImHp -W
962) 5'-W A C C AA W-3' PyPyPyPyPy-y-HpHpImImHp 963) 5'-W A C C AG W-3' PyPyPyPyIm-y-PyHpImImHp 964) 5' A C C AC W-3' PyPyPyPyPy-y-ImHpImImHp -W
965) 5' A C C GT W-3' PyPyPyImHp-y-PypyImImHp -W
966) 5' A C C GA W-3' PyPyPyImPy-y-HpPyImImHp -W
967) 5' A C C CT W-3' PyPyPyPyHp-y-PyImImImHp -W
968) 5' A C C CA W-3' PyPyPyPyPy-y-HpImImImHp -W
969) 5'-W A C G GG W-3' PyPyImImIm-y-PyPyPyImHp 970) 5'-W A C G GC W-3' PyPyImImPy-y-ImPyPyImHp 971) 5' A C G CG W-3' PyPyImPyIm-y-PyImPyImHp -W
972) 5' A C G CC W-3' PyPyImPyPy-y-ImImPyImHp -W
973) 5'-W A C C GG W-3' PyPyPyImIm-y-PyPyImImHp 974) 5'-W A C C GC W-3' PyPyPyImPy-y-ImPyImImHp 975) 5'-W A C C CG W-3' PyPyPyPyIm-y-PyImImImHp 976) 5'-W A C C CC W-3' PyPypypypy-y-ImImImImHp TABLE 44:
10-ring Hairpin Poiyamides for recognition of 7-by 5'-WTGWNNW-3' DNA aromatic amino acid sequence sequence 977 ) 5' -WT G T TT W-3 ' HpImHpHpHp-y-PyPYPYPyPy 978) ~5' -WT G T TA W-3' HpImHpHpPy-y-HpPyPyPYPy 979) 5' -WT G T TG W-3' HpImHpHpIm-y-PYPyPyPypy 980) 5' -WT G T TC W-3' HpImHpHpPy-y-ImPyPyPyPy 981) 5' -WT G T AT W-3' HpImHpPyHp-y-PYHpPYPyPy 982) 5' -WT G T AA W-3' HpImHppyPy-y-HpHpPyPYPy 983) 5' -WT G T AG W-3' HpImHpPyIm-y-PyHpPyPYPy 984) 5' -WT G T AC W-3' HpImHpPyPy-y-ImHpPYPYpy 985) 5' -WT G T GT W-3' HpImHpImHp-y-PYpyPYpypY
986) 5' -WT G T GA W-3' HpImHpImPy-y-HpPYPyPyPy 987) 5' -WT G T GG W-3' HpImHpImIm-y-PyPYPyPYPy IS 988) 5' -WT G T GC W-3' HpImHpImPy-y-ImPyPYPyPy 989) 5' -WT G T CT W-3' HpImHpPyHp-y-PYImPyPyPy 990) 5' -WT G T CA W-3' HpImHpPyPy-y-HpImPyPyPy 991) 5' -WT G T CG W-3' HpImHpPyIm-y-PyImPyPyPy 992) 5' -WT G T CC W-3' HpImHpPYPy-y-ImImPyPYPy 993) 5' -WT G A TT W-3' HpImPyHpHp-y-pypyHpPyPy 994) 5' W HpImPyHpPy-y-HpPyHpPyPy T
G
A
T
A
W-3' 995) 5' -WT G A TG W-3' HpImPyl3plm-y-PyPyHpPypy 996) 5' -WT G A TC W-3' HpImPyHpPy-y-ImPyHpPyPy 997) 5' -WT G A AT W-3' HpImPYPyHp-y-PyHpHpPyPy 998) 5' -WT G A AA W-3' HpImPYPyPy-y-HpHpHpPyPy 999) 5' -WT G A AG W-3' HpImPyPyIm-y-PyHpHpPyPy 1000) 5' -WT G A AC W-3' HpImPyPyPy-y-ImHpHpPYPy 1001) 5' -WT G A GT W-3' Hpln,pyl~p-y_pypYHppypy 1002) 5' -WT G A GA W-3' HpImPyImPy-y-HpPyHpPyPy 1003 5' -WT G A GG W-3 ' HpImPYImIm-y-PyPyHpPyPy ) 1004) 5' -WT G A GC W-3' HpImPyImPy-y-ImPyHpPyPy 1005) 5' -WT G A CT W-3' HpImPyPyHp-y-PYImHpPyPy 1006) 5' -WT G A CA W-3' HpImPYPYPy-y-HpImHpPyPy 1007) 5' -WT G A CG W-3' HpImPyPyIm-y-PyImHpPypy 1008) 5' -WT G A CC W-3' HpImPyPyPy-y-ImImHpPyPy TABLE
45:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGSNNW-3' DNA aromatic amino acid sequence sequence 1009) 5' -W T GG T T W-3' HpImImHpHp-y-PyPyPyPyPy 1010) 'S'-W T GG T A W-3' HpImImHpPy-y-HpPyPyPyPy 1011) 5' -W T GG T G W-3' HpImImHpIm-y-PyPyPyPyPy 1012) 5' -W T GG T C W-3' HpImImHpPy-y-ImPyPyPyPy 1013) 5' -W T GG A T W-3' HpImImPyHp-y-PyHpPyPyPy 1014) 5' -W T GG A A W-3' HpImImPyPy-y-HpHpPyPyPy 1015) 5' -W T GG A G W-3' HpImImPyIm-y-PyHpPyPyPy 1016) 5' -W T GG A C W-3' HpImImPyPy-y-ImHpPyPyPy 1017) 5' -W T GG G T W-3' HpImImImHp-y-PyPyPyPyPy 1018) 5' -W T GG G A W-3' HpImImImPy-~/-HpPyPyPyPy 1019) 5' -W T GG C T W-3' HpImImPyHp-y-PyImPyPyPy 1020) 5' -W T GG C A W-3' HpImImPyPy-y-HpImPyPyPy 1021) 5' -W T GC T T W-3' HpImPyHpHp-y-PyPyImPyPy 1022) 5' -W T GC T A W-3' HpImPyHpPy-y-HpPyImPyPy 1023 5' -W T GC T G W-3 ' HpImPyHpIm-y-PyPyImPyPy ) 1024) 5' -W T GC T C W-3' HpImPyHpPy-y-ImPyImPyPy 1025) 5' -W T GC A T W-3' HpImPyPyHp-y-PyHpImPyPy 1026) 5' -W T GC A A W-3' HpImPyPyPy-y-HpHpImPyPy 1027) 5' -W T GC A G W-3' HpImPyPyIrn-y-PyHpImPyPy 1028) 5' -W T GC A C W-3' HpImPyPyPy-y-ImHpImPyPy 1029) 5' -W T GC G T W-3' HpImPyImHp-y-PyPyImPyPy 1030) 5' -W T GC G A W-3' HpImPyImPy-y-HpPyImPyPy 1031) 5' -W T GC C T W-3' HpImPyPyHp-y-PyImImPyPy 1032) 5' -W T GC C A W-3' HpImPyPyPy-y-HpImImPyPy 1033) 5' -W T GG G G W-3' HpImImImIm-y-PyPyPyPyPy 1034) 5' -W T GG G C W-3' HpImImImPy-y-ImPyPyPyPy 1035) 5' -W T GG C G W-3' HpImImPyIm-y-PyImPyPyPy 1036) 5' -W T GG C C W-3' HpImImPyPy-y-ImImPyPyPy 1037 5' -W T GC G G W-3 ' HpImPyImIm-y-PyPyImPyPy ) 1038) 5' -W T GC G C W-3' HpImPyImPy-y-ImPyImPyPy 1039) 5' -W T GC C G W-3' HpImPyPyIm-y-PyImImPyPy 104 0 5' -W T GC C C W-3 ' HpImPyPyPy-y-ImImImPyPy ) WO 98/3?067 PCT/US98/01714 _71_ TABLE
46:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTWNNW-3' DNA aromatic amino acid sequence sequence 1041) 5' -WT T T T T W-3' HpHpHpHpHp-y-PyPyPypypy 1042) '5'-W T T T T A W-3' HpHpHpHpPy-y-HpPyPyPypy 1043) 5' -WT T T T G W-3' HpHpHpHpIm-y-PyPyPyPyPy 1044) 5' -WT T T T C W-3' HpHpHpHpPy-y-ImPyPyPyPy 1045) 5' -WT T T A T W-3' HpHpHpPyHp-y-PyHpPyPyPy 1046) 5' -WT T T A A W-3' HpHpHpPyPy-y-HpHpPyPyPy 1047) 5' -WT T T A G W-3' HpHpHpPyIm-y-PyHpPyPyPy 1048) 5' -WT T T A C W-3' HpHpHpPyPy-y-ImHpPyPyPy 1049) 5' -WT T T G T W-3' HpHpHpImHp-y-Pypypypypy 1050) 5' -WT T T G A W-3' HpHpHpImPy-y-HpPyPyPyPy 1051) 5' -WT T T G G W-3' HpHpHpImIm-y-PyPypypypy 1052) 5' -WT T T G C W-3' HpHpHpImPy-y-ImPyPyPyPy 1053) 5' -WT T T C T W-3' HpHpHpPyHp-y-PyImPyPyPy 1054) 5' -WT T T C A W-3' HpHpHpPyPy-y-HpImPyPyPy 1055) 5' -WT T T C G W-3' HpHpHpPyIm-y-PyImPyPyPy 1056) 5' -WT T T C C W-3' HpHpHpPyPy-y-ImTmPyPyPy 1057) 5' -WT T A T T W-3' HpHpPyHpHp-y-PypyHpPyPy 1058) 5' -WT T A T A W-3' HpHpPyHpPy-y-HpPyHpPyPy 1059) 5' -WT T A T G W-3' HpHpPyHpIm-y-PyPyHpPyPy 1060) 5' -WT T A T C W-3' HpHpPyHpPy-y-ImPyHpPyPy 1061) 5' -WT T A A T W-3' HpHpPyPyHp-y-pyHpHpPyPy 1062) 5' -WT T A A A W-3' HpHpPyPyPy-y-HpHpHpPyPy 1063) 5' -WT T A A G W-3' HpHpPyPyIm-y-PyHpHpPyPy 1064) 5' -WT T A A C W-3' HpHpPyPyPy-y-ImHpHpPyPy 1065) 5' -WT T A G T W-3' HpHpPyImHp-y-PyPyHpPyPy 1066) 5' -WT T A G A W-3' HpHpPyImPy-y-HpPyHpPyPy 1067) 5' -WT T A G G W-3' HpHpPyImIm-y-PyPyHpPyPy 1068) 5' -WT T A G C W-3' HpHpPyImPy-y-ImPyHpPyPy 1069) 5' -WT T A C T W-3' HpHpPyPyHp-y-PyImHpPyPy 1070) 5' -WT T A C A W-3' HpHpPyPyPy-y-HpImHpPyPy 1071} 5' -WT T A C G W-3' HpApPyPyIm-y-PyImHpPyPy 1072) 5' -WT T A C C W-3' HpApPyPyPy-y-ImImHpPyPy TABLE
47:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' DNA aromatic amino acid sequence sequence 1073) 5'-W T T G TT W-3' HpHpImHpHp-y-PyPyPyPYPy 1074) -5'-WT T G TA W-3' HpHpImHpPy-y-HpPyPyPYPy 1075) 5' T T G TG W-3' HpHpImHpIm-y-Pypypypypy -W
1076) 5'-W T T G TC W-3' HpHpImHpPy-y-ImPyPyPyPy 1077) 5'-W T T G AT W-3' HpHpImPYHp-y-pygppyPyPy 1078) 5'-W T T G AA W-3' HpHpImPyPy-y-HpHpPYPyPy 1079) 5' T T G AG W-3' HpHpImPyIm-y-PYHpPyPyPy -W
1080) 5' T T G AC W-3' HpHpImPyPy-y-ImHpPYPYPy -W
1081) 5' T T G GT W-3' HpHpImImHp-y-pypypypypy -W
1082) 5' T T G GA W-3' HpHpImImPy-y-HpPyPyPyPy -W
1083) 5'-W T T G CT W-3' HpHpImPYHp-y-PyImPyPyPy 1084) 5'-W T T G CA W-3' HpHpImPyPy-y-HpImPyPyPy 1085) 5' T T G GG W-3' HpHpImImIm-y-pypypypypy -W
1086) 5' T T G GC W-3' HpHpImImPy-y-ImPyPyPYPy -W
1087) 5'-W T T G CG W-3' HpHpImPYIm-y-PyImPyPyPy 1088) 5' T T G CC W-3' HpHpImPyPy-y-ImImPyPYPy -W
1089) 5'-W T T C TT W-3' HpHpPyHpHp-y-PypyImPYPy 1090) 5' T T C TA W-3' HpHpPYHpPy-y-HpPYImPyPy -W
1091) 5' T T C TG W-3' HpHpPyHpIm-y-PypyImPyPy -W
1092) 5'-W T T C TC W-3' HpHpPyHpPy-y-ImPyImPyPy 1093) 5'-W T T C AT W-3' HpHpPyPyHp-y-PyHpImPYPy 1094) 5'-W T T C AA W-3' HpHpPyPyPy-y-HpHpImPyPy 1095) 5' T T C AG W-3' ' HpHpPyPyIm-y-PYHpImPypy -W
1096) 5'-W T T C AC W-3' HpHpPYPYPy-y-ImHpImPYPY
1097) 5'-W T T C GT W-3' HpgppYl~p_y_pypylmpypy 1098) 5' T T C GA W-3' HpHpPyImPy-y-HpPyImPyPy -W
1099) 5' T T C CT W-3' HpHpPyPyHp-y-PyImImPyPy -W
1100) 5' T T C CA W-3' HpHpPyPyPy-y-HpImImPYPy -W
1101) 5' T T C GG W-3' HpHpPyImIm-y-PyPyImPyPy -W
1102) 5'-W T T C GC W-3' HpHpPyImPy-y-ImPyImPyPy 1103) 5'-W T T C CG W-3' HpHpPyPyIm-y-PyImImPyPy 1104) 5'-W T T C CC W-3' HpHpPyPyPy-y-ImImImPyPy . , TABLE
48:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTAWNNW-3' DNA aromatic amino acid sequence sequence 1105) 5' -WT A T T T W-3' HpPyHpHpHp-y-PyPyPyHpPy S 1106) ~5'-WT A T T A W-3' HpPyHpHpPy-y-HpPyPyHpPy 1107) 5' -WT A T T G W-3' HpPyHpHpIm-y-PypyPyHpPy 1108) 5' -WT A T T C W-3' HpPyHpHpPy-y-ImPyPyHpPy 1109) 5' -WT A T A T W-3' HpPyHpPyHp-y-PyHpPyHpPy 1110) 5' -WT A T A A W-3' HpPyHpPyPy-y-HpHpPyHpPy 1111) 5' -WT A T A G W-3' HpPyHpPyIm-y-PyHpPyHpPy 1112) 5' -WT A T A C W-3' HpPyHpPyPy-y-ImHpPyHpPy 1113) 5' -WT A T G T W-3' HpPyHpImHp-y-PyPyPyHpPy 1114) 5' -WT A T G A W-3' HpPyHpImPy-y-HpPyPyHpPy 1115) 5' -WT A T G G W-3' HpPyHpImIm-y-PyPyPyHpPy 1116) 5' -WT A T G C W-3' HpPyHpImPy-y-ImPyPyHppy 1117) 5' -WT A T C T W-3' HpPyHpPyHp-y-PyImPyHpPy 1118) 5' -WT A T C A W-3' HpPyHpPyPy-y-HpImPyHpPy 1119) 5' -WT A T C G W-3' HpPyHpPyIm-y-PyImPyHpPy 1120) 5' -WT A T C C W-3' HpPyHpPyPy-y-ImImPyHpPy 1121) 5' -WT A A T T W-3' HpPyPyHpHp-y-PyPyHpHpPy 1122) 5' -WT A A T A W-3' HpPyPyHpPy-y-HpPyHpHpPy 1123) 5' -WT A A T G W-3' HpPyPyHpIm-y-PyPyHpHpPy 1124) 5' -WT A A T C W-3' HpPyPyHpPy-y-ImPyHpHpPy 1125) 5' -WT A A A T W-3' HpPyPyPyHp-y-PyHpHpHpPy 1126) 5' -WT A A A A W-3' HpPyPyPyPy-y-HpHpHpHpPy 1127) 5' -WT A A A G W-3' HpPyPyPyIm-y-PyHpHpHpPy 1128) 5' -WT A A A C W-3' HpPyPyPyPy-y-ImHpHpHpPy 1129) 5' -WT A A G T W-3' HpPyPyImHp-y-PyPyHpHpPy 1130) 5' -WT A A G A W-3' HpPyPyImPy-y-HpPyHpHpPy 1131) 5' -WT A A G G W-3' HpPyPyImIm-y-PyPyHpHpPy 1132) 5' -WT A A G C W-3' HpPyPyImPy-y-ImPyHpHpPy 1133) 5' -WT A A C T W-3' HpPyPyPyHp-y-PyImHpHpPy 1134) 5' -WT A A C A W-3' HpPyPyPyPy-y-HpImHpHpPy 1135) 5' -WT A A C G W-3' HpPyPyPyIm-y-PyImHpHpPy 1136) 5' -WT A A C C W-3' HpPyPyPyPy-y-ImImHpHpPy TABLE
49:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTASNNW-3' DNA aromatic amino acid sequence sequence 1137 ) 5' -WT A G T T W-3 HpPyImHpHp-y-PyPypyHpPy ' S 1138) ~5'-WT A G T A W-3' HpPyImHpPy-y-HpPyPyHpPy 1139) 5' -WT A G T G W-3' HpPyImHpIm-y-PyPyPyHpPy 1140) 5' -WT A G T C W-3' HpPyImHpPy-y-ImPypyHpPy 1141) 5' -WT A G A T W-3' HpPyImPyHp-y-PyHpPyHpPy 1142) 5' -WT A G A A W-3' HpPyImPyPy-y-HpHpPyHpPy 1143) 5' -WT A G A G W-3' HpPyImPyIm-y-PyHpPyHpPy 1144) 5' -WT A G A C W-3' HpPyImPyPy-y-ImHpPyI-IpPy 1145) 5' -WT A G G T W-3' HpPyImImHp-y-PyPyPyHpPy 1146) 5' -WT A G G A W-3' HpPyImImPy-y-HpPyPyHpPy 1147) 5' -WT A G C T W-3' HpPyImPyHp-y-PyImPyI-IpPy 1148) 5' -WT A G C A W-3' HpPyImPyPy-y-HpImPyHpPy 1149) 5' -WT A G G G W-3' HpPyImImIm-y-PyPyPyHpPy 1150) 5' -WT A G G C W-3' HpPyImImPy-y-ImPyPyHpPy 1151) 5' -WT A G C G W-3' HpPyImPyIm-y-PyImPyHpPy 1152) 5' -WT A G C C W-3' HpPyImPyPy-y-ImImPyHpPy 1153) 5' -WT A C T T W-3' HpPyPyHpHp-y-PyPyImHppy 1154) 5' -WT A C T A W-3' HpPyPyHpPy-y-HpPyImHpPy 1155) 5' -WT A C T G W-3' HpPyPyHpIm-y-PyPyImHpPy 1156 ) 5' -WT A C T C W-3 HppyPyHpPy-y-ImPyImHpPy ' 1157) 5' -WT A C A T W-3' HpPyPyPyHp-y-PyHpImHpPy 1158) 5' -WT A C A A W-3' HpPyPyPyPy-y-HpHpImHpPy 1159) 5' -WT A C A G W-3' HpPyPyPyIm-y-PyHpImHpPy 1160) 5' -WT A C A C W-3' HpPyPyPyPy-y-ImHpImHpPy 1161) 5' -WT A C G T W-3' HppyPyImHp-y-PyPyImHpPy 1162) 5' -WT A C G A W-3' HpPyPyImPy-y-HpPyImHpPy 1163) 5' -WT A C C T W-3' HpPyPyPyHp-y-PyImImHpPy 1164 ) 5' -WT A C C A W-3 HpPyPyPyPy-y-HpImImHpPy ' 1165) 5' -WT A C G G W-3' HpPyPyImIm-y-PyPyImHpPy 1166 ) 5' -WT A C G C W-3 HpPyPyImPy-y-ImPyImHpPy ' 1167) 5' -WT A C C G W-3' HpPyPyPyIm-y-PyImImHpPy 1168) 5' -WT A C C C W-3' HpPyPyPyPy-y-ImImImHpPy l Al3LH
50:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCWNNW-3' DNA aromatic amino acid sequence sequence 1169) 5'-W T C TT T W-3' HpPyHpHpHp-y-PypypylmPy 1170) ~5'-W T C TT A W-3' HpPyHpHpPy-y-HpPyPyImPy 1171) 5'-W T C TT G W-3' HpPyHpHpIm-y-Pypypylmpy 1172) 5'-W T C TT C W-3' HpPyHpHpPy-y-ImPyPyImPy 1173) 5'-W T C TA T W-3' HPPYHPPYHP-Y-PYHPPYImPy 1174) 5'-W T C TA A W-3' HpPyHpPyPy-y-HpHpPyImPy 1175) 5'-W T C TA G W-3' HpPyHpPyIm-y-PyHpPyImPy 1176) 5'-W T C TA C W-3' HpPyHpPypy-y-ImHppyImPy 1177) 5'-W T C TG T W-3' HppyHpl~p_Y-pypypylmPy 1178) 5'-W T C TG A W-3' HpPyHpImPy-y-HpPyPyImPy 1179) 5'-W T C TG G W-3' HpPyHpImIm-y-PyPyPyImPy 1180) 5'-W T C TG C W-3' HpPyHpImPy-y-ImPyPyImPy 1181) 5'-W T C TC T W-3' HpPyHpPyHp-y-PyImPyImPy 1182) 5'-W T C TC A W-3' HpPyHpPypy-y-HpImPyImPy 1183) 5'-W T C TC G W-3' HpPyHpPyIm-y-PyImPyImPy 1184) 5'-W T C TC C W-3' HpPyHpPyPy-y-ImImPyImPy 1185) 5'-W T C AT T W-3' HpPyPyHpHp-y-PyPyHpImPy 1186) 5'-W T C AT A W-3' HpPyPyHpPy-y-HpPyHpImPy 1187) 5'-W T C AT G W-3' HpPyPyHpIm-y-PyPyHpImPy 1188) 5'-W T C AT C W-3' HpPyPyHpPy-y-ImPyHpImPy 1189) 5'-W T C AA T W-3' HpPyPyPyHp-y-PyHpHpImPy 1190) 5'-W T C AA A W-3' HpPyPyPyPy-y-HpHpHpImPy 1191) 5'-W T C AA G W-3' ~ HpPyPyPyIm-y-PyHpHpImPy 1192) 5'-W T C AA C W-3' HpPyPyPyPy-y-ImHpHpImPy 1193) 5'-W T C AG T W-3' HpPyPyImHp-y-PyPyHpImPy 1194) 5'-W T C AG A W-3' HpPyPyImPy-y-HpPyHpImPy 1195) 5'-W T C AG G W-3' HpPyPyImIm-y-PyPyHpImPy 1196) 5'-W T C AG C W-3' HpPyPyImPy-y-ImPyHpImPy 1197) 5'-W T C AC T W-3' HpPyPyPyHp-y-PyImHpImPy 1198) 5'-W T C AC A W-3' HpPyPyPyPy-y-HpImHpImPy 1199) 5'-W T C AC G W-3' HpPyPyPyIm-y-PyImHpImPy 1200) 5'-W T C AC C W-3' HpPyPyPyPy-y-ImImHpImPy WO 98/37067 PCTlUS98/01714 TABLE
51:
l0~ring Hairpin Polyamides for recognition of 7-by 5'-WTCSNNW-3' DNA aromatic amino acid sequence sequence 1201) 5' -W T CG T T W-3' HpPyImHpHp-y-PyPyPyImPy 1202) ~5'-W T CG T A W-3' HpPyImHpPy-y-HpPyPyImPy 1203) 5' -W T CG T G W-3' HpPyImHpIm-y-PyPyPyImPy 1204) 5' -W T CG T C W-3' HpPyImHpPy-y-ImPyPyImPy 1205) 5' -W T CG A T W-3' HpPyImPyHp-y-PyHpPyImPy 1206) 5' -W T CG A A W-3' HpPyImPyPy-y-HpHpPyImPy 1207) 5' -W T CG A G W-3' HpPyImPyIm-y-PyHpPyImPy 1208) 5' -W T CG A C W-3' HpPyImPyPy-y-ImHpPyImPy 1209) 5' -W T CG G T W-3' HpPyImImHp-y-PyPyPyImPy 1210) 5' -W T CG G A W-3' HpPyImImPy-y-HpPyPyImPy 1211) 5' -W T CG C T W-3' HpPyImPyHp-y-PyImPyImPy 1212) 5' -W T CG C A W-3' HpPyImPyPy-y-HpImPyImPy 1213) 5' -W T CC T T W-3' HpPyPyHpHp-y-PyPyImImPy 1214) 5' -W T CC T A W-3' HpPyPyHpPy-y-HpPyImImPy 1215) 5' -W T CC T G W-3' HpPyPyHpIm-y-PyPyImImPy 1216 5' -W T CC T C W-3 ' HpPyPyHpPy-y- ImPyImImPy ) 1217 5' -W T CC A T W-3 ' HpPyPyPyHp-y-PyHpImImPy ) 1218) 5' -W T CC A A W-3' HpPyPyPyPy-y-HpHpImImPy 1219) 5' -W T CC A G W-3' HpPyPyPyIm-y-PyHpImImPy 1220) 5' -W T CC A C W-3' HpPyPyPyPy-y-ImHpImImPy 1221) 5' -W T CC G T W-3' HpPyPyImHp-y-PyPyImImPy 1222 5' -W T CC G A W-3' HpPyPyImPy-y-HpPyImImPy ) 1223 5' -W T CC C T W-3 ' HpPyPyPyHp-y-PyImImImPy ) 1224) 5' -W T CC C A W-3' HpPyPyPyPy-y-HpImImImPy 1225) 5' -W T CG G G W-3' HpPyImImIm-y-PyPyPyImPy 1226) 5' -W T CG G C W-3' HpPyImImPy-y-ImPyPyImPy 1227) 5' -W T CG C G W-3' HpPyImPyIm-y-PyImPyImPy 1228) 5' -W T CG C C W-3' HpPyImPyPy-y-ImImPyImPy 1229) 5' -W T CC G G W-3' HpPyPyImIm-y-PyPyImImPy 1230) 5' -W T CC G C W-3' HpPyPyImPy-y-ImPyImImPy 1231) 5' -W T CC C G W-3' HpPyPyPyIm-y-PyImImImPy 1232 5' -W T CC C C W-3 ' HpPyPyPyPy-y-ImImImImPy ) _77_ TABLE 52 :
10-ring Hairpin Yolyamides for recognition of 7-by 5'-WGGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 243(3) 5' G G T TG W-3' ImIm-~-HpIm-y-PYpypypypY
-W
243~3p) '5' G G T TG W-3' ImIm-[3-HpIm-y-PYPy-~3-pypy -W
247(3) 5' G G T AG W-3' Imlm-J3-PyIm-y-PyHpPyPyPy -W
247~p) 5' G G T AG W-3' ImIm-~-PyIm-y-PYHp-(3-PyPy -W
249(3) 5' G G T GT W-3' ImIm-(3-ImHp-y-Pypypypypy -W
249(3p) 5' G G T GT W-3' ImIm-~3-ImHp-y-Pypy-~3-pypY
-W
2503) 5' G G T GA W-3' ImIm-~i-ImPy-y-HpPyPyPyPy -W
250(3p) 5' G G T GA W-3' ImIm-(3-ImPy-y-HpPy-~i-PypY
-W
2513) 5' G G T GG W-3' ImIm-(3-ImIm-y-pypypypypy -W
251(3p) 5' G G T GG W-3' Imlm-(3-Imlm-y-PyPy-(3-PyPy -W
252(3) 5' G G T GC W-3' Imlm-/3-ImPy-y-ImPyPyPyPy -W
252(3p) 5' G G T GC W-3' Imam-(3-ImPy-y-ImPy-(3-Pypy -W
255(3) 5' G G T CG W-3' ImIm-~-Pylm-y-pyImPyPyPy -W
255~ip) 5' G G T CG W-3' ImIm-(3-PYIm-y-PyIm-a-PyPy -W
2593) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPyHpPyPy -W
259~3p) 5' G G A TG W-3' ImIm-(3-HpIm-y-PyPy-(3-PyPy -W
263(3) 5' G G A AG W-3' ImIm-p-PyIm-y-PyHpHpPyPy -W
263(3p) 5' G G A AG W-3' ImIm-(3-PyIm-y-PyHp-~3-PyPy -W
2653) 5' G G A GT W-3' ImIm-(3-ImHp-y-PypyHppypy -W
265(3p) 5' G G A GT W-3' Imlm-(3-ImHp-y-PyPy-p-PyPy -W
266(3) 5' G G A GA W-3' ImIm-(3-ImPy-y-HpPyHpPyPy -W
266~3p) 5' G G A GA W-3' Imlm-~3-ImPy-y-HpPy-(3-PyPy -W
267(3) 5' G G A GG W-3' ImIm-(3-ImIm-y-PyPyHpPyPy -W
267(3p) 5' G G A GG W-3' ImIm-/3-ImIm-y-Pypy-~-pypy -W
2683) 5' G G A GC W-3' Imlm-~3-ImPy-y-ImpyHpPyPy -W
268~3p) 5' G G A GC W-3' ImIm-(3-ImPy-y-ImPy-~3-PyPy -W
271(3) 5' G G A CG W-3' ImIm-~3-PyIm-y-PyImHpPyPy -W
271(3p) 5' G G A CG W-3' Imlm-(3-PyIm-y-PyIm-j3-PyPy -W
WO 98I370b7 PCT/US98/01714 _78_ TABLE
53: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 273(3) 5' G G G TT W-3' ImImIm-p-Hp-y-PyPyPyPyPy -W
273~3p) ~ G G G TT W-3' ImImIm-(3-Hp-y-Py-(3-PyPyPy 5' -W
274(3) 5' G G G TA W-3' ImImIm-(3-Py-y-HpPyPyPyPy -W
274~3p) 5' G G G TA W-3' ImImIm-~3-Py-y-Hp-(3-PyPyPy -W
275(3) 5' G G G TG W-3' ImImIm-~3-Im-y-PyPyPyPyPy -W
275~3p) 5' G G G TG W-3' ImImIm-~3-Im-y-Py-(3-PyPyPy -W
276(3) 5' G G G TC W-3' ImImIm-(3-Py-y-ImPyPyPyPy -W
276(3p) 5' G G G TC W-3' ImImIm-(3-Py-y-Im-(3-PyPyPy -W
277(3) 5'-W G G G AT W-3' ImImIm-(3-Hp-y-PyHpPyPyPy 277~3p) 5' G G G AT W-3' ImImIm-(3-Hp-y-Py-~3-PyPyPy -W
2783) 5' G G G AA W-3' ImImIm-(3-Py-y-HpHpPyPyPy -W
278(3p) 5' G G G AA W-3' ImImIm-~-Py-y-Hp-/3-PyPyPy -W
279(3) 5' G G G AG W-3' ImImIm-(3-Im-y-PyHpPyPyPy -W
279~3p) 5' G G G AG W-3' ImImIm-~-Im-y-Py-[3-PyPyPy -W
280(3) 5' G G G AC W-3' ImImIm-(3-Py-y-ImHpPyPyPy -W
280(3p) 5' G G G AC W-3' ImImIm-(3-Py-y-Im-~3-PyPyPy -W
283(3) 5' G G G CT W-3' ImImIm-p-Hp-y-PyImPyPyPy -W
284(3) 5' G G G CA W-3' ImImIm-(3-Py-y-HpImPyPyPy -W
285(3) 5' G G C TT W-3' ImImPylipHp-y-Py-p-ImPyPy -W
285(3p) 5' G G C TT W-3' ImImPy-(3-Hp-y-Py-(3-ImPyPy -W
286(3) 5' G G C TA W-3' ImImPyHpPy-y-Hp-~i-ImPyPy -W
286~3p) 5' G G C TA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy -W
287~i) 5' G G C TG W-3' ImIm-~3-HpIm-y-Py-(3-ImPyPy -W
288(3) 5' G G C TC W-3' ImImPyHpPy-y-Im-(3-ImPyPy -W
288~ip) 5' G G C TC W-3' ImImPy-(3-Py-y-Im-(3-ImPyPy -W
289(3) 5' G G C AT W-3' ImImPyPyHp-y-Py-p-ImPyPy -W
289(3p) 5' G G C AT W-3' ImImPy-/3-Hp-y-Py-(3-ImPyPy -W
290(3) 5' G G C AA W-3' ImImPyPyPy-y-Hp-~-ImPyPy -W
290~ip) 5' G G C AA W-3' ImImPy-(3-Py-y-Hp-(3-ImPyPy -W
_79_ TABLE 53 (cont.): ecogmrion of 7-by 5'-WGGSNNW-3' 10-ring Hairpin with ~3 substitutions Polyamides for r .
DNA aromatic amino acid sequence sequence 291(3) 5'-W GG C A G W-3' ImIm-(3-PyIm-y-py-(3-ImPyPy 292(3) 5' GG C A C W-3' TmImPyPyPy-y-Im-(3-ImPyPy -W
292(3p) ~ GG C A C W-3' ImImPy-(3-Py-y-Im-~i-ImPyPy 5' -W
293(3) 5' GG C G T W-3' Imam-(3-ImHp-y-Py-(3-ImPyPy -W
294(3) 5' GG C G A W-3' ImIm-(3-ImPy-y-Hp-(3-ImPyPy -W
295x) 5'-W GG C C T W-3' ImImPyPyHp-y-pylmlm-(3-Py 2963) 5' GG C C A W-3' ImImPyPypy-y-HpImIm-p-Py -W
619(3) 5' GG G C G W-3' ImImIm-(3-Im-y-PyImPyPyPy -W
G20(3) 5' GG G C C W-3' ImImIm-(3-Py-y-ImImPypyPy -W
G21(3) 5' GG C G G W-3' Imlm-/3-Imlm-y-Py-(3-ImPyPy -W
G22(3) 5' GG C G C W-3' ImIm-(3-Impy-y-Im-~3-ImPyPy -W
G23~3) 5' GG C C G W-3' Imlm-(3-Pylm-y-PyImIm-(3-Py -W
G24(3) 5' GG C C C W-3' ImImPyPyPy-y-ImImIm-(3-Py -W
TABLE :
54 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 299(3) 5' G T T T G W-3' ImHp-(3-HpIm-y-PyPyPyPyPy -W
299~3p) 5' G T T T G W-3' ImHp-J3-HpIm-y-PyPy-(3-PyPy -W
303(3) ' G T T A G W-3' ImHp-(3-PyIm-y-PyHpPyPyPy 5' -W
303~3p) 5' G T T A G W-3' ImHp-(3-PyIm-y-PyHp-(3-PyPy -W
305(3) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPyPyPyPy -W
305(3p) 5' G T T G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy -W
306(3) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPyPyPyPy -W
306(3p) 5' G T T G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy -W
3073) 5' G T T G G W-3' ImHp-(3-ImIm-y-PyPyPyPyPy -W
307~p) 5' G T T G G W-3' ImHp-J3-ImIm-y-PyPy-~3-PyPy -W
3083) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPyPyPyPy -W
308~3p) 5' G T T G C W-3' ImHp-(3-ImPy-y-ImPy-p-PyPy -W
3113) 5' G T T C G W-3' ImHp-~3-PyIm-y-PyImPyPyPy -W
311(3p) 5' G T T C G W-3' ImHp-(3-Pylm-y-Pylm-~i-PyPy -W
3153) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPyHpPyPy -W
315(3p) 5' G T A T G W-3' ImHp-p-HpIm-y-PyPy-(3-PyPy -W
3193) 5' G T A A G W-3' ImHp-(3-Pylm-y-PyHpHpPyPy -W
319(3p) 5' G T A A G W-3' ImHp-~3-PyIm-y-PyHp-(3-PyPy -W
321~i) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPyApPyPy -W
321(3p) 5' G T A G T W-3' ImHp-(3-ImHp-y-PyPy-(3-PyPy -W
322(3) 5' G T A G A W-3' ImHp-~i-ImPy-y-HpPyHpPyPy -W
322(3p) 5' G T A G A W-3' ImHp-~3-ImPy-y-HpPy-(3-PyPy -W
323(3) 5' G T A G G W-3' ImHp-~3-Imlm-y-PyPyHpPyPy -W
323(3p) 5' G T A G G W-3' ImHp-~3-ImIm-y-PyPy-(3-PyPy -W
324(3) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPyHpPyPy -W
324~p) 5' G T A G C W-3' ImHp-(3-ImPy-y-ImPy--PyPy -W
327(3) 5' G T A C G W-3' ImHp-(3-PyIm-y-PyImHpPyPy -W
327(3p) 5' G T A C G W-3' ImHp-(3-PyIm-y-Pylm-(3-PyPy -W
'TABLE
55: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGTSNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 3293) 5' G T G T T W-3' Im-(3-ImHpHp-y-PyPyPYPYPy -W
329(3P) '5'-WG T G T T W-3' Im-(3-ImHpHp-y-Pypypy-p-py 3303) 5' G T G T A W-3' Im-J3-ImHpPy-y-Hppypypypy -W
330(3p 5' G T G T A W-3' Im-(3-ImHpPy-Y-HpPYPy-~3-py -W
3313) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPyPYPyPy -W
331(3p) 5' G T G T G W-3' Im-(3-ImHpIm-y-PyPYPy-~3-Py -W
332J3) 5' G T G T C W-3' Im-a-ImHpPy-y-ImPyPyPYPy -W
332(3p) 5' G T G T C W-3' Im-~-ImHpPy-y-ImPYPy-/3-Py -W
333(3) 5' G T G A T W-3' Im-(3-ImPyHp-Y-PYHpPyPyPy -W
333~ip) 5' G T G A T W-3' Im-~3-ImPYHp-y-PyHpPy-(3-Py -W
334(3) 5' G T G A A W-3' Im-~3-ImPyPy-y-HpHpPYPYPy -W
334(3p) 5' G T G A A W-3' Im-(3-ImPyPy-y-HpHpPy-p-Py -W
335~i) 5' G T G A G W-3' Im-(3-ImPyIm-y-PyHpPYPYPy -W
335pp) 5' G T G A G W-3' Im-p-ImPyIm-Y-PyHpPy-(3-Py -W
3363) 5' G T G A C W-3' Im-p-ImPyPy-y-ImHpPYPYPy -W
336(3p) 5' G T G A C W-3' Im-(3-ImPyPy-y-ImHppy-p-Py -W
337(3) 5' G T G G T W-3' Im-(3-ImImHp-y-PyPypypypy -W
337(3p) 5' G T G G T W-3' Im-~3-ImImHp-y-PYPyPy-(3-Py -W
338(3) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPYPYPYPy -W
338~3p) 5' G T G G A W-3' Im-(3-ImImPy-y-HpPyPy-(3-Py -W
339(3) 5' G T G C T W-3' Im-~-ImPyHp-y-PYImPyPyPy -W
339~p) 5' G T G C T W-3' Im-~3-ImPYHp-y-PyImPy-p-Py -W
3403) 5' G T G C A W-3' ~ Im-p-ImPyPy-y-HpImPyPyPy -W
340(3p) 5' G T G C A W-3' Im-p-ImPyPy-Y-HpImPy-~3-Py -W
3413) 5' G T G G G W-3' Im-p-ImImIm-y-PyPyPyPyPy -W
341(3p) 5' G T G G G W-3' Im-~3-ImImIm-y-PypyPy-(3-PY
-W
342(3) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPYPyPy -W
342(3p) 5' G T G G C W-3' Im-(3-ImImPy-y-ImPyPy-(3-Py -W
343(3) 5' G T G C G W-3' Im-(3-ImPyIm-y-PyImPyPypy -W
TABLE 55 Polyamides (cont.): for 10-ring recognition Hairpin of 7-by 5'-WGTS1VNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 343(3p) 5' G T GC G W-3' Im-(3-ImPyIm-y-PyImPy-(3-Py -W
344(3) 5' G T GC C W-3' Im-(3-ImPyPy-y-ImImPyPyPy -W
344(3p) '5' G T GC C W-3' Im-p-ImPyPy-y-ImImPy-(3-Py -W
345(3) 5' G T CT T W-3' ImHpPyI~IpHp-y-Py-~3-ImPyPy -W
345~3p) 5' G T CT T W-3' ImHpPy-~3-Hp-y-Py-(3-ImPyPy -W
346(3) 5' G T CT A W-3' ImHpPyHpPy-y-Hp-(3-ImPyPy -W
346(3p) 5' G T CT A W-3' ImHpPy-~3-Py-y-Hp-(3-ImPyPy -W
3473} 5' G T CT G W-3' ImHp-(3-HpIm-y-Py-p-ImPyPy -W
3483) 5' G T CT C W-3' ImHpPyHpPy-y-Im-(3-ImPyPy -W
348(3p) 5' G T CT C W-3' ImHpPy-(3-Py-y-Im-~3-ImPyPy -W
349(3) 5' G T CA T W-3' ImHpPypyHp-y-Py-~-ImPyPy -W
349(3p) 5' G T CA T W-3 T ImHpPyPyHp-y-Py--ImPyPy -W
350(3) 5' G T CA A W-3' ImHpPyPyPy-y-Hp-~3-ImPyPy -W
350~3p) 5' G T CA A W-3' ImHpPy-(3-Py-y-Hp-~i-ImPyPy -W
351(3} 5' G T CA G W-3' ImHp-~3-PyIm-y-Py-(3-ImPyPy -W
3523) 5' G T CA C W-3' ImHpPyPyPy-y-Im-~3-ImPyPy -W
352(3p) 5' G T CA C W-3' ImHpPy-(3-Py-y-Im-(3-ImPypy -W
3533) 5' G T CG T W-3' ImHp-(3-ImHp-y-Py-(3-ImPyPy -W
354(3) 5' G T CG A W-3' ImHp-~-Impy-y-Hp--ImPypy -W
3553) 5' G T CC T W-3' ImHpPypyHp-y-PyImIm-(3-Py -W
355~3p) 5' G T CC T W-3' Im-(3-PyPyHp-y-PyImIm-[3-Py -W
3563) 5' G T CC A W-3' ImHppyPyPy-y-HpImIm-p-Py -W
356~3p) 5' G T CC A W-3' Im-~3-PyPyPy-y-HpImIm-(3-Py -W
357(3) 5' G T CG G W-3' ImHp-(3-ImIm-y-Py-p-ImPyPy -W
358(3) 5' G T CG C W-3' ImHp-(i-ImPy-y-Im-(3-ImPyPy -W
359(3) 5' G T CC G W-3' ImHp-/3-Pylm-y-PyImIm-(i-Py -W
360(3) 5' G T CC C W-3' ImHpPyPyPy-y-ImImIm-~3-Py -W
360~ip) 5' G T CC C W-3' Im-p-PyPyPy-y-ImImIm-p-Py -W
_g3_ TABLE 56: l0-ring Hairpin Polyamides for recognition of 7-by 5'-WGAWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 363(3) 5' G A T T G W-3' ImPy-~-HpIm-y-Pypypygppy -W
363~3p) 5' G A T T G W-3' ImPy-(3-HpIm-y-Pypy-(3-Hppy -W
3673) ' G A T A G W-3' ImPy-(3-PyIm-y-pyHpPYHpPy S' -W
367pp) 5' G A T A G W-3' ImPy-p-PyIm-y-PYHp-(3-HpPy -W
369(3) 5' G A T G T W-3' ImPy-~3-ImHp-y-PyPYPYHpPy -W
369(3p) 5' G A T G T W-3' ImPy-~3-ImHp-y-pypy-(3-HpPy -W
370(3) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPYPYHpPy -W
370~p) 5' G A T G A W-3' ImPy-(3-ImPy-y-HpPy-~3-HpPy -W
371~i) 5' G A T G G W-3' ImPy-p-ImIm-y-PyPypyHpPy -W
371(3p) 5' G A T G G W-3' ImPy-(3-ImIm-y-Pypy-~-HpPy -W
372(3) 5' G A T G C W-3' -W ImPy- (3 - ImPy-y- ImPYPyHpPy 372(3p) 5' G A T G C W-3' ImPy-p-ImPy-y-ImPy-~3-HpPy -W
375(3) 5' G A T C G W-3' ImPy-(3-Pylm-y-PyImPYHpPy -W
375~3p) 5' G A T C G W-3' ImPy-(3-PyIm-y-pylm-(3-HpPy -W
379(3) 5' G A A T G W-3' ImPy-~-HpIm-y-PYPYHpHpPy -W
379(3p) 5' G A A T G W-3' ImPy-p-HpIm-y-PyPy-(3-HpPy -W
383(3) 5' G A A A G W-3' ImPy-~3-PyIm-y-PYHpHpHpPy -W
383(3p) 5' G A A A G W-3' ImPy-~3-PYIm-y-pyHp-(3-HpPy -W
385(3) 5' G A A G T W-3' ImPy-~3-ImHp-y-PyPYHpHpPy -W
385(3p) 5' G A A G T W-3' ImPy-(3-ImHp-y-Pypy-~3-HppY
-W
386(3) 5' G A A G A W-3' -W ImPy-(3-ImPy-y-HpPyHpHpPy 386(3p) 5' G A A G A W-3' ImPy-~3-ImPy-y-HpPy-(3-HpPy -W
387(3) 5' G A A G G W-3' ImPy-(3-Imlm-y-PyPYHpHpPy -W
387(3p) 5'-WG A A G G W-3' ImPy-(3-ImIm-y-PyPy-(3-HpPy 3883) 5' G A A G C W-3' ImP
-W y-~3-ImPy-y-ImPyHpHpPy 388(3p) 5' G A A G C W-3' ImPy-~3-ImPy-y-ImPy-/3-HpPy -W
391~i) 5'-WG A A C G W-3' ImPy-~-PyIm-y-PyImHpHpPy 391(3p) 5' G A A C G W-3' ImPy-(3-Pylm-y-PyIm-~-HpPy -W
TABLE
57: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 393) 5' G A G TT W-3' Im--ImHpHp-y-PyPyPyHpPy -W
394(3p) 5'-W G A G TA W-3' Im--ImHpPy-y-Hppypy--py 395(3) ~ G A G TG W-3' Im--ImHpIm-y-PyPyPyHpPy 5' -W
395~3p) 5'-W G A G TG W-3' Im--ImHpIm-y-PyPyPy--Py 396) 5'-W G A G TC W-3' Im--ImHpPy-y-ImPyPyHpPy 396p) 5' G A G TC W-3' Im--ImHpPy-y-ImPyPy--Py -W
397) 5' G A G AT W-3' Im--ImPyHp-y-PyHpPyHpPy -W
397~p) 5' G A G AT W-3' Im-~i-ImpyHp-y-PyHpPy--Py -W
398) 5' G A G AA W-3' Im--ImPyPy-y-HpHpPyHpPy -W
398p) 5'-W G A G AA W-3' Im--ImPyPy-y-HpHpPy--Py 399(3) 5' G A G AG W-3' Im--ImPyIm-y-PyI-ippyHpPy -W
399~3p) 5' G A G AG W-3' Im-(3-ImPyIm-y-PyHpPy--Py -W
400(3) 5' G A G AC W-3' Im--ImpyPy-y-ImHpPyHpPy -W
400(3p) 5'-W G A G AC W-3' Im-~-ImpyPy-y-ImHppy-p-Py 401(3) 5' G A G GT W-3' Im--ImImHp-y-PypyPyHpPy -W
401p) 5'-W G A G GT W-3' Im--ImImHp-y-PyPypy--py 402) 5' G A G GA W-3' Im--ImImPy-y-HppyPyHpPy -W
402p) 5'-W G A G GA W-3' Im--ImImPy-y-HpPyPy--Py 403 ) 5'-W G A G CT W-3' Im--ImPyHp-y-PyImPyHpPy 403(3p) 5' G A G CT W-3' Im--ImPyHp-y-PyImPy--Py -W
404) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPyHpPy 404~3p) 5'-W G A G CA W-3' Im--ImPyPy-y-HpImPy--Py 405(3) 5' G A G GG W-3' Im--ImImIm-y-PyPyPyHpPy -W
405p) 5'-W G A G GG W-3' 'Im--ImImIm-y-PyPyPy--Py 406(3) 5' G A G GC W-3' Im-(3-ImImPy-y-ImPyPyHpPy -W
406~ip) 5' G A G GC W-3' Im--ImImPy-y-ImPyPy--Py -W
407(3) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPyHpPy 407(3p) 5'-W G A G CG W-3' Im--ImPyIm-y-PyImPy--Py 408) 5' G A G CC W-3' Im-(3-ImPyPy-y-ImImPyHpPy -W
408(3p) 5' G A G CC W-3' Im--ImPyPy-y-ImImPy-(3-Py -W
1 AliLlr S / (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGASNNW-3' with (3 substitutions.
D NA aromatic amino acid sequence sequence 4093) 5'-W G AC T T W-3' ImPyPyHpHp-y-py-(3-I~pPy 409(3p) 5' G AC T T W-3' ImPyPy-~3-Hp-y-Py-(3-ImHpPy -W
4103) 'S' G AC T A W-3' ImPyPyHpPy-y-Hp-(3-ImHpPy -W
410(3p) 5' G AC T A W-3' ImPyPy-(3-Py-y-Hp-(3-ImHpPy -W
411(3) 5' G AC T G W-3' ImPy-~i-HpIm-y-Py-(3-ImHpPy -W
412(3) 5'-W G AC T C W-3' ImPYPyHpPy-y-Im-(3-ImHpPy 412pp) 5'-W G AC T C W-3' ImPYPy-~-py-y-Im-~-ImHpPy 413(3) 5' G AC A T W-3' ImPYPyPyHp-y-py-(3-I~ppy -W
413~3p) 5' G AC A T W-3' ImPyPy-~3-Hp-y-Py-(~_ImHppy -W
414(3) 5' G AC A A W-3' Impypypypy_y-Hp-~-I~ppy -W
414(3p) 5' G AC A A W-3' ImPyPy-(3-Py-y-Hp-(3-I~ppY
-W
415(3) 5' G AC A G W-3' ImPy-~3-Pylm-y-Py-(3-ImHpPy -W
416(3) 5' G AC A C W-3' ImPypypypy-y-Im-/3-ImHpPy -W
416(3p) 5' G AC A C W-3' ImPyPy-(3-Py-y-Im-(3-ImHpPy -W
417(3) 5' G AC G T W-3' ImPy-(3-ImHp-y-Py-(3-ImHpPy -W
4183) 5' G AC G A W-3' ImPy-~3-ImPy-y-Hp-~3-ImHppy -W
419(3) 5' G AC C T W-3' Im-~-PyPyHp-y-PyImIm-(3-Py -W
419(3p) 5' G AC C T W-3' ImPYPYPyHp-y-PyImIm-(3-Py -W
4200 5' G AC C A W-3' Im-p-Pypypy-y-HpImIm-(3-Py -W
420(3p) 5' G AC C A W-3' ImPYPyPypy-y-HpImIm-~3-Py -W
421(3) 5' G AC G G W-3' ImPy-~3-Imlm-y-Py-~3-ImHpPy -W
422(3) 5' G AC G C W-3' ImPy-y-ImPy-y-Im-(3-ImHpPy -W
423(3) 5' G AC C G W-3' ImPy-(3-Pylm-y-PyImIm-~3-Py -W
424(3) 5' G AC C C W-3' ImPyPyPyPy-y-ImImIm-(3-Py -W
424(3p) 5' G AC C C W-3' Im-(3-PyPyPy-y-ImImIm-~i-Py -W
TABLE 58:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 425(3) 5' G CT T T W-3' ImPyHpHpHp-y-PyPy-(3-ImPy -W
425(3p) ' G CT T T W-3' ImPy-~3-HpHp-y-PyPy-(3-ImPy 5' -W
426x) 5' G CT T A W-3' ImPyHpHpPy-y-HpPy-(3-ImPy -W
426(3p) 5' G CT T A W-3' ImPy-J3-HpPy-y-HpPy-(3-ImPy -W
427(3) 5' G CT T G W-3' ImPy-~3-Hp lm-y-PyPy-(3-Impy -W
428(3) 5' G CT T C W-3' ImPyHpHpPy-y-ImPy-~3-ImPy -W
428(3p) 5' G CT T C W-3' Impy-(3-HpPy-y-ImPy-(3-Impy -W
429(3) 5' G CT A T W-3' ImPyHpPyHp-y-PyHp-(3-ImPy -W
429(3p) 5' G CT A T W-3' ImPy-(3-PyHp-y-PyHp-(3-ImPy -W
4303) 5' G CT A A W-3' ImPyHpPyPy-y-HpHp-(3-ImPy -W
430(3p) 5' G CT A A W-3' ImPy-(3-PyPy-y-HpHp-(3-ImPy -W
431(3) 5' G CT A G W-3' ImPy-~i-Pylm-y-PyHp-(3-ImPy -W
432(3) 5' G CT A C W-3' ImPyHpPyPy-y-ImHp-~i-ImPy -W
432(3p) 5' G CT A C W-3' ImPy-(3-PyPy-y-ImHp-(3-ImPy -W
433(3) 5' G CT G T W-3' ImPy-(3-ImHp-y-Pypy-(3-ImPy -W
434(3) 5' G CT G A W-3' ImPy-(3-ImPy-y-HpPy-a-ImPy -W
435~i) 5' G CT G G W-3' ImPy-(3-ImIm-y-PyPy-~i-ImPy -W
436(3) 5' G CT G C W-3' ImPy-(3-ImPy-y-ImPy-(3-ImPy -W
437(3) 5' G CT C T W-3' ImPyHpPyHp-y-Pylm-(3-ImPy -W
437(3p) 5' G CT C T W-3' ImPy-(3-PyHp-y-PyIm-(3-ImPy -W
438~i) 5' G CT C A W-3' ImPylipPyPy-y-Hplm-(3-ImPy -W
438(3p) 5' G CT C A W-3' ImPy-(3-PyPy-y-Hplm-~i-ImPy -W
439(3) 5'-W G CT C G W-3' Impy-(3-PyIm-y-PyIm-~i-ImPy 4403) 5' G CT C C W-3' ImPyHpPyPy-y-ImIm-ji-ImPy -W
440(3p) 5' G CT C C W-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy -W
441(3) 5' G CA T T W-3' ImPyPyHpHp-y-PyPy-~i-ImPy -W
441~p) 5' G CA T T W-3' ImPy-(3-HpHp-y-PyPy-/3-ImPy -W
442(3} 5' G CA T A W-3' ImPyPyHpPy-y-HpPy-~3-ImPy -W
442(3p) 5' G CA T A W-3' ImPy-~3-HpPy-y-HpPy-(3-ImPy -W
443(3) 5' G CA T G W-3' ImPy-(3-Hplm-y-PyPy-(3-ImPy -W
-87_ TABLE 58 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 444(3) 5' G C A T CW-3' ImPyPyHpPy-y-ImPy-~3-ImPy -W
444~3p) 5' G C A T CW-3' ImPy-(3-HpPy-y-ImPy-(3-Impy -W
445(3) ' G C A A TW-3' ImPyPyPyHp-y-PyHp-(3-ImPy 5' -W
445(3p) 5' G C A A TW-3' ImPy-(3-PyHp-y-PyHp-R-ImPy -W
446(3) 5' G C A A AW-3' ImPyPyPyPy-y-HpHp-(3-ImPy -W
446~3p) 5' G C A A AW-3' ImPy-(3-pypy-y-HpHp-a-ImPy -W
447(3) 5' G C A A GW-3' ImPy-(3-Pylm-y-PyHp-(3-ImPy -W
4483) 5' G C A A CW-3' ImPyPypypy-y-ImHp-(3-ImPy -W
448(3p) 5'-W G C A A CW-3' ImPy-(3-PyPy-y-ImHp-~i-ImPy 449(3) 5'-W G C A G TW-3' ImPy-~3-ImHp-y-PyPy-(3-ImPy 450(3) 5' G C A G AW-3' ImPy-~-ImPy-y-Hppy-(3-Impy -W
4513) 5' G C A G GW-3' ImPy-(3-ImIm-y-PyPy-(3-ImPy -W
4523) 5' G C A G CW-3' ImPy-J3-ImPy-y-ImPy-~i-ImPy -W
4533) 5' G C A C TW-3' ImPyPyPyHp-y-Pylm-(3-ImPy -W
453~3p) 5' G C A C TW-3' ImPy-(3-PyHp-y-Pylm-p-ImPy -W
4540 5' G C A C AW-3' ImPyPyPyPy-y-HpIm-~3-ImPy -W
454(3p) 5' G C A C AW-3' ImPy-~3-PyPy-y-Hplm-(3-ImPy -W
455(3) 5' G C A C GW-3' ImPy-(3-PyIm-y-PyIm-(3-ImPy -W
4563) 5' G C A C CW-3' ImpyPyPypy-y-Imam-(3-ImPy -W
456(3p) 5' G C A C CW-3' ImPy-(3-PyPy-y-Imlm-(3-ImPy -W
_88_ TABLE 59:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 457) 5' G C GT T W-3' Im--ImHpHp-y-PyPy--ImPy -W
458(3) ~ G C GT A W-3' Im--ImHpPy-y-HpPy--ImPy 5' -W
4593) 5' G C GT G W-3' Im--ImHpIm-y-PyPy--ImPy -W
460(3) 5' G C GT C W-3' Im--ImHpPy-y-ImPy--ImPy -W
461) 5' G C GA T W-3' Im--ImPyHp-y-PyHp--ImPy -W
462(3) 5' G C GA A W-3' Im--ImPyPy-y-HpHp--ImPy -W
463) 5' G C GA G W-3' Im--ImPyIm-y-PyHp--ImPy -W
4643) 5' G C GA C W-3' Im--ImPyPy-y-ImHp--ImPy -W
465(3) 5' G C GG T W-3' Im--ImImHp-y-PyPy--ImPy -W
466(3) 5' G C GG A W-3' Im-(3-ImImPy-y-HpPy--ImPy -W
467(3) 5' G C GG T W-3' Im--ImPyHp-y-PyIm--ImPy -W
468(3) 5' G C GC A W-3' Im--ImPyPy-y-HpIm--ImPy -W
469) 5'-W G C CT T W-3' ImPyPyHpHp-y-Py-~-ImImPy 469~3p) 5'-W G C CT T W-3' ImPyPy--Hp-y-Py--ImImPy 470) 5' G C CT A W-3' ImPyPyHpPy-y-Hp--ImImPy -W
470p) 5' G C CT A W-3' ImPyPy--Py-y-Hp--ImImPy -W
4710 5' G C CT G W-3' ImPy--Hplm-y-Py--ImImPy -W
472(3) 5' G C CT C W-3' ImPyPyHpPy-y-Im--ImImPy -W
472(3p) 5' G C CT C W-3' ImPyPy--Py-y-Im--ImImPy -W
473(3) 5' G C CA T W-3' ImPyPyPyHp-y-Py--ImImPy -W
473p) 5'-W G C CA T W-3' ImPyPy--Hp-y-Py--ImImPy 474~i) 5' G C CA A W-3' ImPyPyPyPy-y-Hp--ImImPy -W
474pp) 5'-W G C CA A W-3' ImPyPy--Py-y-Hp--ImImPy 4753) 5' G C CA G W-3' ImPy--Pylm-y-Py--ImImPy -W
476(3) 5' G C CA C W-3' ImPyPyPyPy-y-Im--ImImPy -W
476(3p) 5' G C CA C W-3' ImPyPy--Py-y-Im--ImImPy -W
4773) 5' G C CG T W-3' ImPy--ImHp-y-Py--ImImPy -W
478(3) 5' G C CG A W-3' ImPy--ImPy-y-Hp--ImImPy -W
TABLE 59 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WGCSNNW-3' with ~i substihrtions.
DNA aromatic amino acid sequence sequence G25(3) 5' GC G G W-3' Im-(3-ImImIm-y-PyPy-~3-ImPy -W G
G26(3) 5' GC G C W-3' Im-(3-ImImPy-y-ImPy-p-ImPy -W G
G27~3) ~5' GC C G W-3' Im-(3-ImPyIm-y-Pylm-(3-ImPy -W G
G28(3) 5' GC C C W-3' Im-~3-ImPyPy-y-ImIm-~i-ImPy -W G
G29(3) 5'-W GC G G W-3' ImPy-~3-Imlm-y-Py-(3-ImImPy C
G30(3) 5' GC G C W-3' ImPy-(3-ImPy-y-Im-~3-ImImPy -W C
G31(3) 5' GC C G W-3' ImPy-(3-Pylm-y-PyImImImPy -W C
TABLE 60: 10-ring Hairpin Polyamides for recognition of 7-by S'-WCGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 4810 5' C G T T T W-3' PyImHpHpHp-y-PyPy-(3-PyIm -W
481(3p) '5' C G T T T W-3' PyIm-(3-HpHp-y-PyPy-(3-PyIm -W
4823) 5' C G T T A W-3' PyImHpHpPy-y-HpPy-(3-PyIm -W
482~3P) 5' C G T T A W-3' Pylm-/3-Hppy-y-Hppy-~3-pylm -W
4833) 5' C G T T G W-3' PyIm-~3-HpIm-y-Pypy-p-Pylm -W
484(3) 5' C G T T C W-3' PyImHpHppy-y-ImPy-/3-PyIm -W
484(3p} 5'-WC G T T C W-3' Pylm-(3-HpPy-y-ImPy-(3-PyIm 4853) 5' C G T A T W-3' PyImHpPyHp-y-PyHp-[3-PyIm -W
485(3p) 5' C G T A T W-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm -W
486(3) 5' C G T A A W-3' PyImHpPyPy-y-HpHp-(3-pylm -W
486(3p) 5' C G T A A W-3' PyIm-~3-Pypy-Y-HpHp-(3-pylm -W
4873) 5' C G T A G W-3' PyIm-J3-Pylm-y-PyHp-(3-Pylm -W
488J3) 5' C G T A C W-3' PyImHpPyPy-y-ImHp-~3-Pylm -W
488(3p) 5' C G T A C W-3' PyIm-(3-PyPy-y-ImHp-(3-PyIm -W
489(3} 5' C G T G T W-3' PyIm-~-ImHp-Y-Pypy-~3-pylm -W
490(3) 5' C G T G A W-3' Pylm-(3-Impy-y-HpPy-(3-PyIm -W
491(3) 5' C G T G G W-3' PyIm-~-ImIm-y-pyPy-(3-pyIm -W
492(3) 5' C G T G C W-3' PyIm-[3-ImPy-y-Impy-~3-PyIm -W
493x) 5' C G T C T W-3' PyImHpPyHp-y-PyIm-p-PyIm -W
493(3p) 5' C G T C T W-3' Pylm-(3-PyHp-y-PyIm-(3-PyIm -W
4943) 5' C G T C A W-3' PyImHpPyPy-y-HpIm-~3-PyIm -W
494(3p) 5' C G T C A W-3' PyIm-J3-PyPy-y-HpIm-(3-PyIm -W
495(3) 5' C G T C G W-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm -W
496(3) 5' C G T C C W-3' PyImHpPyPy-y-Imlm-~i-PyIm -W
496(3p) 5' C G T C C W-3' PyIm-~3-PyPy-y-ImIm-~3-PyIm -W
4973) 5' C G A T T W-3' PyImPyHpHp-y-Pypy-(3-pyIm -W
497(3p) 5' C G A T T W-3' PyIm-~3-HpHp-y-PyPy-(3-pyIm -W
498(3) 5' C G A T A W-3' PyImPyHpPy-y-HpPy-p-PyIm -W
498(3p) 5' C G A T A W-3' Pylm-~i-HpPy-y-HpPy-(3-PyIm -W
TABLE 60 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 499(3) 5' C G A T GW-3' Pylm-(3-Hplm-y-Pypy-(3-pylm -W
500(3) 5' C G A T CW-3' PyImPyHpPy-y-ImPy-(3-pylm -W
500(3p) ~ C G A T CW-3' PyIm-(3-HpPy-y-ImPy-~_pyln~
5' -W
501~i) 5' C G A A TW-3' PyImPyPyHp-y-PyHp-(3-PyIm -W
501(3p) 5' C G A A TW-3' PyIm-(3-PyHp-y-PyHp-(3-PyIm -W
5023) 5' C G A A AW-3' PyImPyPyPy-y-HpHp-~3-Pylm -W
502~3p) 5' C G A A AW-3' PyIm-(3-Pypy-y-HpHp-~-PyIm -W
5030 5' C G A A GW-3' PyIm-(3-PyIm-y-PyHp-~3-Pylm -W
504 ) 5' C G A A CW-3' -W PyImPyPyPy-y-ImHp-(3-PyIm 504(3p) 5' C G A A CW-3' Pyim-(3-PyPy-y-ImHp-~3-pylm -W
505(3) 5' C G A G TW-3' -W Pylm-(3-ImHp-y-PyPy-(3-PyIm 5063) 5' C G A G AW-3' PyIm-p-ImPy-y-HpPy-p-pyIm -W
507(3) 5' C G A G GW-3' PyIm-(3-Imlm-y-Pypy-(3-pylm -W
50B(3} 5' C G A G CW-3' PyIm-~i-ImPy-y-ImPy-(3-PyIm -W
5093) 5' C G A C TW-3' PyImPyPyHp-y-PyIm-(3-PyIm -W
509~p) 5'-W C G A C TW-3' PyIm-(3-PyHp-y-pylm-(3-PyIm 5100 5' C G A C AW-3' PyImPyPyPy-y-Hplm-~3-Pylm -W
510(3p} 5' C G A C AW-3' PyIm-~3-PyPy-y-HpIm-(3-PyIm -W
511~i) 5' C G A C GW-3' PyIm-(3-PyIm-y-PyIm-(3-PyIm -W
5123) 5' C G A C CW-3' PyImPyPyPy-y-ImIm-~3-PyIm -W
5I2~3p) 5' C G A C CW-3' PyIm-~3-PyPy-y-ImIm-(3-PyIm -W
TABLE 61:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 513(3) 5' C G GT T W-3' PyImIm-(3-Hp-y-PyPy-(3-PyIm -W
514(3) -5' C G GT A W-3' PyImIm-~i-Py-y-HpPy-(3-Pylm -W
515(3) 5' C G GT G W-3' PyImIm-(3-Im-y-PyPy-(3-Pylm -W
516(3) 5' C G GT C W-3' PyImIm-(3-Py-y-ImPy-(3-Pylm -W
517(3) 5' C G GA T W-3' PyImIm-(3-Hp-y-PyHp-~3-Pylm -W
518(3) 5' C G GA A W-3' PyImIm-(3-Py-y-HpHp-(3-PyIm -W
5193) 5' C G GA G W-3' PyImIm-(3-Im-y-PyHp-(3-PyIm -W
520(3) 5' C G GA C W-3' PyImIm-~3-Py-y-ImHp-~3-PyIm -W
521~i) 5' C G GG T W-3' PyImImImHp-y-PyPy-(3-PyIm -W
522(3) 5' C G GG A W-3' PyImImImPy-y-HpPy-~3-PyIm -W
523(3) 5' C G GC T W-3' PyImIm-~-Hp-y-PyIm-~3-PyIm -W
524(3) 5' C G GC A W-3' PyImIm-~3-Py-y-HpIm-(3-PyIm -W
5250 5' C G CT T W-3' PyImPyHpHp-y-Py-~3-ImPyIm -W
525(3p) 5' C G CT T W-3' PyImPy-(3-Hp-y-Py-(3-ImPyIm -W
526(3) 5' C G CT A W-3' PyImPyHpPy-y-Hp-~3-ImPyIm -W
526(3p) 5' C G CT A W-3' PyImPy-(3-Py-y-Hp-p-ImPyIm -W
5273) 5' C G CT G W-3' Pylm-(3-Hplm-y-Py-p-ImPyIm -W
528(3) 5' C G CT C W-3' PyImPyHpPy-y-Im-(3-ImPyIm -W
528(3p) 5' C G CT C W-3' PyImPy-(3-Py-y-Im-(3-ImPyIm -W
529(3) 5' C G CA T W-3' PyImPyPyHp-y-Py-(3-ImPyIm -W
529(3p) 5' C G CA T W-3' PyImPy-(3-Hp-y-Py-~3-ImPyIm -W
530(3) 5' C G CA A W-3' PyImPyPyPy-y-Hp-(3-ImPyIm -W
530(3p) 5' C G CA A W-3' PyImPy-~3-Py-y-Hp-~3-ImPyIm -W
531(3) 5' C G CA G W-3' PyIm-(3-Pylm-y-Py-[3-ImPyIm -W
532(3) 5'-W C G CA C W-3' PyImPyPyPy-y-Im-p-ImPyIm 532(3p) 5' C G CA C W-3' PyImPy-~3-Py-y-Im-p-ImPyIm -W
533(3) 5' C G CG T W-3' Pylm-p-ImHp-y-Py-p-ImPyIm -W
5343) 5' C G CG A W-3' Pylm-~3-ImPy-y-Hp-(3-ImPyIm -W
TABLE 61 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCGSNNW-3' with p substitutions .
DNA aromatic amino acid sequence sequence 5353) 5' C G C C TW-3' PyImPyPyHp-y-PyImIm-p-Im -W
536(3) ~5' C G C C AW-3' PyImPyPyPy-y-HpImIm-(3-Im -W
G33(3) 5' C G G G GW-3' PyImImImIm-y-PyPy-(3-PyIm -W
G34(3) 5' C G G G CW-3' PyImImImPy-y-ImPy-(3-PyIm -W
G35~3) 5' C G G C GW-3' PyImIm-~-Im-y-Pylm-(3-PyIm -W
G36(3) 5' C G G C CW-3' PyImIm-~3-Py-y-ImIm-(3-PyIm -W
G37(3) 5'-W C G C G GW-3' Pylm-(3-ImIm-y-Py-(3-ImPyIm G38(3) 5' C G C G CW-3' PyIm-~3-ImPy-y-Im-(3-ImPyIm -W
G39(3) 5' C G C C GW-3' PyIm-(3-PyIm-y-PyImIm-~i-Im -W
G40(3) 5' C G C C CW-3' PyImPyPyPy-y-ImImIm-(3-Im -W
WO 98/37067. PCT/US98/01714 TABLE 62:
I 0-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 537(3) 5' C T TT T W-3' PyHpHpHpHp-y-PyPy-(3-Pylm -W
537(3p) 'S' C T TT T W-3' PyHp-(3-HpHp-y-PyPy-(3-PyIm -w 538~i) 5' C T TT A W-3' PyHpHpHpPy-y-HpPy-(3-PyIm -W
538(3p) 5' C T TT A W-3' PyHp-(3-HpPy-y-HpPy-~3-Pylm -W
539(3) 5' C T TT G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyIm -W
540~i) 5' C T TT C W-3' PyHpHpHpPy-y-ImPy-(3-PyIm -W
540(3p) 5' C T TT C W-3' PyAp-(3-HpPy-y-ImPy-~3-PyIm -W
541R) 5' C T TA T W-3' PyHpHpPyHp-y-PyHp-(3-PyIm -W
541(3p) 5' C T TA T W-3' PyHp-(3-PyHp-y-PyHp-(3-PyIm -W
5420 5' C T TA A W-3' PyHpHpPyPy-y-HpHp-(3-PyIm -W
542(3p) 5' C T TA A W-3' PyHp-p-PyPy-y-HpHp-(3-PyIm -W
543~i) 5' C T TA G W-3' PyHp-~i-PyIm-y-PyHp-~-PyIm -W
544(3) 5' C T TA C W-3' PyHpHpPyPy-y-ImHp-(3-Pylm -W ~
544(3p) 5' C T TA C W-3' PyHp-(3-PyPy-y-ImHp-~3-Pylm -W
545(3) 5' C T TG T W-3' PyHp-(3-ImI-Ip-y-PyPy-(3-PyIm -W
5463) 5' C T TG A W-3' PyHp-(3-ImPy-y-HpPy-~-PyIm -W
547(3) 5' C T TG G W-3' PyHp-(3-Imlm-y-PyPy-(3-Pylm -W
548(3) 5' C T TG C W-3' PyHp-(3-ImPy-y-ImPy-(3-PyIm -W
549(3) 5' C T TC T W-3' PyHpHpPyHp-y-PyIm-~3-Pylm -W
549(3p) 5' C T TC T W-3' PyHp-~3-PyHp-y-PyIm-~3-PyIm -W
550(3) 5' C T TC A W-3' PyHpHpPyPy-y-HpIm-[3-PyIm -W
550~3p) 5' C T TC A W-3' PyHp-[3-PyPy-y-HpIm-(3-PyIm -W
5513) 5' C T TC G W-3' PyHp-~i-Pylm-y-PyIm-~3-Pylm -W
5523) 5' C T TC C W-3' PyHpHpPyPy-y-ImIm-(3-PyIm -W
552(3p) 5' C T TC C W-3' PyHp-(3-PyPy-y-Imlm-(3-PyIm -W
553(3) 5' C T AT T W-3' PyHpPyHpHp-y-PyPy-~i-PyIm -W
553(3p) 5' C T AT T W-3' PyHp-~i-HpHp-y-PyPy-~i-PyIm -W
554(3) 5' C T AT A W-3' PyHpPyHpPy-y-HpPy-(3-PyIm -W
(cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 554(3p) 5' C TA T A W-3' PyHp-(3-HpPy-y-HpPy-~i-Pylm -W
555(3) ~ C TA T G W-3' PyHp-(i-Hplm-y-PyPy-p-pyIm 5' -W
5563) 5' C TA T C W-3' PyHpPyHpPy-Y-ImPy-~3-PyIm -W
556(3p) 5' C TA T C W-3' PyHp-(3-HpPy-y-ImPy-(3-PyIm -W
557(3) 5' C TA A T W-3' PyHpPyPyHp-Y-PyHp-(3-PyIm -W
557~3p) 5' C TA A T W-3' PyHp-(3-PyHp-y-PyHp-(3-Pylm -W
5580 5' C TA A A W-3' PyHpPyPyPy-Y-HpHp-/3-PyIm -W
558~ip) 5' C TA A A W-3' PyHp-(3-PyPy-y-HpHp-(3-PyIm -W
559(3) 5' C TA A G W-3' PyHp-~-PyIm-y-PyHp-(3-PyIm -W
5603) 5' C TA A C W-3' PyHpPyPyPy-y-ImHp-(3-PYIm -W
560(3p) 5' C TA A C W-3' PyHp-(3-PyPy-y-ImHp-(3-Pylm -W
5613) 5' C TA G T W-3' PyHp-(3-ImHp-y-PYPy-(3-pylm -W
562~i) 5' C TA G A W-3 T PyHp-(3-ImPy-y-HpPy-(3-PyIm -W
563(3) 5' C TA G G W-3' PyHp-(3-ImIm-y-PyPy-(3-PyIm -W
564~i) 5' C TA G C W-3' PyHp-~3-ImPy-y-ImPy-~3-PyIm -W
565(3) 5' C TA C T W-3' PyHpPyPyHp-y-PyIm-(3-PyIm -W
565~3p) 5' C TA C T W-3' PyHp-(3-PyHp-Y-PyIm-(3-PyIm -W
5663) 5' C TA C A W-3' PyHppyPyPy-Y-HpIm-(3-PyIm -W
566(3p) 5' C TA C A W-3' PyHp-~i-PyPy-y-Hplm-(3-PyIm -W
567(3) 5' C TA C G W-3' PyHp-(3-PyIm-y-PyIm-(3-PyIm -W
5683) 5'-W C TA C C W-3' PyHpPyPyPy-y-ImIm-(3-PyIm 568pp) 5' C TA C C W-3' PyHp-yPYPY-y-Imlm-(3-Pylm -W
TABLE
63: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCTSNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 5693) 5' C T GT T W-3' Py-(3-ImHpHp-y-PyPy-(3-PyIm -W
570(3) 'S' C T GT A W-3' Py-(3-ImHpPy-y-HpPy-~i-PyIm -W
571(3) 5' C T GT G W-3' Py-~i-ImHpIm-y-PyPy-(3-Pylm -W
572(3) 5' C T GT C W-3' Py-(3-ImHpPy-y-ImPy-(3-Pylm -W
5733) 5' C T GA T W-3' Py-(3-ImPyHp-y-PyHp-(3-PyIm -W
574(3) 5' C T GA A W-3' Py-(3-ImPyPy-y-HpHp-(3-PyIm -W
5753) 5' C T GA G W-3' Py-(3-ImPyIm-y-PyHp-(3-PyIm -W
576(3) 5' C T GA C W-3' Py-(3-ImPyPy-y-ImHp-(3-PyIm -W
577(3) 5' C T GG T W-3' Py-~3-ImImHp-y-PyPy-(3-PyIm -W
578(3) 5' C T GG A W-3' Py-(3-ImImPy-y-HpPy-(3-PyIm -W
579(3) 5' C T GC T W-3' Py-(3-ImPyHp-y-PyIm-~-PyIm -W
5803) 5' C T GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-PyIm -W
581(3) 5' C T GG G W-3' Py-~3-ImImIm-y-PyPy-(3-Pylm -W
5823) 5' C T GG C W-3' Py-(3-ImImPy-y-ImPy-p-PyIm -W
583(3) 5' C T GC G W-3' Py-(3-ImPyIm-y-PyIm-p-PyIm -W
584(3) 5' C T GC C W-3' Py-(3-ImPyPy-y-ImIm-~-PyIm -W
5853) 5' C T CT T W-3' PyHpPyHpHp-y-Py-(3-ImPyIm -W
585~3p) 5' C T CT T W-3' PyHpPy-/3-Hp-y-Py-(3-ImPyIm -W
586(3) 5' C T CT A W-3' PyHpPyHpPy-y-Hp-p-ImPyIm -W
586(3p) 5' C T CT A W-3' PyHpPy-(3-Py-y-Hp-(3-ImPyIm -W
587(3) 5' C T CT G W-3' PyHp-p-HpIm-y-Py-(3-ImPyIm -W
5883) 5' C T CT C W-3' PyHpPyHpPy-y-Im-a-ImPyim -W
588(3p} 5' C T CT C W-3' PyHpPy-(3-Py-y-Im-(3-ImPyIm -W
589(3) 5' C T CA T W-3' PyHpPyPyAp-y-Py-~3-ImPyIm -W
589(3p) 5' C T CA T W-3' PyHpPy-(3-Hp-y-Py-~3-ImPyIm -W
590(3) 5' C T CA A W-3' PyHpPyPyPy-y-Hp-(3-ImPyIm -W
590(3p) 5' C T CA A W-3' PyHpPy-~3-Py-y-Hp-~-ImPyIm -W
591(3) 5' C T CA G W-3' PyHp-(3-PyIm-y-Py-(3-ImPyIm -W
_97_ TABLE 63 (cont): in 10-ring Hairp Polyamides for recognition of 7-by 5'-WCTSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 592(3) 5' C TC A C W-3' PyHpPyPyPy-y-Im-~3-ImPyIm -W
592(3p) 5' C TC A C W-3' PyHpPy-(3-Py-y-Im-~i-ImPyIm - -W
593R) 'S'-WC TC G T W-3' PYHP-~-I~P-y-PY-~-ImPYIm 594(3) 5' C TC G A W-3' PyHp-(3-ImPy-y-Hp-~3-ImPYIm -W
595~i) 5' C TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Im -W
595(3p) 5' C TC C T W-3' Py-~3-PypyHp-y-PyImIm-~-Im -W
596(3) 5' C TC C A W-3' PyHpPyPyPy-y-HpImIm-(3-Im -W
596(3p) 5' C TC C A W-3' Py-~3-Pypypy-y-HpImIm-~3-Im -W
5973) 5' C TC G G W-3' PyHp-p-ImIm-y-Py-(3-ImPyIm -W
598(3) 5' C TC G C W-3' P H
-W Y p-~3-ImPy-y-Im-(3-ImPyIm 599(3) 5' C TC C G W-3' PyHp-~i-Pylm-y-pylmIm-~3-Im -W
600R) 5'-W C TC C C W-3' PyHpPyPYPy-y-ImImIm-(3-Im 600(3p) 5' C TC C C W-3' Py-(3-PyPyPy-y-ImImIm-~-Im -W
TABLE 64:
10-ring Hairpin Polyamides for recognition of 7-by S'-WCAWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 6013) 5' C AT T T W-3' PyPyHpHpHp-y-PyPy-/3-HpIm -W
601(3p) '5' C AT T T W-3' PyPy-R-HpHp-y-PyPy-(3-HpIm -W
6023) 5' C AT T A W-3' PyPyHpHpPy-y-HpPy-(3-HpIm -W
602(3p) 5' C AT T A W-3 ' PyPy-(3-HpPy-y-HpPy-~i-Hplm -W
603(3) 5' C AT T G W-3' PyPy-~3-HpIm-y-PyPy-~i-Hplm -W
6040 5' C AT T C W-3' PyPyHpHpPy-y-ImPy-(3-HpIm -W
604~3p) 5' C AT T C W-3' PyPy-R-HpPy-y-ImPy-(3-Hplm -W
6053) 5' C AT A T W-3' PyPyHpPyHp-y-PyHp-~i-HpIm -W
605~3p) 5' C AT A T W-3' PyPy-(3-PyHp-y-PyHp-J3-Hplm -W
6063) 5' C AT A A W-3' PyPyHpPyPy-y-HpHp-(3-HpIm -W
606(3p) 5' C AT A A W-3' PyPy-(3-PyPy-y-HpHp-(3-Hplm -W
607(3) 5' C AT A G W-3' PyPy-(3-Pylm-y-PyHp-(3-Hplm -W
608~i) 5' C AT A C W-3' PyPyHpPyPy-y-ImHp-(3-HpIm -W
608(3p) 5' C AT A C W-3' PyPy-(3-PyPy-y-ImHp-(3-HpIm -W
609(3) 5' C AT G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpIm -W
610(3) 5' C AT G A W-3' PyPy-(3-ImPy-y-HpPy-~i-HpIm -W
611(3) 5' C AT G G W-3' PyPy-(3-ImIm-y-PyPy-(3-HpIm -W
612(3) 5' C AT G C W-3' PyPy-(3-ImPy-y-ImPy-(3-HpIm -W
613(3) 5' C AT C T W-3' PyPyHpPyHp-y-PyIm-[3-HpIm -W
613~p) 5' C AT C T W-3' PyPy-p-PyHp-y-PyIm-(3-HpIm -W
6143) 5' C AT C A W-3 ' PyPyHpPyPy-y-HpIm-~3-HpIm -W
614~3p) 5' C AT C A W-3' PyPy-j3-PyPy-y-HpIm-(3-HpIm -W
615(3) 5' C AT C G W-3' PyPy-(3-PyIm-y-PyIm-~i-HpIm -W
6163) 5' C AT C C W-3' PyPyHpPyPy-y-ImIm-(3-HpIm -W
616~3p) 5' C AT C C W-3' PyPy-~i-PyPy-y-ImIm-~-HpIm -W
6I7~3) 5' C AA T T W-3' PyPyPyHpHp-y-PyPy-(3-HpIm -W
617~p) 5' C AA T T W-3' PyPy-(3-HpHp-y-PyPy-~i-HpIm -W
6180 5' C AA T A W-3' PyPyPyHpPy-y-HpPy-p-HpIm -W
618(3p) 5' C AA T A W-3' PyPy-~-HpPy-y-HpPy-(3-HpIm -W
_9c~_ . TABLE 64 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCAWNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence 619(3) 5' C A A T G W-3' Pypy--Hplm-y-pypy_-Hplm -W
620) 5' C A A T C W-3' PyPyPyHpPy-~-ImPy--HpIm -W
620~ip) ~ C A A T C W-3' Pypy--HpPy-y-ImPy-(3-Hplm 5' -W
6Z1) 5'-W C A A A T W-3' PyPyPyPyHp-r-PyHp--HpIm 621(3p) 5' C A A A T W-3' PyPy-(3-PyHp-y-PyHp-(3-HpIm -W
622(3) 5'-W C A A A A W-3' PyPyPyPyPy-y-HpHp--Hplm 622p) 5' C A A A A W-3' PyPy--Pypy-y-Hpgp-(3-HpIm -W
623) 5' C A A A G W-3' PyPy--Pylm-y-PyHp--HpIm -W
6243) 5' C A A A C W-3' PyPyPyPyPy-'y-ImHp--Hplm -W
624p) 5' C A A A C W-3' PyPy--pypy-~-ImHp_-Hplm -W
625) 5' C A A G T W-3' PyPy--ImHp-y-PyPy--HpIm -W
626) 5' C A A G A W-3' PyPy--ImPy-y-HpPy--HpIm -W
IS 627(3) 5' C A A G G W-3' PyPy--ImIm-y-PyPy--Hplm -W
6283) 5' C A A G C W-3' PyPy--ImPy-y-ImPy--HpIm -W
6293) 5'-W C A A C T W-3' PyPyPyPyHp-y-PyIm--HpIm 629p) 5'-W C A A C T W-3' PyPy--PyHp-y-PyIm--HpIm 630(3) 5' C A A C A W-3' PyPyPyPyPy-y-HpIm--HpIm -W
630p) 5'-W C A A C A W-3' PyPy--PyPy-y-HpIm--HpIm 631) 5'-W C A A C G W-3' PyPy--PyIm-y-PyIm--HpIm 632(3) 5' C A A C C W-3' PyPyPyPyPy-y-Imlm--HpIm -W
632p) 5'-W C A A C C W-3' PyPy--PyPy-y-ImIm--HpIm TABLE 65:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 633~i) 5' C A G TT W-3' Py-(3-ImHpHp-y-PyPy-(3-HpIm -W
6343) ' C A G TA W-3' Py-(3-ImHppy-y-Hppy-/3-Hpim 5' -W
635~i) 5' C A G TG W-3' Py-~3-ImHpIm-y-PyPy-(3-Hplm -W
636(3) 5' C A G TC W-3' Py-(3-ImHpPy-y-ImPy-(3-HpIm -W
637(3) 5' C A G AT W-3' Py-(3-ImPyHp-y-PyHp-(3-HpIm -W
638(3) 5' C A G AA W-3' Py-(3-ImPyPy-y-HpHp-(3-Hplm -W
6393) 5' C A G AG W-3' Py-~i-ImPyIm-y-PyHp-~3-HpIm -W
640(3) 5' C A G AC W-3' Py-(3-ImPyPy-y-ImHp-(3-HpIm -W
641(3) 5' C A G GT W-3' Py-(3-ImImHp-y-PyPy-(3-HpIm -W
6423) 5' C A G GA W-3' Py-(3-ImImPy-y-HpPy-~3-HpIm -W
643(3) 5' C A G CT W-3' Py-(3-ImPyHp-y-PyIm-~3-Hplm -W
644(3) 5' C A G CA W-3' Py-(3-ImPyPy-y-HpIm-(3-HpIm -W
645(3) 5' C A G GG W-3' Py-(3-ImImIm-y-PyPy-(3-Hplm -W
6463) 5' C A G GC W-3' Py-(3-ImImPy-y-ImPy-(3-HpIm -W
647(3) 5' C A G CG W-3' Py-(3-ImPyIm-y-Pylm-(3-Hplm -W
6483) 5' C A G CC W-3' Py-(3-ImPyPy-y-Imlm-(3-Hplm -W
6493) 5'-W C A C TT W-3' PyPyPyHpHp-y-Py-(3-ImHpIm 649(3p) 5' C A C TT W-3' PyPyPy-(3-Hp-y-Py-~i-ImHpIm -W
6503) 5' C A C TA W-3' PyPyPyHpPy-y-Hp-(3-ImHpIm -W
650(3p) 5' C A C TA W-3' PyPyPy-(3-Py-y-Hp-~i-ImHpIm -W
651(3) 5' C A C TG W-3' PyPy-(3-HpIm-y-Py-(3-ImHpIm -W
652~i) 5' C A C TC W-3' PyPyPyHpPy-y-Im-~3-ImHpIm -W
652(3p) 5' C A C TC W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm -W
653(3) 5' C A C AT W-3' PyPyPyPyHp-y-Py-(3-ImHpIm -W
653(3p) 5' C A C AT W-3' PyPyPy-(3-Hp-y-Py-p-ImHpIm -W
654(3) 5' C A C AA W-3' PyPyPyPyPy-y-Hp-(3-ImHpIm -W
654(3p) 5' C A C AA W-3' PyPyPy-(3-Py-y-Hp-(3-ImHpIm -W
655(3) 5' C A C AG W-3' PyPy-(3-PyIm-y-Py-(3-ImHpIm -W
. TABLE 65 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCASNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 656(3) 5' C A C A C W-3' PyPyPyPyPy-y-Im-(3-ImHpIm -W
656(3p) 5' C A C A C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpIm -W
6573) '5' C A C G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpIm -W
658(3p) 5' C A C G A W-3' PyPy-~-ImPy-y-Hp-~_ImHpIm -W
6590 5' C A C C T W-3' PyPyPyPyHp-y-PyImIm-(3-Im -W
659(3p) 5' C A C C T W-3' Py-(3-PyPyHp-r-PyImIm-(3-Im -W
660(3) 5' C A C C A W-3' PyPyPyPyPy-y-HpImIm-~-Im -W
660(3p) 5' C A C C A W-3' Py-/3-PyPyPy-y-HpImIm-(3-Im -W
6613) 5' C A C G G W-3' PyPy-/3-ImIm-y-Py-(3-ImHpIm -W
662(3) 5' C A C G C W-3' PyPy-(3-ImPy-y-Im-j3-ImHpIm -W
6633} 5' C A C C G W-3' PyPy-(3-pylm-y-PyImIm-(i-Im -W
664(3} 5' C A C C C W-3' PyPyPyPyPy-y-ImImIm-(3-Im -W
664~3p) 5' C A C C C W-3' Py-p-Pypypy-y-ImImIm-(3-Im -W
TABLE 66:
10-ring Hairpin Polyamides for recognition of 7-by S'-WCCWNNW-3' with ~
substitutions.
DNA aromatic amino acid sequence sequence 665(3) 5' C C TT T W-3' PyPyHpHpHp-y-PyPy-(3-ImIm -W
665(3p) '5' C C TT T W-3' PyPy-(3-HpHp-y-PyPy-~3-ImIm -W
666(3) 5' C C TT A W-3' PyPyHpHpPy-y-HpPy-~-ImIm -W
666(3p) 5' C C TT A W-3' PyPy-(3-HpPy-y-HpPy-p-ImIm -W
667(3) 5' C C TT G W-3' PyPy-(3-HpIm-y-PyPy-(3-ImIm -W
668(3) 5' C C TT C W-3' PyPyHpHpPy-y-ImPy-~3-Imlm -W
668(3p) 5' C C TT C W-3' PyPy-(3-HpPy-y-ImPy-(3-ImIm -W
669(3) 5' C C TA T W-3' PyPyHpPyHp-y-PyHp-(3-ImIm -W
669(3p) 5' C C TA T W-3' PyPy-[3-PyAp-y-PyHp-(3-ImIm -W
670(3) 5' C C TA A W-3' PyPylipPyPy-y-HpHp-(3-ImIm -W
670~3p) 5' C C TA A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImIm -W
671(3) 5' C C TA G W-3' PyPy-(3-PyIm-y-PyHp-(3-ImIm -W
672(3) 5' C C TA C W-3' PyPyHpPyPy-y-ImHp-(3-ImIm -W
672(3p) 5' C C TA C W-3' PyPy-[3-PyPy-y-ImHp-~3-ImIm -W
673(3) 5' C C TG T W-3' PyPy-(3-ImHp-y-PyPy-(3-Imlm -W
674(3) 5' C C TG A W-3' PyPy-~-ImPy-y-HpPy-(3-ImIm -W
6753) 5' C C TG G W-3' PyPy-~3-ImIm-y-PyPy-(3-ImIm -W
676(3) 5' C C TG C W-3' PyPy-p-ImPy-y-ImPy-(3-ImIm -W
677(3) 5' C C TC T W-3' PyPyHpPyHp-y-PyIm-(3-ImIm -W
677(3p) 5' C C TC T W-3' PyPy-(3-PyHp-y-PyIm-/3-ImIm -W
678(3) 5'-W C C TC A W-3' PyPyHpPyPy-y-Hplm-(3-ImIm 678(3p) 5' C C TC A W-3' PyPy-p-PyPy-y-Hplm-~i-ImIm -W
679p) 5' C C TC G W-3' PyPy-p-PyIm-y-Pylm-(3-ImIm -W
680(3) 5' C C TC C W-3' PyPyHpPyPy-y-Imlm-~i-Imlm -W
680~3p) 5' C C TC C W-3' PyPy-(3-PyPy-y-Imlm-(3-Imlm -W
681R) 5' C C AT T W-3' PyPyPyHpHp-y-PyPy-~3-ImIm -W
681~p) 5' C C AT T W-3' PyPy-(1-HpHp-y-PyPy-~-ImIm -W
682(3) 5' C C AT A W-3' PyPyPyHpPy-y-HpPy-~3-ImIm -W
682(3p) 5' C C AT A W-3' PyPy-~i-HpPy-y-HpPy-(3-ImIm -W
TABLE 66: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 683(3) 5' C C A TG W-3' Pypy-(3-HpIm-y-PyPy-~-ImIm -W
684(3) '5'-WC C A TC W-3' PyPyPyHpPy-y-ImPy-~3-ImIm 684(3p) 5' C C A TC W-3' PyPy-~i-HpPy-y-ImPy-(3-ImIm -W
6853) 5' C C A AT W-3' PyPyPyPyHp-y-PyHp-(3-ImIm -W
685(3p) 5' C C A AT W-3' PyPy-(3-PyHp-y-PyHp-p-ImIm -W
686(3) 5' C C A AA W-3' PyPyPyPyPy-y-HpHp-(3-ImIm -W
686(3p) 5' C C A AA W-3' PyPy-~3-PyPy-y-HpHp-~-ImIm -W
687(3) 5' C C A AG W-3' PyPy-p-PyIm-y-PyHp-(3-ImIm -W
6883) 5' C C A AC W-3' PyPyPyPyPy-y-ImHp-(3-ImIm -W
688~3p) 5' C C A AC W-3' PyPy-(3-pypy-y-I~p_~_ImIm -W
689(3) 5' C C A GT W-3' PyPy-j3-ImHp-y-PyPy-/3-ImIm -W
690(3) 5' C C A GA W-3' PyPy-(3-ImPy-y-HpPy-(3-ImIm -W
691(3) 5' C C A GG W-3' PyPy-(3-ImIm-y-PyPy-(3-ImIm -W
6923) 5' C C A GC W-3' PyPy-(3-ImPy-y-ImPy-(3-Imlm -W
693(3) 5' C C A CT W-3' PyPyPyPyHp-y-PyIm-(3-ImIm -W
693~ip) 5' C C A CT W-3' Pypy-(3-PyHp-y-Pylm-(3-ImIm -W
694(3) 5' C C A CA W-3' PyPyPyPyPy-y-Hplm-/3-ImIm -W
694(3p) 5' C C A CA W-3' PyPy-~i-PyPy-y-Hplm-[3-Imlm -W
695(3) 5' C C A CG W-3' PyPy-(3-PyIm-y-Pylm-~3-ImIm -W
696(3) 5' C C A CC W-3' PyPyPyPyPy-y-ImIm-p-ImIm -W
696~ip) 5' C C A CC W-3' PyPy-(3-PyPy-y-ImIm-(3-Imlm -W
TABLE
67: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 697(3) 5' C C G T TW-3' Py-~3-ImHpHp-y-PyPy-~3-ImIm -W
698(3) '5' C C G T AW-3' Py-~3-ImHpPy-y-HpPy-(3-ImIm -W
6993) 5' C C G T GW-3' Py-~i-ImHpIm-y-PyPy-p-Imlm -W
700(3) 5' C C G T CW-3' Py-~3-ImHpPy-y-ImPy-(3-ImIm -W
701(3) 5' C C G A TW-3' Py-[3-ImPyHp-y-PyHp-(3-ImIm -W
702(3) 5' C C G A AW-3' Py-(3-ImPyPy-y-HpHp-p-ImIm --W
703(3) 5' C C G A GW-3' Py-~i-ImPyIm-y-PyHp-p-Imlm -W
7043? 5'-W C C G A CW-3' p y-p-ImPyPy-y-ImHp-(3-ImIm 705(3) 5' C C G G TW-3' p -W y-(3-ImImHp-y-PyPy-(3- ImIm 706(3) 5' C C G G AW-3' Py-~-ImImPy-y-HpPy-(3-ImIm -W
707(3) 5' C C G C TW-3' Py-(3-ImPyHp-y-PyIm-R-ImIm -W
708(3) 5' C C G C AW-3' Py-(3-ImPyPy-y-Hplm-~i-Imlm -W
709~i) 5' C C C T TW-3' PyPypyHpHp-y-Py-(3-ImImIm -W
709~ip) 5' C C C T TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm -W
710(3) 5'-W C C C T AW-3' PyPyPyHpPy-y-Hp-~i-ImImIm 710(3p) 5' C C C T AW-3' PyPyPy-~3-Py-y-Hp-~i-ImImIm -W
7113) 5'-W C C C T GW-3' PyPy-(3-HpIm-y-Py-(3-ImImIm 7123) 5' C C C T CW-3' PyPyPyHpPy-y-Im-(3-ImImIm -W
712(3p) 5' C C C T CW-3' PyPyPy-~i-Py-y-Im-~3-ImImIm -W
713(3) 5' C C C A TW-3' PyPyPyPyHp-y-Py-(3-ImImIm -W
713~3p) 5' C C C A TW-3' PyPyPy-(3-Hp-y-Py-(3-ImImIm -W
714(3) 5' C C C A AW-3' PyPyPyPyPy-y-Hp-(3-ImImIm -W
714(3p) 5' C C C A AW-3' PyPyPy-(3-Py-y-Hp-~i-ImImIm -W
715(3) 5' C C C A GW-3' PyPy-~3-Pylm-y-Py-(3-ImImIm -W
716(3) 5' C C C A CW-3' PyPypypypy-y-Im-(3-ImImIm -W
716(3p) 5' C C C A CW-3' PyPyPy-(3-Py-y-Im-~i-ImImIm -W
717(3) 5' C C C G TW-3' PyPy-(3-ImHp-y-Py-(3-ImImIm -W
718)3) 5' C C C G AW-3' PyPy-p-ImPy-y-Hp-(3-ImImIm -W
WO 98!37067 PCT/US98/01714 TABLE 67 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WCCSNNW-3' with ~3 substitutions.
DNA sequence aromatic amino acid sequence G4l~i) 5' C C G G G W-3' Py-(~-ImImIm-y-PyPy-(3-ImIm -W
G42~3) 5' C C G G C W-3' Py-(3-ImImPy-y-ImPy-(3-ImIm -W
G43(3) '5' C C G C G W-3' Py-[3-ImPyIm-y-Pylm-p-Imlm -W
G44(3) 5' C C G C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImIm -W
645(3) 5' C C C G G W-3' PyPy-p-ImIm-y-Py-(3-ImImIm -W
G46~3) 5' C C C G C W-3' PyPy-(3-ImPy-y-Im-~3-ImImIm -W
G47(3) 5'-W C C C C G W-3' PyPy-(3-Pylm-y-PyImImImIm TABLE 68:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 7230 5'-W A G TT G W-3' Pylm-(3-HpIm-y-PyPyPyPyHp 723(3p) '5'-W A G TT G W-3' PyIm-~3-HpIm-y-PyPy-(3-PyHp 727(3) 5'-W A G TA G W-3' PyIm-(3-Pylm-y-PyHpPyPyHp 727~3p) 5'-W A G TA G W-3' PyIm-(3-PyIm-y-PyHp-(3-PyHp 729(3) 5'-W A G TG T W-3' Pylm-~3-ImHp-y-PyPyPyPyHp 729(3p) 5'-W A G TG T W-3' PyIm-(3-ImHp-y-PyPy-(3-PyHp 730(3) 5'-W A G TG A W-3' PyIm-[3-ImPy-y-HpPyPyPyHp 730(3p) 5'-W A G TG A W-3' PyIm-~i-ImPy-y-HpPy-~-PyHp 7313) 5'-W A G TG G W-3' PyIm-(3-ImIm-y-PyPyPyPyHp 731(3p) 5'-W A G TG G W-3' PyIm-~i-Imlm-y-PyPy-(3-PyHp 732(3) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPyPyPyHp 732(3p) 5'-W A G TG C W-3' PyIm-(3-ImPy-y-ImPy-J3-PyHp 735(3) 5'-W A G TC G W-3' Pyim-~-PyIm-y-PyImPyPyHp 735(3p) 5'-W A G TC G W-3' Pylm-(3-Pylm-y-Pylm-(3-PyHp 739(3) 5'-W A G AT G W-3' PyIm-p-HpIm-y-PyPyHpPyIip 739~p) 5'-W A G AT G W-3' PyIm-~3-HpIm-y-PyPy-~3-PyHp 743(3) 5'-W A G AA G W-3' PyIm-(3-PyIm-y-PyHpHpPyHp 743~ip) 5'-W A G AA G W-3' PyIm-(3-Pylm-y-PyHp-p-PyHp 745(3) 5'-W A G AG T W-3' PyIm-(3-ImHp-y-PyPyHpPyHp 745(3p) 5'-W A G AG T W-3' PyIm-~i-ImHp-y-PyPy-(3-PyHp 7463) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPyHpPyHp 746(3p) 5'-W A G AG A W-3' PyIm-(3-ImPy-y-HpPy-~3-PyHp 747(3) 5'-W A G AG G W-3' PyIm-~i-ImIm-y-PyPyHpPyHp 747~3p) 5'-W A G AG G W-3' PyIm-p-ImIm-y-PyPy-(3-PyHp 748(3) 5'-W A G AG C W-3' PyIm-p-ImPy-y-ImPyHpPyHp 748(3p) 5'-W A G AG C W-3' Pylm-(3-ImPy-y-ImPy-~3-PyHp 751(3) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-PyImHpPyHp 751(3p) 5'-W A G AC G W-3' PyIm-(3-PyIm-y-Pylm-~i-PyHp TABLE :
69 10-ring Hairpin Polyamides for recognition of 7-by 5'-WAGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 753(3) 5' A G G T TW-3' PyImIm-(3-Hp-y-pypypypyHp -W
753~3P) '5'-WA G G T TW-3' PyIrttIm-J3-Hp-y-py-(3-pypyHp 754(3) 5' A G G T AW-3' PyImIm-~3-Py-y-HpPyPyPyHp -W
754~3p) 5' A G G T AW-3' PyImIm-(3-Py-y-Hp-~-PypyHp -W
755(3) 5' A G G T GW-3' PyImIm-(3-Im-y-PyPypypyHp -W
755pp) 5' A G G T GW-3' PyImIm-(3-Im-y-Py-~3-pypyHp -W
7563) 5' A G G T CW-3' PyImIm-~3-py-y-ImPyPyPyHp -W
756(3p) 5' A G G T CW-3' PyImIm-(3-Py-y-Im-(3-PyPyHp -W
757(3) 5' A G G A TW-3' PyImIm-~3-Hp-y-PyHpPyPyHp -W
757~3P) 5' A G G A TW-3' PyImIm-(3-Hp-y-Py-(3-pypyHp -W
7583) 5' A G G A AW-3' PyImIm-(3-Py-y-HpHpPyPyHp -W
758(3p) 5' A G G A AW-3' PyImIm-(3-Py-y-Hp-(3-PyPyHp -W
759(3) 5' A G G A GW-3' PyImIm-p-Im-y-PyHpPyPyHp -W
759~3p) 5' A G G A GW-3' PyImIm-~3-Im-y-Py-~-pypygp -W
760(3) 5' A G G A CW-3' PyImIm-(3-Py-y-ImHpPyPyHp -W
760~p) 5' A G G A CW-3' PyImIm-(3-Py-y-Im-~-PyPyHp -W
763(3) 5' A G G C TW-3' PyImIm-(3-Hp-y-PyImPyPyHp -W
7643) 5' A G G C AW-3' Pylmim-(3-Py-y-HpImPyPyHp -W
765(3) 5' A G C T TW-3' PyImPyHpHp-y-Py-~3-ImPyHp -W
765pp) 5' A G C T TW-3' PyImPy-(3-Hp-y-py-(3-ImPyHp -W
7663) 5' A G C T AW-3' PyImPyHpPy-y-Hp-(3-ImPyHp -W
766(3p) 5' A G C T AW-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp -W
7673) 5' A G C T GW-3' PyIm-(3-HpIm-y-Py-(3-ImPyAp -W
768(3) 5' A G C T CW-3' PyImPyHpPy-y-Im-~3-ImPyHp -W
768~ip) 5' A G C T CW-3' PyImPy-(3-Py-y-Im-~-ImPyHp -W
769(3) 5' A G C A TW-3' PyImPyPyHp-y-Py-p-ImPyHp -W
769(3p) 5' A G C A TW-3' PyImPy-~i-Hp-y-py-(3-ImPyHp -W
770(3) 5' A G C A AW-3' PyImPyPyPy-y-Hp-(3-ImPyHp -W
lAIiLL by (cont):
IU-ring Hairpin Polyamides for recognition of 7-by 5'-WAGSNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 770~3p) 5'-WA G C A A W-3' PyImPy-(3-Py-y-Hp-(3-ImPyHp 771(3) .5'-WA G C A G W-3' PyIm-~3-PyIm-y-Py-(3-ImPyHp 772(3) 5'-WA G C A C W-3' PyImPyPyPy-y-Im-(3-ImPyHp 772(3p) 5'-WA G C A C W-3' PyImPy-(3-Py-y-Im-~3-ImPyHp 7733) 5'-WA G C G T W-3' PyIm-(3-ImHp-y-Py-~-ImPyHp 7743) 5'-WA G C G A W-3' Pylm-(3-ImPy-y-Hp-(3-ImPyHp 775(3) 5'-WA G C C T W-3' PyImPyPyHp-y-PyImIm-/3-Hp 776~i) 5'-WA G C C A W-3' PyImPyPyPy-y-HpImIm-~3-Hp 7793) 5'-WA G G C G W-3' PyImIm-(3-Im-y-PyImPyPyHp 780(3) 5'-WA G G C C W-3' PyImIm-~3-Py-y-ImImPyPyHp 781(3) 5'-WA G C G G W-3' PyIm-~-ImIm-y-Py-~i-ImPyHp 782(3) 5'-WA G C G C W-3' Pylm-/3-ImPy-'y-Im-~-ImPyHp 783(3) 5'-WA G C C G W-3' Pylm-(3-Pylm-y-PyImIm-(3-Hp 784(3) 5'-WA G C C C W-3' PyImPyPyPy-y-ImImIm-a-Hp TABLE 70:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WATWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 7873) 5'-WA T T T G W-3' PyHp_R_Hplm-y-PypyPypyHp 787(3p) . -WA T T T G W-3' PyHp-~3-HpIm-y-PyPy-(3-PyHp 5' 791(3) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHpPyPyHp 791(~p) 5'-WA T T A G W-3' PyHp-(3-PyIm-y-PyHp-p-PyHp 793(3) 5'-WA T T G T W-3' PyHp-~i-ImHp-y-PyPyPyPyHp 793~P) 5'-WA T T G T W-3' pyHp-~_I~p_y_pypy-~j-pyHp 7943) 5'-WA T T G A W-3' PyHp-p-ImPy-y-HpPyPyPyHp 794(3p) 5'-WA T T G A W-3' PyHp-~-ImPy-y-HpPy-~3-PyHp 795(3) 5'-WA T T G G W-3' PyHp-~3-Imlm-y-PypypypyHp 795~3P) 5'-WA T T G G W-3' PyHp-~-ImPy-y-ImPyPyPyHp 796(3p) 5'-WA T T G C W-3' Pylip-p-ImPy-y-ImPy-/3-PyHp 799(3) 5'-WA T T C G W-3' PyHp-p-pyIm-y-PyImPyPyHp 799(3p) 5'-WA T T C G W-3' PyHp-(3-Pylm-y-PyIm-p-PyHp 803~i) 5'-WA T A T G W-3' PyHp-/3-HpIm-y-PypyHpPyHp 803(3p) 5'-WA T A T G W-3' PyHp-~3-HpIm-y-PyPy-~3-PyHp 8073) 5'-WA T A A G W-3' PyHp-~-PyIm-y-PyHpHpPyHp 807(3p) 5'-WA T A A G W-3' PyHp-(3-PyIm-y-PyHp-~3-PyHp 8093) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPYHpPyHp 809(3p) 5'-WA T A G T W-3' PyHp-(3-ImHp-y-PYPy-p-PyHp 810(3) 5'-WA T A G A W-3 ' PyHp-(3-ImPy-y-HpPyHpPyHp 810~3p) 5'-WA T A G A W-3' PyHp-~-ImPy-y-HpPy-(3-PyHp 811~i) 5'-WA T A G G W-3' PyHp-[3-ImIm-y-pypyHpPyHp 811~3P) 5'-WA T A G G W-3' PyHp-/3-ImIm-y-PyPy-(3-PyHp 812~i) 5'-WA T A G C W-3' p H
Y P-p-ImPy-y-ImPyHpPyHp 812~ip) 5'-WA T A G C W-3' PyHp-(3-Impy-y-Impy-p-PyHp 815(3) 5'-WA T A C G W-3' PyHp-(3-pylm-y-PyImHpPyHp 815~3p) 5'-WA T A C G W-3' PyHp-p-PyIm-y-Pylm-~i-PyHp TABLE 71:
I 0-ring Hairpin Polyamides for recognition of 7-by S'-WATSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 817~i) 5'-W A T GT T W-3' Py-J3-ImHpHp-y-PyPyPyPyHp 817(3p) ' -W A T GT T W-3' py-(3-I~pgp_y_pypypy_p-Hp S' 8183) 5'-W A T GT A W-3 Py-(3-ImHpPy-y-HpPyPyPyHp 818(3p) 5'-W A T GT A W-3' Py-(3-ImHpPy-y-HpPyPy-~3-Hp 8193) 5'-W A T GT G W-3' Py-(3-ImHpIm-y-PyPyPyPyHp 819~3p) 5'-W A T GT G W-3' Py-/3-ImHpIm-y-PyPyPy-(3-Hp 820(3) 5'-W A T GT C W-3' Py-~3-ImHppy-y-ImPyPyPyHp 820(3p) 5'-W A T GT C W-3' py-(3-ImHpPy-y-ImPyPy-~3-Hp 821(3) 5'-W A T GA T W-3' Py-(3-ImPyHp-y-PyHpPyPyHp 821(3p) 5'-W A T GA T W-3' Py-/3-ImPyHp-y-PyHpPy-(3-Hp 822(3} 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHppyPyHp 822(3p) 5'-W A T GA A W-3' Py-(3-ImPyPy-y-HpHpPy-~3-Hp 823(3) 5'-W A T GA G W-3' Py-p-ImPyIm-y-PyHpPyPyHp 823(3p) 5'-W A T GA G W-3' Py-/3-ImPyIm-y-PyHpPy-~i-Hp 824(3) 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPyPyHp 824(3p} 5'-W A T GA C W-3' Py-(3-ImPyPy-y-ImHpPy-(3-Hp 825(3) 5'-W A T GG T W-3' Py-(3-ImImHp-y-PypyPyPyHp 825~3p} 5'-W A T GG T W-3' Py-(3-ImImHp-y-PyPyPy-(3-Hp 826(3) 5'-W A T GG A W-3' Py-~3-ImImPy-y-HpPyPyPyHp 826(3p) 5'-W A T GG A W-3' Py-(3-ImImPy-y-HpPyPy-p-Hp 8273) 5'-W A T GC T W-3' Py-p-ImPyHp-y-PyImPyPyHp 827(3p) 5'-W A T GC T W-3' Py-~3-ImPyHp-y-PyImPy-p-Hp 8283) 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPyPyHp 828(3p} 5'-W A T GC A W-3' Py-p-ImPyPy-y-HpImPy-~3-Hp 8290 5'-W A T GG G W-3' Py-(3-ImImIm-y-PypyPyPyHp 829~p) 5'-W A T GG G W-3' Py-(3-ImImIm-y-PyPyPy-(3-Hp 830(3) 5'-W A T GG C W-3' Py-j3-ImImPy-y-ImPyPyPyHp 830(3p) 5'-W A T GG C W-3' Py-(3-ImImPy-y-ImPyPy-(3-Hp 831(3) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPyPyHp 831(3p) 5'-W A T GC G W-3' Py-(3-ImPyIm-y-PyImPy-~3-Hp TABLE 71:
I 0-ring Hairpin Polyamides for recognition of 7-by 5'-WATSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 8323) 5'-W A TG C C W-3' Py-~-ImPyPy-y-ImImPyPyHp 832~3p) ' -W A TG C C W-3' Py-~-ImPyPy-y-ImImPy-~3-Hp 5' 833(3) 5'-W A TC T T W-3' PyHpPyHpHp-y-Py-~3-ImPyHp 833~p) 5'-W A TC T T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp 8340 5'-W A TC T A W-3' PyHpPyHpPy-y-Hp-(3-ImPyHp 834~3p) 5'-W A TC T A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp 8353) 5'-W A TC T G W-3' PyHp-(3-HpIm-y-Py-(3-ImPyHp 836~i) 5'-W A TC T C W-3' PyHpPyHpPy-y-Im-(3-ImPyHp 836(3p) 5'-W A TC T C W-3' PyHpPy-~3-py-y-Im-(3-ImPyHp 837(3) 5'-W A TC A T W-3' PyHpPyPyHp-y-Py-(3-ImPyHp 837~3p) 5'-W A TC A T W-3' PyHpPy-(3-Hp-y-Py-(3-ImPyHp 8383) 5'-W A TC A A W-3' PyHpPyPyPy-y-Hp-(3-ImPyHp 838(3p) 5'-W A TC A A W-3' PyHpPy-~3-Py-y-Hp-(3-ImPyHp 839(3) 5'-W A TC A G W-3' PyHp-~3-PyIm-y-Py-(3-ImPyHp $40(3) 5'-W A TC A C W-3' PyHpPyPyPy-y-Im-p-ImPyHp 840~p) 5'-W A TC A C W-3' PyHpPy-~i-Py-y-Im-~3-ImPyHp 841(3) 5'-W A TC G T W-3' PyHp-(3-ImHp-y-Py-(3-ImPyHp 842(3) 5'-W A TC G A W-3' PyHp-~-ImPy-y-Hp-~-ImPyHp 8430 5'-W A TC C T W-3' PyHpPyPyHp-y-PyImIm-(3-Hp 843(3p) 5'-W A TC C T W-3' py-(3-pypygp-y-pylmIm-~3-Hp 8443) 5'-W A TC C A W-3' PyHppyPyPy-y-HpImIm-(3-Hp 844(3p) 5'-W A TC C A W-3' py-p-pypypy-y-HpImIm-(3-Hp 845 ) 5'-W A TC G G W-3' PyHp-(3-ImIm-y-Py-(3-ImPyHp 8463) 5'-W A TC G C W-3' PyHp-(3-ImPy-y-Im-(3-ImPyHp 8473) 5'-W A TC C G W-3' PyHp-(3-PyIm-y-PyImIm-(3-Hp - 8483) 5'-W A TC C C W-3' PyHpPyPyPy-y-ImImIm-~3-Hp 848(3p) 5'-W A TC C C W-3' Py-(3-PyPyPy-y-ImImIm-(3-Hp TABLE 72:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WAAWNNW-3' with ~3 substitutions.
DNA aromatic amino acid sequence sequence 851(3) 5' -WA AT T G W-3' PyPy-~3-Hp lm-y-PyPyPyHpHp 851~3p) ' -WA AT T G W-3' PyPy-J3-Hplm-y-PyPy-~3-HpHp 5' 8553) 5' -WA AT A G W-3' PyPy-~3-Pylm-y-PyHppyHpHp 855(3p) 5' -WA AT A G W-3' Pypy-p-PyIm-y-PyHp-~3-HpHp 857(3) 5' -WA AT G T W-3' PyPy-~3-ImHp-y-PyPyPyHpHp 857(3p) 5' -WA AT G T W-3' PyPy-~-ImHp-y-PyPy-(3-HpHp 858(3) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-HpPyPyHpHp 858(3p) 5' -WA AT G A W-3' PyPy-(3-ImPy-y-Hppy-(3-HpHp 8593) 5' -WA AT G G W-3' Pypy-(3-Imlm-y-PyPyPyHpHp 859~3p) 5' -WA AT G G W-3' PyPy-(3-Imlm-y-Pypy-~-HpHp 8603) 5' -WA AT G C W-3' PyPy-(3-ImPy-y-ImPyPyHpHp 860(3p) 5' -WA AT G C W-3' PyPy-[3-ImPy-y-ImPy-(3-HpHp 8633) 5' -WA AT C G W-3' PyPy-(3-PyIm-y-PyImPyHpHp 863(3p) 5' -WA AT C G W-3' PyPy-(3-Pylm-y-PyIm-(3-HpHp 8673) 5' -WA AA T G W-3' PyPy-(3-HpIm-y-PyPyHpHpHp 867(3p) 5' -WA AA T G W-3' PyPy-(3-Hplm-y-PyPy-(3-HpHp 871(3) 5' -WA AA A G W-3' PyPy-(3-PyIm-y-PyHpHpHpHp 871~3p) 5' -WA AA A G W-3' PyPy-p-PyIm-y-PyHp-(3-HpAp 8733) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPyHpHpHp 873(3p) 5' -WA AA G T W-3' PyPy-(3-ImHp-y-PyPy-(3-HpHp 874(3) 5' -WA AA G A W-3' PyPy-p-ImPy-y-HpPyHpHpHp 874~p) 5' -WA AA G A W-3' PyPy-(i-ImPy-y-HpPy-(3-HpHp 875(3) 5' -WA AA G G W-3' PyPy-p-ImIm-y-PyPyHpHpHp 875(3p) 5' -WA AA G G W-3' PyPy-~3-Imlm-y-PyPy-~i-HpHp 876(3) 5' -WA AA G C W-3' Pypy-(3-ImPy-y-ImPyHpHpHp 876~ip) 5' -WA AA G C W-3' PyPy-~i-ImPy-y-ImPy-(3-HpHp 8793) 5' -WA AA C G W-3' PyPy-~i-PyIm-y-PyImHpHpHp 879(3p) 5' -WA AA C G W-3' PyPy-(3-PyIm-y-PyIm-(3-HpHp TABLE
73: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WAASNNW-3' with substitutions.
DNA aromatic amino acid sequence sequence ' 881) 5' A A GT T W-3' Py--IrnHpHp-y-PyPyPyHpHp -W
881p) '5' A A GT T W-3' py__I~pHp-y-pyPypy--Hp -W
882) 5' A A GT A W-3' Py--ImHpPy-y-HpPyPyHpHp -W
882P) 5' A A GT A W-3' py--I~ppy_y-Hppypy--Hp -W
883) 5' A A GT G W-3' Py--ImHpIm-y-PyPypyHpHp -W
883(3p) 5'-W A A GT G W-3' Py--ImHpIm-y-PyPyPy--Hp 884) 5'-W A A GT C W-3' p y--ImHpPy-y-ImPyPyHpHp 884(3p) 5' A A GT C W-3' p -W y--ImHppy-y-ImPyPy--Hp 8853) 5' A A GA T W-3' -W Py--ImPyHp-y-PyHpPyHpHp 885p) 5' A A GA T W-3' Py--ImPyHp-y-PyHpPy--Hp -W
886(3) 5' A A GA A W-3' -W Py--ImPyPy-y-HpHpPyHpHp 886p) 5'-W A A GA A W-3' Py--ImPyPy-y-HpHpPy--Hp 887) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPyHpHp -W
887(3p) 5' A A GA G W-3' Py--ImPyIm-y-PyHpPy--Hp -W
888) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPyI-IpHp -W
888~iP) 5' A A GA C W-3' Py--ImPyPy-y-ImHpPy--Hp -W
889) 5'-W A A GG T W-3' Py--ImImHp-y-PyPyPyHpHp 889p) 5'-W A A GG T W-3' Py--ImImHp-y-PyPyPy--Hp 890(3) 5'-W A A GG A W-3' Py--ImImPy-y-HpPyPyHpHp 890p) 5'-W A A GG A W-3' Py--ImImPy-y-HpPyPy--Hp 891) 5' A A GC T W-3' Py--ImPyHp-y-PyTmPyHpHp -W
891p) 5' A A GC T W-3' Py--ImPyHp-y-PyImPy--Hp -W
892) 5'-W A A GC A W-3' Py--ImPyPy-y-HpImPyHpHp 892p) 5'-W A A GC A W-3' Py--ImPyPy-y-HpImPy--HP
893(3) 5' A A GG G W-3' Py--ImImIm-y-PyPyPyHpHp -W
893p) 5' A A GG G W-3' Py--ImImIm-y-PyPyPy--Hp -W
894) 5' A A GG C W-3' Py--ImImPy-y-ImPyPyHpHp -W
894p) 5'-W A A GG C W-3' Py--ImImPy-y-ImPyPy--Hp 895(3) 5' A A GC G W-3' Py--ImPyIm-y-PyImPyHpHp -W
895p) 5'-W A A GC G W-3' Py--ImPyIm-y-PyImPy--Hp TABLE 73 (cont); Polyamides 10-ring Hairpin for recognition of 7-by 5'-WAASNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 896(3) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPyHpHp 896(3p) 5'-W A AG C C W-3' Py-p-ImPyPy-y-ImImPy-(3-Hp 8973) ~ -W A AC T T W-3' PyPyPyHpHp-y-Py-~i-ImHpHp 5' 897(3p) 5'-W A AC T T W-3' pypypy_R_Hp_y_py_~_I~pHp 898(3) 5'-W A AC T A W-3' PyPyPyHpPy-y-Hp-(3-ImHpHp 898~3p) 5'-W A AC T A W-3' PyPyPy-(3-py-y-Hp_(3-ImApHp 899(3) 5'-W A AC T G W-3' PyPy-(3-HpIm-y-Py-(3-ImHpHp 900(3) 5'-W A AC T C W-3' PyPyPyHpPy-y-Im-~3-ImHpHp 900(3p) 5'-W A AC T C W-3' PyPyPy-(3-Py-y-Im-(3-ImHpHp 901(3) 5'-W A AC A T W-3' PyPyPyPyHp-y-Py-(3-ImHpHp 901(3p) 5'-W A AC A T W-3' PyPyPy-(3-Hp-y-py_~3-ImHpHp 902(3) 5'-W A AC A A W-3' PyPyPypypy-y-Hp_~-ImHpHp 902~3p) 5'-W A AC A A W-3' pypypy_~_py_y_Hp-~-I~pHp 903~i) 5'-W A AC A G W-3' PyPy-(3-pylm_y_py_~_I~pHp 904(3) 5'-W A AC A C W-3' PyPyPyPyPy-y-Im-~3-ImHpHp 904(3p) 5'-W A AC A C W-3' PyPyPy-~3-Py-y-Im-(3-ImHpHp 905(3) 5'-W A AC G T W-3' PyPy-(3-ImHp-y-Py-p-ImHpHp 9063) 5'-W A AC G A W-3' PyPy-(3-ImPy-y-Hp-(3-ImHpHp 9073) 5'-W A AC C T W-3' PyPypypyHp-y-PyImIm-p-Hp 907(3p) 5'-W A AC C T W-3' Py-(3-PyPyHp-y-PyImIm-(3-Hp 908(3) 5'-W A AC C A W-3' PyPyPyPyPy-y-HpImIm-(3-Hp 908~3p) 5'-W A AC C A W-3' Py-(3-PyPyPy-y-HpImIm-p-Hp 9093) 5'-W A AC G G W-3' PyPy-(3-Imlm-y-Py-(3-ImHpHp 910(3) 5'-W A AC G C W-3' PyPy-(3-ImPy-y-Im-(3-ImHpHp 9113) 5'-W A AC C G W-3' PyPy-~3-PyIm-y-PyImIm-(3-Hp 912(3) 5'-W A AC C C W-3' PyPyPyPyPy-y-ImImIm-(3-Hp 912~3p) 5'-W A AC C C W-3' Py-(3-pypypy-y-ImImIm-p-Hp ' TABLE
74: 30-ring Hairpin Polyamides for recognition of 7-by 5'-WACWNNW-3' with ~3 substitutions .
DNA aromatic amino acid sequence sequence 913(3) 5' -WA C T TT W-3' PyPyHpHpHp-y-PyPy-(3-ImFip 913(3p) .5'-WA C T TT W-3' PyPy-(3-HpHp-y-Pypy-(3-ImHp 914(3) 5' -WA C T TA W-3' PyPyHpHpPy-y-HpPy-(3-ImHp 914(3p) 5' -WA C T TA W-3' pyPy-p-HpPy-y-HpPy-j3-ImHp 9153) 5' -WA C T TG W-3' PyPy-(3-HpIm-y-PyPy-(3-ImHp 916(3) 5' -WA C T TC W-3' PyPyHpHpPy-Y-ImPy-(3-ImHp 916(3p) 5' -WA C T TC W-3' PyPy-(3-HpPy-y-ImPy-(3-ImHp 9173) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-~3-ImHp 9I7(3p) 5' -WA C T AT W-3' PyPyHpPyHp-y-PyHp-(3-ImHp 918~i) 5' -WA C T AA W-3' PyPyHpPyPy-y-HpHp-(3-ImHp 918~3p) 5' -WA C T AA W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp 9193) 5' -WA C T AG W-3' PyPy-p-pylm-y-PyHp-~i-ImHp 920(3) 5' -WA C .TAC W-3' PyPyHpPyPy-Y-ImHp-(3-ImHp 920(3p) 5' -WA C T AC W-3' PyPy-(3-PyPy-y-ImIip-(3-ImHp 921(3) 5' -WA C T GT W-3' pypy-~-Imp-y_pypy-a_I~p 922(3) 5' -WA C T GA W-3' PyPy-~3-ImPy-y-HpPy-(3-ImHp 923(3) 5' -WA C T GG W-3' PyPy-(3-Imlm-y-PyPy-(3-ImHp 924(3) 5' -WA C T GC W-3' PyPy-~3-ImPy-y-ImPy-(3-ImHp 925(3) 5' -WA C T CT W-3' PyPyHpPyHp-y-PyIm-~3-ImHp 925~3p) 5' -WA C T CT W-3' PyPy-(1-PyHp-Y-pylm-(3-ImHp 9260 5' -WA C T CA W-3' PyPyHpPyPy-y-HpIm-(3-ImHp 926(3p) 5' -WA C T CA W-3' PyPy-(3-PyPy-Y-Hplm-~3-ImHp 927(3) 5' -WA C T CG W-3' PyPy-(3-PyIm-y-PyIm-(3-ImHp 928(3) 5' -WA C T CC W-3' PyPyHpPyPy-y-ImIm-[3-ImHp 928~3p) 5' -WA C T CC W-3' PyPy-(3-pypy-y-Imlm-~3-ImHp 929(3) 5' -WA C A TT W-3' PyPyPyHpHp-y-PyPy-/3-ImHp ' 30 929~3p) 5' -WA C A TT W-3' pypy-(3-gpgp_y_pypy_~_I~p 9303) 5' -WA C A TA W-3' PyPyPyHpPy-Y-HpPy-(3-ImHp 930~3p) 5' -WA C A TA W-3' pypy-(3-Hppy-y-HpPy-p-ImHp 9313) 5' -WA C A TG W-3' Pypy-(3-Hplm-Y_pypy_p-I~p TABLE 74 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WACWNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 932(3) 5'-W A CA T C W-3' PyPyPyHpPy-y-ImPy-(3-ImHp 932(3p) '5'-W A CA T C W-3' PyPy-(3-HpPy-y-ImPy-[3-ImHp 9333) 5'-W A CA A T W-3' PyPyPyPyHp-y-PyHp-(3-ImHp 933(3p) 5'-W A CA A T W-3' PyPy-(3-PyHp-y-PyHp-(3-ImHp 934(3) 5'-W A CA A A W-3' PyPyPyPyPy-y-HpHp-(3-ImHp 934(3p) 5'-W A CA A A W-3' PyPy-(3-PyPy-y-HpHp-(3-ImHp 1(? 935~i) 5'-W A CA A G W-3' PyPy-(3-PyIm-y-PyHp-p-ImHp 936(3) 5'-W A CA A C W-3' PyPypypypy-y-I~p-~-I~p 936(3p) 5'-W A CA A C W-3' PyPy-(3-PyPy-y-ImHp-(i-ImHp 937(3) 5'-W A CA G T W-3' PyPy-(3-ImHp-y-PyPy-p-ImHp 938(3) 5'-W A CA G A W-3' PyPy-(3-ImPy-y-HpPy-~3-ImHp 9393) 5'-W A CA G G W-3' PyPy-~3-Imlm-y-PyPy-(3-ImHp 940(3) 5'-W A CA G C W-3' PyPy-(3-ImPy-y-ImPy-(3-ImHp 941(3) 5'-W A CA C T W-3' PyPyPyPyHp-y-PyIm-(3-ImAp 941~p) 5'-W A CA C T W-3' PyPy-(3-PyHp-y-Pylm-(i-ImFip 942(3) 5'-W A CA C A W-3' PyPyPyPyPy-y-HpIm-(3-ImHp 942(3p) 5'-W A CA C A W-3' PyPy-(3-PyPy-y-HpIm-~3-ImHp 943(3) 5'-W A CA C G W-3' PyPy-(3-PyIm-y-PyIm-~-ImHp 9443) 5'-W A CA C C W-3' PyPyPyPyPy-y-ImIm-(3-ImHp 944(3p) 5'-W A CA C C W-3' PyPy-(3-Pypy-y-ImIm-(3-ImHp TABLE
75: 10-ring Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' with (3 substitutions.
D1~1A aromatic amino acid sequence sequence 9453) 5' -WA C GT T W-3' Py-(3-ImHpHp-Y-Pypy-(3-Imp 9463) '5'-WA C GT A W-3' py_~3_I~ppy_y-Hppy_~-I~p 9473) 5' -WA C GT G W-3' Py-(3-ImHpIm-y-Pypy-a-ImHp 948(3) 5' -WA C GT C W-3' Py-(3-ImHpPy-y-ImPy-~3-ImHp 949(3) 5' -WA C GA T W-3' Py-(3-ImPyHp-y-pyHp-/3-ImHp 950(3) 5' -WA C GA A W-3' Py-~3-ImPyPy-y-HpHp-~-ImHp 9513) 5' -WA C GA G W-3' Py-J3-ImPyIm-y-PyHp-[3-ImHp 952(3) 5' -WA C GA C W-3' Py-(3-ImPyPy-Y-ImHp-(3-ImHp 9533) 5' -WA C GG T W-3' Py-(3-ImImHp-y-PyPy-p-I~p 954(3) 5' -WA C GG A W-3' Py-(3-ImImPy-y-Hppy-(3-ImHp 9553) 5' -WA C GC T W-3' Py-(3-ImPyHp-y-Pylm-(3-ImHp 9563) 5' -WA C GC A W-3' Py-(3-ImPyPy-y-Hplm-(3-ImHp 9573) 5' -WA C CT T W-3' PyPypyHpHp-y-Py-(3-ImImHp 957(3p) 5' -WA C CT T W-3' PyPyPy-~3-Hp-Y-Py-~3-ImImHp 958(3) 5' -WA C CT A W-3' PyPyPyHpPy-y-Hp-(3-ImImHp 958~3p) 5' -WA C CT A W-3' PyPypy-~3-py-y-Hp-~-ImImHp 959p) 5' -WA C CT G W-3' PyPy-j3-HpIm-y-Py-(3-ImImHp 960(3) 5' -WA C CT C W-3' PyPyPyHpPy-y-Im-~-ImImHp 960pp) 5' -WA C CT C W-3' Pypypy-(3-py-y-Im_~-ImImHp 961~i) 5' -WA C CA T W-3' PyPyPyPyHp-y-Py-~3-ImImHp 961(3p) 5' -WA C CA T W-3' PyPyPy-/3-Hp-y-Py-(3-ImImHp 9623) 5' -WA C CA A W-3' pypypypypy_y_Hp_~-ImImHp 962~3p) 5' -WA C CA A W-3' pypypy-(3-py-y-Hp-~-ImImHp 9633) 5' -WA C CA G W-3' PyPy-(3-pylm-y-Py-(3-ImImHp 964) 5' -WA C CA C W-3' PyPyPyPyPy-y-Im-~3-ImImHp 964(3p) 5' -WA C CA C W-3' PyPypy-(3-Py-y-Im_~3-ImImHp 965(3) 5' -WA C CG T W-3' PyPy-~3_ImHp-y-Py-~i-ImImHp 966(3) 5' -WA C CG A W-3' Pypy-~-Impy-y-Hp-~3-ImImHp 969(3) 5' -WA C GG G W-3' Py-(3-ImImIm-y-Pypy-~3-I~p 970~i) 5' -WA C GG C W-3' Py-(3-ImImPy-y-ImPy-~3-ImHp TABLE 75 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WACSNNW-3' with (3 substitutions.
DNA sequence aromatic amino acid sequence 9713) 5' -W A C G W-3' Py-(3-ImPyIm-y-PyIm-~-ImHp C G
972(3) 5' -W A C C W-3' Py-(3-ImPyPy-y-ImIm-(3-ImHp C G
973(3) ' 5' -W G G W-3' PyPy-(3-Imlm-y-Py-~-ImImHp A C C
974(3) 5' -W A G C W-3' PyPy-~-ImPy-y-Im-(3-ImImHp C C
9753) 5' -W A C G W-3' PyPy-(3-PyIm-y-PyImImImHp C C
TABLE 76:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGWNNW-3' with (3 substitutions.
DNA aromatic amino acid sequence sequence 979(3) 5' -WT G T T GW-3' Hplm-(3-HpIm-y-PyPyPyPyPy 979(3p) ~ -WT G T T GW-3' HpIm-~3-HpIm-y-PyPy-(3-PyPy 5' 9833) 5' -WT G T A GW-3' HpIm-/3-PyIm-y-PyHpPypyPy 983(3p) 5' -WT G T A GW-3' Hplm-~3-PyIm-y-PyHp-(3-PyPy 985(3) 5' -WT G T G TW-3' HpIm-p-ImHp-y-PyPyPyPyPy 985(3p) 5' -WT G T G TW-3' HpIm-(3-ImHp-y-PyPy-~i-PyPy 9863) 5' -WT G T G AW-3' HpIm-~3-ImPy-y-HpPypypypy 986~3p) 5' -WT G T G AW-3' HpIm-(3-ImPy-~y-HpPy-~3-PyPy 987(3) 5' -WT G T G GW-3' Hplm-p-Imlm-y-PyPyPyPyPy 987(3p) 5' -WT G T G GW-3' HpIm-(3-Imlm-y-PyPy-p-PyPy 988(3) 5' -WT G T G CW-3' HpIm-(3-ImPy-y-ImPyPYPyPy IS 988(3p) 5' -WT G T G CW-3' Hplm-~-ImPy-y-ImPy-p-Pypy 9913) 5' -WT G T C GW-3' Hplm-~i-Pylm-y-PyImPypyPy 991(3p) 5' -WT G T C GW-3' Hplm-(3-Pylm-y-Pylm-~3-PyPy 9953) 5' -WT G A T GW-3' Hplm-(3-HpIm-y-PyPyHpPyPy 995~p) 5' -WT G A T GW-3' HpIm-(3-HpIm-y-PyPy-(3-PyPy 999(3) 5' -WT G A A GW-3' HpIm-(3-Pylm-y-PyHpHpPyPy 999~3p) 5' -WT G A A GW-3' HpIm-(3-PyIm-y-PyHp-~3-PyPy 1001(3) 5' -WT G A G TW-3' HpIm-(3-ImHp-y-PyPyHpPyPy 1001~3p) 5' -WT G A G TW-3' HpIm-p-ImHp-y-PyPy-(3-PyPy 1002(3) 5' -WT G A G AW-3' Hplm-(3-ImPy-y-HpPyHpPyPy 1002~3p) 5' -WT G A G AW-3' HpIm-(3-ImPy-y-HpPy-(3-PyPy 1003(3) 5' -WT G A G GW-3' HpIm-~3-Imlm-y-PyPyHpPyPy 1003~3p) 5' -WT G A G GW-3' HpIm-~3-ImIm-y-PyPy-(3-PyPY
10043) 5' -WT G A G CW-3' HpIm-(3-ImPy-y-ImPyHpPyPy - 1004~ip) 5' -WT G A G CW-3' Hplm-~3-ImPy-y-ImPy-(3-PyPy 10073) 5' -WT G A C GW-3' HpIm-(3-PyIm-y-PyImHpPyPy 1007(3p) 5' -WT G A C GW-3' Hplm-(3-PyIm-y-Pylm-(3-PyPy TABLE 77:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTGSNNW-3' with substitutions.
DNA sequence aromatic amino acid sequence 1009(3) 5'-W T GG T T W-3' HpImIm--Hp-y-PyPyPyPyPy 1009p)' 5'-W T GG T T W-3' HpImIm--Hp-y-Py--PyPyPy 1010(3) 5'-W T GG T A W-3' HpImIm--Py-y-HpPyPyPyPy 1010(3p) 5'-W T GG T A W-3' HpImIm--Py-y-Hp--PyPyPy 10113) 5'-W T GG T G W-3' HpImIm--Im-y-PyPyPyPyPy 1011(3p) 5'-W T GG T G W-3' HpImIm--Im-y-Py--PyPyPy 1012(3) 5'-W T GG T C W-3' HpImIm--Py-y-ImPyPyPyPy 1012~p) 5'-W T GG T C W-3' HpImIm--Py-y-Im--PyPyPy 1013(3) 5'-W T GG A T W-3' HpImIm--Hp-y-PyHpPyPyPy 1013p) 5'-W T GG A T W-3' HpImIm--Hp-y-Py--PyPyPy 1014(3) 5'-W T GG A A W-3' HpImIm--Py-y-HpHpPyPyPy 1014p) 5'-W T GG A A W-3' HpImIm--Py-y-Hp--PyPyPy 10153) 5'-W T GG A G W-3' HpImIm--Im-y-PyHpPyPyPy 1015(3p) 5'-W T GG A G W-3' HpImIm--Im-y-Py-(3-PyPyPy 10163) 5'-W T GG A C W-3' HpImIm--Py-y-ImHpPyPyPy 1016(3p) 5'-W T GG A C W-3' HpImIm-(3-Py-y-Im--PyPyPy 1019(3) 5'-W T GG C T W-3' HpImIm--Hp-y-PyImPyPyPy 10203) 5'-W T GG C A W-3' HpImIm--Py-y-HpImPyPyPy 1021(3) 5'-W T GC T T W-3' HpImPyHpHp-y-Py--ImPyPy 1021(3p) 5'-W T GC T T W-3' HpImPy--Hp-y-Py--ImPyPy 1022(3) 5'-W T GC T A W-3' HpImPyHpPy-y-Hp--ImPyPy 1022(3p) 5'-W T GC T A W-3' HpImPy-(3-Py-y-Hp--ImPyPy 1023) 5'-W T GC T G W-3' HpIm--Hplm-y-Py--ImPyPy 10243) 5'-W T GC T C W-3' HpImPyHpPy-y-Im-/3-ImPyPy 1024p) 5'-W T GC T C W-3' HpImPy--Py-y-Im--ImPyPy 1025(3) 5'-W T GC A T W-3' HpImPyPyHp-y-Py-(i-ImPyPy 1025(3p) 5'-W T GC A T W-3' HpImPy--Hp-y-Py--ImPyPy 1026(3) 5'-W T GC A A W-3' HpImPyPyPy-y-Hp--ImPyPy 1026~p) 5'-W T GC A A W-3' HpImPy--Py-y-Hp--ImPyPy 10273) 5'-W T GC A G W-3' HpIm--PyIm-y-Py--ImPyPy TABLE 77 (cont): Polyamides 10-ring Hairpin for recognition of 7-by 5'-WTGSNNW-3' with p substitutions.
DNA aromatic amino acid sequence sequence 1028(3) 5' -WT G C A C W-3' HpImPyPyPy-y-Im-~3-ImPyP
1028(3p)' 5' -WT G C A C W-3' HpImPy-(3-Py-y-Im-~i-ImPyPy 1029(3) 5' -WT G G G T W-3' HpIm-(3-ImHp-y-py-(3-ImPypy 1030(3) 5' -WT G C G A W-3' Hplm-~-ImPy-y-Hp-(3-ImPyPy 1031(3) 5' -WT G C C T W-3' HpImPyPyHp-y-PyImIm-~i-Py 1031(3p) 5' -WT G C C T W-3' HpImPy-p-Hp-y-PyImIm-(3-Py 10323) 5' -WT G C C A W-3' HpImPyPyPy-y-HpImIm-(3-Py 1032~3p) 5' -WT G C C A W-3' HpImPy-(3-Py-y-HpImIm-(3-Py 1035(3) 5' -WT G G C G W-3' HpImIm-(3-Im-y-PyImPyPyPy 1036) 5' -WT G G C C W-3' HpImIm-~3-Py-y-ImImPyPyPy 1037(3) 5' -WT G C G G W-3' HpIm-(3-ImIm-y-Py-(3-ImPyPy 1038(3) 5' -WT G C G C W-3' Hplm-(3-ImPy-y-Im-(3-ImPyPy 1039~i) 5' -WT G C C G W-3' Hplm-(3-Pylm-y-pylmlm-(3-Py 1040(3) 5' -WT G C C C W-3' HpImPyPyPy-y-ImImIm-~3-Py TABLE 78:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTWIVNW-3' with p substitutions.
DNA sequence aromatic amino acid sequence 10433) 5'-WT T T T G W-3' HpHp-(3-Hplm-y-PyPyPyPyPy 1043(3p)' 5'-WT T T T G W-3 HpHp-(3-HpIm-y-PyPy-(3-PyPy T
10473) 5'-WT T T A G W-3' HpHp-(3-PyIm-y-PyHpPyPyPy 1047(3p) 5'-WT T T A G W-3' HpHp-~i-Pylm-y-PyHp-(3-PyPy 1049(3) 5'-WT T T G T W-3' HpHp-~i-ImHp-y-PyPyPyPyPy 1049~3p) 5'-WT T T G T W-3' HpHp-p-ImHp-y-PyPy-(3-PyPy 1050(3) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPyPyPyPy 1050(3p) 5'-WT T T G A W-3' HpHp-(3-ImPy-y-HpPy-p-PyPy 1051(3) 5'-WT T T G G W-3' HpHp-(3-Imlm-y-PyPyPyPyPy 1051(3p) 5'-WT T T G G W-3' HpHp-(i-ImIm-y-PyPy-(3-PyPy 1052(3) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPyPyPyPy 1052(3p) 5'-WT T T G C W-3' HpHp-(3-ImPy-y-ImPy-(3-PyPy 1055(3) 5'-WT T T C G W-3' HpHp-(3-Pylm-y-PyImPyPyPy 1055~3p) 5'-WT T T C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy 1059~i) 5'-WT T A T G W-3' HpHp-(3-HpIm-y-PyPyHpPyPy 1059(3p) 5'-WT T A T G W-3' HpHp-~3-HpIm-y-PyPy-R-PyPy 1063(3) 5'-WT T A A G W-3' HpHp-~3-Pylm-y-PyHpHpPyPy 1063~3p) 5'-WT T A A G W-3' HpHp--PyIm-y-PyHp-(3-PyPy 1065(3) 5'-WT T A G T W-3' HpHp-(3-ImHp-y-PyPyHpPyPy 1065(3p) 5'-WT T A G T W-3' HpHp-~-ImHp-y-PyPy-p-PyPy 1066~i) 5'-WT T A G A W-3' HpHp-p-ImPy-y-HpPyHpPyPy 1066(3p) 5'-WT T A G A W-3' HpHp-J3-ImPy-y-HpPy-/3-PyPy 1067(3) 5'-WT T A G G W-3' ~ HpHp-(3-Imlm-y-PyPyHpPyPy 1067(3p) 5'-WT T A G G W-3' HpHp-(3-ImIm-y-PyPy-(3-PyPy 1068(3) 5'-WT T A G C W-3' HpHp-(3-ImPy-y-ImPyHpPyPy 1068(3p) 5'-WT T A G C W-3' HpHp-~3-ImPy-y-ImPy-(3-PyPy 1071(3) 5'-WT T A C G W-3' HpHp-(3-PyIm-y-PyImHpPyPy 1071~ip) 5'-WT T A C G W-3' HpHp-~3-PyIm-y-PyIm-p-PyPy n TABLE 79:
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' with ~i substitutions DNA aromatic amino acid sequence sequence 1073R) 5' -WT T G T TW-3' Hp-~3-I,~pgp-y-pypypypypy 1073~3p)' 5' -WT T G T TW-3' Hp-(3-ImHpAp-y-PyPYPy-(3-py 1074(3) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HppypypypY
1074(3p) 5' -WT T G T AW-3' Hp-(3-ImHpPy-y-HpPYPy-~3_py 1075(3) 5' -WT T G T GW-3' Hp-~3-ImHpIm-y-PyPYPyPyPy 1075(3p) 5' -WT T G T GW-3' Hp-p-ImHpIm-y-PyPYPy-(3-Py 10763) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPyPyPy 1076(3p) 5' -WT T G T CW-3' Hp-(3-ImHpPy-y-ImPyPy-~-Py 1077(3) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PyHpPyPyPy 1077(3p) 5' -WT T G A TW-3' Hp-(3-ImPyHp-y-PYHpPy-(3-Py 1078(3) 5' -WT T G A AW-3' Hp-(3-ImPyPy-y-HpHpPyPyPy I5 1078~3p) 5' -WT T G A AW-3' Hp-~3-ImPyPy-y-HpHpPy-p-Py 1079(3) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PyHpPyPyPy 1079~3p) 5' -WT T G A GW-3' Hp-(3-ImPyIm-y-PYHpPy-~-Py 1080(3) 5' -WT T G A CW-3' Hp-~3-ImPyPy-y-ImHpPyPYPy 1080(3p} 5' -WT T G A CW-3' Hp-(3-ImPyPy-y-ImHpPy-/3-Py 1081(3) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PyPypypypY
1081(3p) 5' -WT T G G TW-3' Hp-(3-ImImHp-y-PYPypy-(3-py 10820 5' -WT T G G AW-3' Hp-(3-ImImPy-y-HpPypyPyPy 1082~p) 5' -WT T G G AW-3' Hp-~-ImImPy-y-HpPYPy-~3-Py 1083(3) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPyPyPy 1083~3p) 5' -WT T G C TW-3' Hp-(3-ImPyHp-y-PyImPy-~-Py 10843) 5' -WT T G C AW-3' Hp-~i-ImPyPy-y-HpImPYPyPy 1084(3p) 5' -WT T G C AW-3' Hp-~3-ImPyPy-y-HpImPy-~3-Py 10850 5' -WT T G G GW-3' Hp-(3-ImImIm-y-PYPypypypy - 1085(3p) 5' -WT T G G GW-3' Hp-J3-ImImIm-y-PyPyPy-~3-Py 10863) 5' -WT T G G CW-3' Hp-~i-ImImPy-y-ImPyPyPyPy 1086(3p) 5' -WT T G G CW-3' Hp-(3-ImImPy-y-ImPyPy-~i-Py 1087) 5' -WT T G C GW-3' Hp-~3-ImPYIm-y-PyImPyPyPy 1087(3p) 5' -WT T G C GW-3' Hp-(3-ImPYIm-y-PyImPy-/3-Py WO 98/370b7 PCT/US98/01714 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTTSNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1088(3) 5'-W T T G CC W-3' Hp-p-ImPyPy-y-ImImPyPyPy 1088(3p)' 5'-W T T G CC W-3' Hp-(3-ImPyPy-y-ImImPy-(3-Py 1089(3) 5'-W T T C TT W-3' HpHpPyHpHp-y-Py-(3-ImPyPy 1089(3p) 5'-W T T C TT W-3' HpHpPy-p-Hp-y-Py-(3-ImPyPy 1090(3) 5'-W T T C TA W-3' HpHpPyHpPy-y-Hp-(3-ImPyPy 1090(3p) 5'-W T T C TA W-3' HpHpPy-(3-Py-y-Hp-(3-ImPyPy 1091~i) 5'-W T T C TG W-3' HpHp-(3-HpIm-y-Py-~i-ImPyPy 10923) 5'-W T T C TC W-3' HpHpPyApPy-y-Im-(3-ImPyPy 1092(3p) 5'-W T T C TC W-3' HpHpPy-(3-Py-y-Im-(3-ImPyPy 10933) 5'-W T T C AT W-3' HpHpPyPyHp-y-Py-~3-ImPyPy 1093(3p) 5'-W T T C AT W-3' HpHpPy-~i-Hp-y-Py-/3-ImPyPy 10943) 5'-W T T C AA W-3' HpHpPyPyPy-y-Hp-(3-ImPyPy 1094(3p) 5'-W T T C AA W-3' HpHpPy-~3-Py-y-Hp-~i-ImPyPy 10953) 5'-W T T C AG W-3' HpHp-(3-Pylm-y-Py-(3-ImPyPy 10963) 5'-W T T C AC W-3' HpHpPyPyPy-y-Im-/3-ImPyPy 1096(3p) 5'-W T T C AC W-3' HpHpPy-(3-Py-y-Im-(i-ImPyPy 1097(3) 5'-W T T C GT W-3' HpHp-(3-ImHp-y-Py-[3-ImPyPy 1098(3) 5'-W T T C GA W-3' HpHp-~3-ImPy-y-Hp-p-ImPyPy 1099) 5'-W T T C CT W-3' HpHpPyPyHp-y-PyimIm-~3-Py 1099(3p) 5'-W T T C CT W-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py 1100(3) 5'-W T T C CA W-3 HpHpPyPyPy-y-HpImIm-p-Py ' 1100~ip) 5'-W T T C CA W-3' Hp-~i-PyPyPy-y-HpImIm-~-Py 1101(3) 5'-W T T C GG W-3' HpHp-(3-ImIm-y-Py-(3-ImPyPy 1102(3) 5'-W T T C GC W-3' HpHp-(3-ImPy-y-Im-~i-ImPyPy 1103(3) 5'-W T T C CG W-3' HpHp-(3-PyIm-y-PyImIm-(3-Py TABLE 80:
10-ring Hairpin Polyamides for recognition of 7-by S'-WTAWNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 11073) 5'-W T A TT G W-3' HpPy-(3-HpIm-y-PypypyHppy S I107(3p)' S'-W T A TT G W-3' HpPy-p-Hplm-y-Pypy-(3-HpPy 1111(3) 5'-W T A TA G W-3' HpPy-~3-Pylm-y-PyHpPyHpPy 1111~p) 5'-W T A TA G W-3' HpPy-~3-PyIm-y-PyHp-(3-HpPy 11133) 5'-W T A TG T W-3' HpPy-(3-ImHp-y-Pypypygppy 1113(3p) 5'-W T A TG T W-3' HpPy-p_ImHp_y_p~,p~,_~_HppY
11143) 5'-W T A TG A W-3' HpPy-p-ImPy-y-HpPYPyHpPy 1114(3p) 5'-W T A TG A W-3' HpPy-(3-ImPy-y-HpPy-(3-HpPy 1115(3) 5'-W T A TG G W-3' HpPy-(3-Imlm-y-Pypypygppy 1115(3p) 5'-W T A TG G W-3' HpPy-(3-ImIm-y-PyPy-(3-HpPy 1116(3) 5'-W T A TG C W-3' HpPy-~3-ImPy-y-ImPyPyHpPy 1S 1116~3p) 5'-W T A TG C W-3' HpPy-R-ImPy-y-ImPy-J3-HpPy 11193) 5'-W T A TC G W-3' HpPy-~i-PYim-y-PyImPyHpPy 1119(3p) 5'-W T A TC G W-3' HpPy-(3-PyIm-y-PyIm-(3-HpPy 11233) 5'-W T A AT G W-3' HpPy-(3-HpIm-y-PyPyHpHpPy 1123(3P) 5'-W T A AT G W-3' HpPy-p-HpIm-y-PyPy-(3-HpPY
1127(3) 5'-W T A AA G W-3' HpPy-(3-PYIm-y-PyHpHpHpPy 1127(3p) 5'-W T A AA G W-3' HpPy-(3-Pylm-y-PyHp-(3-HpPy 1129(3) 5'-W T A AG T W-3' HpPy-(3-ImHp-y-PyPyHpHpPy 1129(3p) 5'-W T A AG T W-3' Hppy-(3_I~p_y_p~,py_a-Hppy 1130(3) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPyHpHpPy 1130(3p) 5'-W T A AG A W-3' HpPy-~3-ImPy-y-HpPy-(3-HpPy 1131(3) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-PyPyI-IpHppy 1131~p) 5'-W T A AG G W-3' HpPy-(3-ImIm-y-Pypy-(3-Hppy 1132(3) 5'-W T A AG C W-3' HpPy-(3-ImPy-y-ImPyHpHpPy 1132(3p) 5'-W T A AG C W-3' HpPy-~i-ImPy-y-ImPy-p-HpPy 1135~i) 5'-W T A AC G W-3' Hppy_~_pylm_y_pYImHpHppy 1135~p) 5'-W T A AC G W-3' HpPy-(3-PyIm-y-PYIm-~i-HpPy TABLE 81: in 10-ring Polyamides Hairp for recognition of 7-by 5'-WTASNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1137(3) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPyHpPy 1137(3p) 5' -W T A GT T W-3' Hp-(3-ImHpHp-y-PyPyPy-~3-Py 1138(3) 5' -W T A GT A W-3' Hp-(3-ImHpPy-y-HpPyPyHpPy 1138~ip) 5' -W T A GT A W-3' Hp-p-ImHpPy-y-HpPyPy-(3-Py 1139(3) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPyHpPy 1139(3p) 5' -W T A GT G W-3' Hp-~3-ImHpIm-y-PyPyPy-(3-Py 11403) 5' -W T A GT C W-3' Hp-~3-ImHpPy-y-ImPyPyHpPy 1140(3p) 5' -W T A GT C W-3' Hp-(3-ImHpPy-y-ImPyPy-(3-Py 1141(3) 5' -W T A GA T W-3' Hp-~3-ImPyHp-y-PyHpPyHpPy 1141(3p) 5' -W T A GA T W-3' Hp-(3-ImPyHp-y-PyHpPy-(3-Py 1142(3) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPyHpPy 1142~ip) 5' -W T A GA A W-3' Hp-(3-ImPyPy-y-HpHpPy-(3-Py 11433) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPyHpPy 1143(3p) 5' -W T A GA G W-3' Hp-(3-ImPyIm-y-PyHpPy-~3-Py 11443) 5' -W T A GA C W-3' Hp-(3-ImPyPy-y-ImHpPyHpPy 1144(3p) 5' -W T A GA C W-3' Hp-~-ImPyPy-y-ImHpPy-~3-Py 11453) 5' -W T A GG T W-3' Hp-~-ImImHp-y-PyPyPyHpPy 1145~3p) 5' -W T A GG T W-3' Hp-p-ImImHp-y-PyPyPy-(3-Py 1146(3) 5' -W T A GG A W-3' Hp-(3-ImImPy-y-HpPyPyHpPy 1146(3p) 5' -W T A GG A W-3' Hp-~-ImImPy-y-HpPyPy-(3-Py 1147(3) 5' -W T A GC T W-3' Hp-~3-ImPyHp-y-PyImPyHpPy 1147~ip) 5' -W T A GC T W-3' Hp-(3-ImPyHp-y-PyImPy-(3-Py 1148(3) 5' -W T A GC A W-3' ~ Hp-~i-ImPyPy-y-HpImPyHpPy 1148(3p) 5' -W T A GC A W-3' Hp-p-ImPyPy-y-HpImPy-~i-Py 11493) 5' -W T A GG G W-3' Hp-(3-ImImIm-y-PyPyPyHpPy 1149(3p) 5' -W T A GG G W-3' Hp-~i-ImImIm-y-PyPyPy-(3-Py 1150(3) 5' -W T A GG C W-3' Hp-(3-ImImPy-y-ImPyPyHpPy 1150(3p) 5' -W T A GG C W-3' Hp-~3-ImImPy-y-ImPyPy-~i-Py 1151(3) 5' -W T A GC G W-3' Hp-p-ImPyIm-y-PyImPyHpPy 1151~3p) 5' -W T A GC G W-3' Hp-(3-ImPyIm-y-PyImPy-~-Py (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTASNNW-3' with (3 substitutions DNA aromatic amino acid sequence sequence 1152(3) 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPyHpPy 1152(3p). 5' -WT A G C CW-3' Hp-(3-ImPyPy-y-ImImPy-~3-Py 1153(3) 5' -WT A C T TW-3' HpPyPyHpHp-y-Py-(3-ImHpPy 1153(3p) 5' -WT A C T TW-3' HpPyPy-(3-Hp-y-Py-(3-ImHpPy 1154(3) 5' -WT A C T AW-3' HpPyPyHpPy-y-Hp-~3-ImHpPy 1154~ip) 5' -WT A C T AW-3' HpPyPy-p-py-y-Hp_p_I~ppy 11553) 5' -WT A C T GW-3' HpPy-(3-HpIm-y-Py-~3-ImHpPy 1156(3) 5' -WT A C T CW-3' HpPyPyHpPy-y-Im-(3-ImHpPy 1156(3p) 5' -WT A C T CW-3' HpPyPy-(3-Py-y-Im-~i-ImApPy 11573) 5' -WT A C A TW-3' HpPyPyPyHp-y-Py-(3-ImHpPy 1157(3p) 5' -WT A C A TW-3' HpPyPy-(3-Hp-y-Py-~3-ImHppy IS 1158~i) 5' -WT A C A AW-3' HpPyPyPyPy-y-Hp-(3-ImHpPy 1158(3p) 5' -WT A C A AW-3' HpPypy-(3-Py-y-Hp-/3-ImHpPy 1159(3) 5' -WT A C A GW-3' HpPy-(i-PyIm-y-Py-(3-ImHpPy 11603) 5' -WT A C A CW-3' HpPyPyPyPy-y-Im-(3-ImHpPy 1160(3p) 5' -WT A C A CW-3' HpPyPy-(3-Py-y-Im-(3-ImHpPy 1161) 5' -WT A C G TW-3' Hppy-~3-I~p_y-py-~_I~ppy 1162(3) 5' -WT A C G AW-3' HpPy-(3-ImPy-y-Hp-~-ImHpPy 1163(3) 5' -WT A C C TW-3' HpPyPyPyHp-y-PyImIm-(3-Py 1163(3p) 5' -WT A C C TW-3' Hp-(3-PyPyHp-y-PyImIm-(3-Py 1164(3) 5' -WT A C C AW-3' HpPyPyPyPy-y-HpImIm-p-Py 1164(3p) 5' -WT A C C AW-3' Hp-~3-PyPyPy-y-HpImIm-(3-Py 1165~i) 5' -WT A C G GW-3' HpPy-(3-ImIm-y-Py-(3-ImHpPy 1166(3) 5' -WT A C G CW-3' HpPy-(3-ImPy-y-Im-~3-ImHpPy 1167(3) 5' -WT A C C GW-3' HpPy-(3-PyIm-y-PyImIm-(3-Py TABLE 82:
10-ring Hairpin Polyamides for recognition of ?-by 5'-WTCWNNW-3' with R
substitutions DNA sequence aromatic amino acid sequence 11703) 5'-W T CT T A W-3' HpPyHpHpPy-y-HpPy-p-ImPy S 1170(3p)' S'-W T CT T A W-3' HpPy-~3-HpPy-y-HpPy-(3-ImPy 1171~i) 5'-W T CT T G W-3' HpPy-(3-HpIm-y-PyPy-~i-ImPy 1I72~i) 5'-W T CT T C W-3' HpPyHpHpPy-y-ImPy-(3-ImPy 1172(3p) 5'-W T CT T C W-3' HpPy-(3-HpPy-y-ImPy-(3-ImPy 1173(3) 5'-W T CT A T W-3' HpPyHpPyHp-y-PyHp-(3-ImPy 1173(3p) 5'-W T CT A T W-3' HpPy-~3-PyHp-y-PyHp-(3-ImPy 1174(3) 5'-W T CT A A W-3' HpPyHpPyPy-y-HpHp-(3-ImPy 1I74(3p) 5'-W T CT A A W-3' HpPy-~3-PyPy-y-HpHp-(3-ImPy 1175(3) 5'-W T CT A G W-3' HpPy-(3-PyIm-y-PyHp-(3-ImPy 1176J3) 5'-W T CT A C W-3' HpPyHpPyPy-y-ImHp-p-ImPy 1176(3p) 5'-W T CT A C W-3' HpPy-(3-PyPy-y-ImHp-(3-ImPy 1177(3) 5'-W T CT G T W-3' HpPy-(3-ImHp-y-PyPy-(3-ImPy 1178(3) 5'-W T CT G A W-3' HpPy-[3-ImPy-y-HpPy-[3-ImPy 11793) 5'-W T CT G G W-3' HpPy-(3-Imlm-y-PyPy-(3-ImPy 1180(3) 5'-W T CT G C W-3' HpPy-(3-ImPy-y-ImPy-(3-ImPy 1181(3) 5'-W T CT C T W-3' HpPyHpPyHp-y-PyIm-p-ImBy 1181~3p) 5'-W T CT C T W-3' HpPy-(3-PyHp-y-PyIm-p-ImPy 1182(3) 5'-W T CT C A W-3' HpPyHpPyPy-y-HpIm-[3-ImPy 1182~3p) 5'-W T CT C A W-3' HpPy-(3-PyPy-y-HpIm-p-ImPy 1183(3) 5'-W T CT C G W-3' HpPy-p-Pylm-y-PyIm-(3-ImPy 1184(3) 5'-W T CT C C W-3' HpPyHpPyPy-y-Imlm-(3-ImPy 1184~3p) 5'-W T CT C C W-3' ~ HpPy-j3-PyPy-y-Imlm-(3-ImPy 1185(3) 5'-W T CA T T W-3' HpPyPyHpHp-y-PyPy-(3-ImPy 1185~3p) 5'-W T CA T T W-3' HpPy-(3-HpHp-y-PyPy-~3-ImPy 1186(3) 5'-W T CA T A W-3' HpPyPyHpPy-y-HpPy-p-ImPy 1186(3p) 5'-W T CA T A W-3' HpPy-(3-HpPy-y-HpPy-(3-ImPy 11873) 5'-W T CA T G W-3' HpPy-p-HpIm-y-PyPy-(3-ImPy TABLE 82 (cont):
10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCWNNW-3' with substitutions DNA sequence aromatic amino acid sequence 1188) 5'-WT C A T CW-3' HpPyPyHpPy-y-ImPy--ImPy 1188p)~ 5'-WT C A T CW-3' HpPy--HpPy-y-ImPy--Impy 1189) 5'-WT C A A TW-3' HpPyPyPyHp-y-PyHp--ImPy 1189p) 5'-WT C A A TW-3' HpPy--pyHp-y-pyHp--ImPy 1190(3) 5'-WT C A A AW-3' HpPyPyPyPy-y-HpHp--ImPy 1190p) 5'-WT C A A AW-3' HpPy--PyPy-y-HpHp--ImPy 1191) 5'-WT C A A GW-3' HpPy--pyIm-y-PyHp--ImPy 1192) 5'-WT C A A CW-3' HppypyPyPy-y-ImHp--ImPy 1192p) 5'-WT C A A CW-3' HpPy--pypy-y-ImHp--ImPy 1193(3) 5'-WT C A G TW-3' HpPy--ImHp-y-PyPy--ImPy 1194) 5'-WT C A G AW-3' HpPy--ImPy-y-HpPy--ImPy IS 11953) 5'-WT C A G GW-3' HpPy--Imlm-y-PyPy--ImPy 1196) 5'-WT C A G CW-3' HpPy--ImPy-y-ImPy--ImPy 1197(3) 5'-WT C A C TW-3' HpPyPyPyHp-y-PyIm--ImPy 1197p) 5'-WT C A C TW-3' HpPy--PyHp-y-Pylm--ImPy 1198) 5'-WT C A C AW-3' HpPyPyPyPy-y-HpIm--ImPy 1198p) 5'-WT C A C AW-3' HpPy--PyPy-y-Hplm--ImPy 1199) 5'-WT C A C GW-3' HpPy--PyIm-y-PyIm--ImPy 1200) 5'-WT C A C CW-3' HpPyPyPyPy-y-ImIm--ImPy 1200p) 5'-WT C A C CW-3' HpPy--pypy-y-ImIm--ImPy TABLE 83:
10-ring Hairpin Polyamides for recognition of 7-by S'-WTCSNNW-3' with ~i substitutions DNA aromatic amino acid sequence sequence 1201(3) 5' -W TC G T T W-3' Hp-(3-ImHpHp-y-PyPy-J3-ImPy 1202(3) 5''-W TC G T A W-3' Hp-(3-ImHpPy-y-HpPy-(3-ImPy 12033) 5' -W TC G T G W-3' Hp-~3-ImHpIm-y-PyPy-/3-ImPy 1204(3) 5' -W TC G T C W-3' Hp-(3-ImHpPy-y-ImPy-(3-ImPy 1205(3) 5' -W TC G A T W-3' Hp-(3-ImPyHp-y-PyHp-~i-ImPy 1206(3) 5' -W TC G A A W-3' Hp-(3-ImPyPy-y-HpHp-(3-ImPy 1207(3) 5' -W TC G A G W-3' Hp-(3-ImPyIm-y-PyHp-~3-ImPy 1208~i) 5' -W TC G A C W-3' Hp-(3-ImPyPy-y-ImHp-(3-ImPy 12093) 5' -W TC G G T W-3' Hp-(3-ImImHp-y-PyPy-(3-ImPy 1210(3) 5' -W TC G G A W-3' Hp-~3-ImImPy-y-HpPy-R-ImPy 1211(3) 5' -W TC G C T W-3' Hp-(3-ImPyHp-y-Pylm-p-ImPy 12123) 5' -W TC G C A W-3' Hp-~3-ImPyPy-y-Hplm-(3-ImPy 12133) 5' -W TC C T T W-3' HpPyPyHpHp-y-Py-p-ImImPy 1213(3p) 5' -W TC C T T W-3' HpPyPy-~i-Hp-y-Py-(3-ImImPy 12143) 5' -W TC C T A W-3' HpPyPyHpPy-y-Hp-~-ImImPy 1214(3p) 5' -W TC C T A W-3' HpPyPy-(3-Py-y-Hp-(3-ImImPy 12153) 5' -W TC C T G W-3' HpPy-(3-HpIm-y-Py-(3-ImImPy 1216(3) 5' -W TC C T C W-3' HpPyPyHpPy-y-Im-~3-ImImPy 1216(3p) 5' -W TC C T C W-3' HpPyPy-~3-Py-y-Im-~3-ImImPy 1217(3) 5' -W TC C A T W-3' HpPyPyPyHp-y-Py-~3-ImImPy 1217~3p) 5' -W TC C A T W-3' HpPyPy-(3-Hp-y-Py-p-ImImPy 1218(3) 5' -W TC C A A W-3' HpPyPyPyPy-y-Hp-[3-ImImPy 1218(3p) 5' -W TC C A A W-3' HpPyP-(3-Py-y-Hp-~-ImImPy 12193) 5' -W TC C A G W-3' HpPy-[3-PyIm-y-Py-(3-ImImPy 1220(3) 5' -W TC C A C W-3' HpPyPyPyPy-y-Im-R-ImImPy 1220~3p) 5' -W TC C A C W-3' HpPyPy-~i-Py-y-Im-~3-ImImPy 1221(3) 5' -W TC C G T W-3' HpPy-p-ImHp-y-Py-(3-ImImPy 1222(3) 5' -W TC C G A W-3' HpPy-~3-ImPy-y-Hp-(3-ImImPy 1225(3) 5' -W TC G G G W-3' Hp-(3-ImImIm-y-PyPy-(3-ImPy TABLE 83 (cont): 10-ring Hairpin Polyamides for recognition of 7-by 5'-WTCSNNW-3' with (3 substitutions DNA sequence aromatic amino acid sequence 1226(3) 5' -W T C G G C W-3' Hp-~3-ImImPy-y-ImPy-(3-ImPy 12273) 5' -W T C G C G W-3' Hp-(3-ImPyIm-y-Pyim-(3-ImPy 12280 5' -W T C G C C W-3' Hp-(3-ImPyPy-y-Imlm-y-ImPy 1229(3) 5' -W T C C G G W-3' H p P Yrj-ImIm-y-Py-(3-ImImPy 1230~i) 5' -W T C C G C W-3' HpPy-(3-ImPy-y-Im-~i-ImImPy 1231(3) 5' -W T C C C G W-3' HpPy-(3-pyIm-y-PyImImImPy If the process described above of designing a preferred polyamide molecule comprising four or five carboxamide binding pairs does not produce a selective polyamide that binds to the target identified DNA sequence with subnanomolar affinity and with a selectivity over mismatch sequences of greater than a factor of ten, a polyamide molecule X1X2X3X4XSX6-Y-X7X8X9X1OX11X12 having six carboxamide binding pairs can be designed that is selective for an eight base pair identified target 5'-WNTI~JNNNW-3' sequence.
The design and synthesis of six binding pair polyamides is essentially the same as that of the 2o four and five binding pair polyamides described above.
The polyamide design process for six carboxamide binding pair polyamides is shown schematically in Figure 10 A and the upper half of l OB. The method for chosing the residues that can be replaced by a (3-alanine residue is shown schematically in the lower half of Figure 10 B and in Figure 11. The 1024 possible 12-ring hairpins which target the 1024 5'-GNNNNN-3' core sequences are listed in Tables 84-I 15. Each DNA sequence entry can be correlated to its corresponding polyamide recognition sequence using the process outlined in this figure. The 1024 possible I2-ring hairpins which target the 1024 5'-CNNNNN-3' core sequences are listed in Tables 116-147. Each DNA sequence entry can be correlated to its corresponding polyamide 3o recognition sequence using the process outlined in this figure.
Figure 11 shows a process for replacement of aromatic amino acid residues with aliphatic (3-aIanine 'spring' residues in order to enhance the DNA binding properties of 12-ring hairpin polyamides. Selective placement of an aliphatic (3-alanine (/3) residue paired side-by-side with either a pyrrole (Py) or imidazoIe (Im) aromatic amino acid or another (3-alanine residue is found to compensate for sequence composition effects for recognition of the minor groove of DNA by hairpin pyrrole-imidazole polyamides. If an all-ring polyamide has been found to have an affinity which is not subnanomolar, or a specificity versus mismatch sequences which is less than 10-fold it may be caused by DNA sequence-composition effects which can be tuned out by replacement of an aromatic amino acid with an aliphatic j3-alanine spring.
Rules have been determined to help determine the exact placement of the (3-spring residues.
For example, within the 12-ring template, it is only beneficial to place ~3-alanine within positions X2, X3, X4, XS, Xg, X9, and X10 X11,. No more than two (3-alanine residues may be placed within a single hairpin structure. No more than a single (3-residue may be placed within each individual to poiyamide subunit. Tables 148-1079 list derivatives of sequences (1233-2224) labeled (1223(3-2224[3) which contain two (3-alanine residues assigned according to the process outlined in Figure 11A & B.
WO 98/37067 , PCT/US98/01714 1 AtiLl; 12-ring 84: Hairpin Polyamides for recognition of 8-by 5'-WGGGWNNW-3' DNA aromatic amino acid sequence sequence 1233) 5'-W GG G T T T W-3' ImImImHpHpHp-y-PYPYPYPYPYpy 1234) 5'~-W GG G T T A W-3' ImImImHpHpPy-y-HpPyPYPyPyPy 1235) 5'-W GG G T T G W-3' ImImImHpHpIm-y-Pypypypypypy 1236) 5'-W GG G T T C W-3' ImTmImHpHppy-y-ImpyPYPypypy 1237) 5'-W GG G T A T W-3' ImImImHpPYHp-y-PyHpPyPyPyPy 1238) 5' GG G T A A W-3' ImImImHpPyPy-y-HpHpPyPYPYPy -W
1239) 5'-W GG G T A G W-3' ImImImHpPyIm-y-PyHpPYpypypY
1240) 5'-W GG G T A C W-3' ImImImHpPyPy-y-ImHpPYPYPYPy 1241) 5'-W GG G T G T W-3' ImImImHpImHp-y-pypypypypypy 1242} 5'-W GG G T G A W-3' ImImImHpImPy-y-HpPyPyPyPyPy 1243) 5'-W GG G T G G W-3' ImImImHpImIm-y-PyPYPyPyPYPy 1244) 5' GG G T G C W-3' ImImImHpImPy-y-ImPyPYPyPyPy -W
1245) 5' GG G T C T W-3' ImImImHpPyHp-y-PyImPyPyPyPy -W
1246) 5'-W GG G T C A W-3' ImImImHpPYPy-y-HpImPYPYPYPy 1247) 5'-W GG G T C G W-3' ImImImHpPyIm-y-pyImPyPyPYPy 1248) 5'-W GG G T C C W-3' ImImImHpPYPy-y-ImImPyPYPyPy 1249) 5'-W GG G A T T W-3' ImImImPyHpHp-y-PYPyHpPyPyPy 1250) 5'-W GG G A T A W-3' ImImImPyHpPy-y-HpPyHpPyPyPy 1251) 5'-W GG G A T G W-3' TmImImPyHpIm-y-PypyHpPyPyPy 1252) 5'-W GG G A T C W-3' ImImImPyHpPy-y-ImPyHpPyPyPy 1253) 5'-W GG G A A T W-3' ImImImPyPyHp-y-PyHpHpPYPyPy 1254) 5'-W GG G A A A W-3' ImImImPyPyPy-y-HpHpHppyPyPy 1255) 5'-W GG G A A G W-3' ImImImPyPyIm-y-PyHpHpPYPyPy 1256) 5'-W GG G A A C W-3' ImImImPyPYPy-y-ImHpHpPYPyPy 1257) 5'-W GG G A G T W-3' ImImImPyImHp-y-PyPyHpPyPYPy 1258) 5'-W GG G A G A W-3' ImImImPyImPy-y-HpPyHpPyPyPy 1259) 5'-W GG G A G G W-3' ImImImPyImIm-y-P
P
H
P
P
p y y p y y y 12 60 5' GG G A G C W-3 ImImImPyImPy-y- ImPYHpPyPyPy ) -W ' 1261) 5'-W GG G A C T W-3' ImImImPyPyHp-y-PyImHpPYPYPY
1262) 5'-W GG G A C A W-3' ImImImPyPypy-y-HpImHpPyPyPy 1263) 5'-W GG G A C G W-3' ImImImPyPyIm-y-PyImHpPypypy 1264) 5'-W GG G A C C W-3' ImImImPyPYPy-y-ImImHpPyPYPy TABLE
85:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGGSNNW-3' ' DNA aromatic amino acid sequence sequence 1265) 5' -W GG G G T T W-3' ImImImImHpHp-y-PyPyPyPyPyPy 1266) 5' -W GG G G T A W-3' ImImImImHpPy-y-HpPyPyPyPyPy S 1267) 5'~-W GG G G T G W-3' ImImImImHpIm-y-PyPyPyPyPyPy 1268} 5' -W GG G G T C W-3' ImImImImHpPy-y-ImPyPyPyPyPy 1269) 5' -W GG G G A T W-3' ImImImImPyHp-y-PyHpPyPyPyPy 1270) 5' -W GG G G A A W-3' ImImImImPyPy-y-HpHpPyPyPyPy 1271) 5' -W GG G G A G W-3' ImImImImPyIm-y-PyHpPyPyPyPy 1272) 5' -W GG G G A C W-3' ImImImImPyPy-y-ImHpPypyPyPy 1273} 5' -W GG G G G T W-3' ImImImImImHp-y-PyPypypypypy 1274) 5' -W GG G G G A W-3' ImImImImImPy-y-HpPyPyPyPyPy 1275) 5' -W GG G G C T W-3' ImImImImPyHp-y-PyImPyPyPyPy 1276) 5' -W GG G G C A W-3' ImImImImPyPy-y-HpImPyPyPyPy 1277) 5' -W GG G C T T W-3' ImImImPyHpHp-y-PyPyImPyPyPy 1278} 5' -W GG G C T A W-3' ImImImPyHpPy-y-HpPyImPyPyPy 1279) 5' -W GG G C T G W-3' ImImImPyHpIm-y-PyPyImPyPyPy 1280) 5' -W GG G C T C W-3' ImImImPyHpPy-y-ImPyImPyPyPy 1281) 5' -W GG G C A T W-3' ImImImPypyHp-y-PyHpImPyPyPy 1282) 5' -W GG G C A A W-3' ImImImPyPyPy-y-HpHpImPyPyPy 1283) 5' -W GG G C A G W-3' ImImImPyPyIm-y-PyHpImPyPyPy 1284) 5' -W GG G C A C W-3' ImImImPyPyPy-y-ImHpImPyPyPy 1285) 5' -W GG G C G T W-3' ImImImPyImHp-y-PyPyImPyPyPy 12 86 5' -W GG G C G A W-3 ImImImPyImPy-y-HpPyImPyPyPy ) ' 1287) 5' -W GG G C C T W-3' ImImImPyPyHp-y-PyImImPyPyPy 1288) 5' -W GG G C C A W-3' ImImImPyPyPy-y-HpImImPyPyPy G4 9 5' -W GG G G G G W-3 ImImImImImIm-y-PyPyPyPyPyPy ) ' G50) 5' -W GG G G G C W-3' ImImImImImPy-y-ImPyPyPyPyPy G51) 5' -W GG G G C G W-3' ImImImImPyIm-y-PyImPyPyPyPy G52) 5' -W GG G G C C W-3' ImImImImPyPy-y-ImImPyPyPyPy G53) 5' -W GG G C G G W-3' ImImImPyImIm-y-PyPyImPyPyPy G54 ) 5' -W GG G C G C W-3 ImImImPyImPy-y-ImPyImPyPyPy ' G55) 5' -W GG G C C G W-3' ImImImPyPyIm-y-PyImImPyPyPy G56) 5' -W GG G C C C W-3' ImImImPypyPy-y-ImImImPyPyPy TABLE
86:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGTWNNW-3' DNA aromatic amino acid sequence sequence 1289) 5' -WG G T T TT W-3' ImImHpHpHpHp-y-PyPyPyPyPypy 1290) 5' '-WG G T T TA W-3' ImImHpHpHpPy-y-HpPyPyPyPyPy 1291) 5' -WG G T T TG W-3' ImImHpHpHpIm-y-PyPyPyPyPyPy 1292) 5' -WG G T T TC W-3' ImImHpApHpPy-y-ImPyPyPyPyPy 1293) 5' -WG G T T AT W-3' ImImHpHpPyHp-y-PyHpPyPyPyPy 12 94 5' -WG G T T AA W-3 ImImHpHpPyPy-y-HpHpPyPyPyPy ) ' 1295) 5' -WG G T T AG W-3' ImImHpHpPyIm-y-PyHpPyPyPyPy 1296) 5' -WG G T T AC W-3' ImImHpHpPyPy-y-ImHppyPyPyPy 1297) 5' -WG G T T GT W-3' ImImHpHpImHp-y-PyPyPyPyPyPy 1298) 5' -WG G T T GA W-3' ImImHpHpImPy-y-HpPypyPyPyPy 1299) 5' -WG G T T GG W-3' ImImHpHpImIm-y-PyPyPyPypypy 1300) 5' -WG G T T GC W-3' ImImHpHpImPy-y-ImpyPyPyPypy 1301) 5' -WG G T T CT W-3' ImImHpHpPyHp-y-PyImPyPyPyPy 1302) 5' -WG G T T CA W-3' ImImHpHpPyPy-y-HpImPyPyPyPy 1303) 5' -WG G T T CG W-3' ImImHpHppylm-y-PyImPyPyPyPy 1304) 5' -WG G T T CC W-3' ImImHpHpPyPy-y-ImImPypyPyPy 1305) 5' -WG G T A TT W-3' ImImHpPyHpHp-y-PyPyHpPyPyPy 1306) 5' -WG G T A TA W-3' ImImHpPyHpPy-y-HpPyHpPyPyPy 1307) 5' -WG G T A TG W-3' ImImHpPyHpIm-y-PyPyHpPyPyPy 1308) 5' -WG G T A TC W-3' ImImHpPyHpPy-y-ImPyHpPyPyPy 1309) 5' -WG G T A AT W-3' ImImHpPyPyHp-y-PyHpHpPyPyPy 1310 5' -WG G T A AA W-3 ImImHpPyPyPy-y-HpHpHpPyPyPy ) ' 1311) 5' -WG G T A AG W-3' ImImHpPyPyIm-y-PyHpHpPyPyPy 1312) 5' -WG G T A AC W-3' ImImHpPyPyPy-y-ImHpHpPyPyPy 1313) 5' -WG G T A GT W-3' ImImHpPyImHp-y-PyPyHpPyPyPy a 1314) 5' -WG G T A GA W-3' ImImHpPyImPy-y-HpPyHpPyPyPy 1315) 5' -WG G T A GG W-3' ImImHpPyImIm-y-PyPyHpPyPyPy 1316) 5' -WG G T A GC W-3' ImImHpPyImPy-y-ImPyHpPyPyPy 1317) 5' -WG G T A CT W-3' ImImHpPyPyHp-y-pyImHpPyPyPy 1318) 5' -WG G T A CA W-3' ImImHpPyPyPy-y-HpImHppyPyPy 1319) 5' -WG G T A CG W-3' ImImHpPyPyIm-y-PyImHpPyPyPy 1320) 5' -WG G T A CC W-3' ImImHpPyPyPy-y-ImImHpPyPyPy TABLE
87:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGTSNNW-3' DNA aromatic amino acid sequence sequence 1321) 5' -W G GT G T T W-3' ImImHpImHpHp-y-PyPyPyPyPyPy 1322) 5' -W G GT G T A W-3' ImImHpImHpPy-y_Hppypypypypy 1323) 5' -W G GT G T G W-3' ImImHpImHpIm-y-PyPyPyPyPyPy 1324) 5' -W G GT G T C W-3' ImImHpImHpPy-y-ImPyPyPyPyPy 1325) 5' -W G GT G A T W-3' ImImHpImPyHp-y-PyHpPyPyPyPy 1326) 5' -W G GT G A A W-3' ImImHpImPyPy-y-HpHpPyPyPyPy 1327) 5' -W G GT G A G W-3' ImImHpImPyIm-y-PyHpPyPyPyPy 1328) 5' -W G GT G A C W-3' ImImHpImPyPy-y-ImHpPyPyPyPy 1329) 5' -W G GT G G T W-3' ImImHpImImHp-y-PyPyPyPyPyPy 1330) 5' -W G GT G G A W-3' ImImHpImImPy-y-HpPyPyPyPyPy 1331) 5' -W G GT G C T W-3' ImImHpImPyHp-y-PyImPyPyPyPy 1332) 5' -W G GT G C A W-3' ImImHpImPyPy-y-HpImPyPyPyPy 1333) 5' -W G GT G G G W-3' ImImApImImIm-y-PyPyPyPyPyPy 1334) 5' -W G GT G G C W-3' ImImHpImImPy-y-ImPyPyPyPyPy 1335) 5' -W G GT G C G W-3' ImImHpImPyIm-y-PyImPyPyPyPy 1336) 5' -W G GT G C C W-3' ImImHpImPyPy-y-ImImPyPyPyPy 1337) 5' -W G GT C T T W-3' ImImHpPyHpHp-y-PyPyImPyPyPy 1338) 5' -W G GT C T A W-3' ImImHpPyHpPy-y-HpPyImPyPyPy 1339) 5' -W G GT C T G W-3' ImImHpPyHpIm-y-PyPyImPyPyPy 1340) 5' -W G GT C T C W-3' ImImHpPyHpPy-y-ImPyImPyPyPy 1341) 5' -W G GT C A T W-3' ImImHpPyPyHp-y-PyHpImPyPyPy 1342) 5' -W G GT C A A W-3' ImImHpPyPyPy-y-HpHpImPyPypy 1343) 5' -W G GT C A G W-3' ImImHpPyPyIm-y-PyHpImPyPyPy 1344) 5' -W G GT C A C W-3' ImImHpPyPyPy-y-ImHpImPyPyPy 1345) 5' -W G GT C G T W-3' ImImHpPyImHp-y-PyPyImPyPyPy 1346) 5' -W G GT C G A W-3' ImImHpPyImPy-y-HpPyImPyPyPy 1347) 5' -W G GT C C T W-3' ImImHpPyPyHp-y-PyImImPyPyPy 1348) 5' -W G GT C C A W-3' ImImHpPyPyPy-y-HpImImPyPyPy 1349) 5' -W G GT C G G W-3' ImImHpPyImIm-y-PyPyimPyPyPy 1350) 5' -W G GT C G C W-3' ImImHpPyImPy-y-ImPyImPyPyPy 1351) 5' -W G GT C C G W-3' ImImHpPyPyIm-y-PyImImpyPyPy 1352) 5' -W G GT C C C W-3' ImImHpPyPyPy-y-ImImImPyPyPy lAt3Ll;
~i8:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGAWNNW-3' DNA aromatic amino acid sequence sequence 1353) 5'-W G G A T TT W-3' ImImPyHpHpHp-y-PyPyPyHpPyPy 1354) 5' G G A T TA W-3' ImImPyHpHpPy-y-HpPyPyHpPyPy -W
1355) 5' G G A T TG W-3' ImImPyHpHpIm-y-PyPyPyHpPyPy -W
1356) 5' G G A T TC W-3' ImImPyHpHpPy-y-ImPyPyHpPyPy -W
1357 5' G G A T AT W-3 ImImPyHpPyHp-y-PyHpPyHpPyPy ) -W ' 1358) 5' G G A T AA W-3' ImImPyHpPyPy-y-HpHpPyHppyPy -W
1359) 5' G G A T AG W-3' ImImPyHpPyIm-y-PyHpPyHpPyPy -W
1360) 5'-W G G A T AC W-3' ImImPyHpPyPy-y-ImHpPyHpPyPy 1361) 5' G G A T GT W-3' ImImPyHpImHp-y-pypypyHpPyPy -W
1362) 5' G G A T GA W-3' ImImPyHpImPy-y-HpPyPyHpPyPy -W
1363) 5'-W G G A T GG W-3' ImImPyHpImIm-y-PyPyPyHpPyPy IS 1364) 5'-W G G A T GC W-3' ImImPyHpImPy-y-ImPyPyHpPyPy 1365) 5' G G A T CT W-3' ImImPyHpPyHp-y-PyImPyHpPyPy -W
1366) 5' G G A T CA W-3' ImImPyHpPyPy-y-HpImPyHpPyPy -W
1367) 5'-W G G A T CG W-3' imImPyHpPyIm-y-PyImPyHpPyPy 1368) 5'-W G G A T CC W-3' ImImPyHpPyPy-y-ImImPyHpPyPy 1369) 5' G G A A TT W-3' ImImPyPyHpHp-y-PyPyHpHpPyPy -W
1370) 5'-W G G A A TA W-3' ImImPyPyHpPy-y-HpPyHpHpPyPy 1371) 5' G G A A TG W-3' ImImPyPyHpIm-y-PyPyHpHpPyPy -W
1372) 5' G G A A TC W-3' ImImPyPyHpPy-y-ImPyHpHpPyPy -W
1373) 5'-W G G A A AT W-3' ImImPyPyPyHp-y-PyHpHpHpPyPy 1374) 5'-W G G A A AA W-3' ImImPyPypypy-y-HpHpHpHpPyPy 1375) 5' G G A A AG W-3' ImImPyPypyIm-y-PyHpHpHpPyPy -W
1376) 5' G G A A AC W-3' ImImPyPyPyPy-y-ImHpHpHpPyPy -W
1377) 5'-W G G A A GT W-3' ImImPyPyImHp-y-PyPyHpHpPyPy 1378) 5' G G A A GA W-3' ImImPyPyImPy-y-HpPyHpHpPyPy -W
1379) 5' G G A A GG W-3' ImImPyPyImIm-y-PyPyHpHpPyPy -W
13 8 5' G G A A GC W- 3 ImImPyPyImPy-y- ImPyHpHpPyPy 0 ) -W ' 1381) 5' G G A A CT W-3' ImImPyPyPyHp-y-PyImApHpPyPy -W
1382) 5' G G A A CA W-3' ImImPypypypy-y_HpI~pHppyPy -W
1383} 5' G G A A CG W-3' ImImPyPyPyIm-y-PyImHpHpPyPy -W
1384) 5'-W G G A A CC W-3' ImImPyPyPyPy-y-ImImHpHpPyPy TABLE
89:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGASNNW-3' DNA aromatic amino acid sequence sequence 1385} 5' -WG G A G TT W-3' ImImPyImHpHp-y-PyPypyHpPyPy 1386) 5' -WG G A G TA W-3' ImImPyImHpPy-y-HpPyPyHpPyPy 1387} 5' -WG G A G TG W-3' ImImPyImHpIm-y-PyPyPyHpPyPy 1388) 5' -WG G A G TC W-3' ImImPyImHpPy-y-ImPyPyHpPyPy 1389) 5' -WG G A G AT W-3' Im3mPyImPyHp-y-PyHpPyHpPyPy 1390} 5' -WG G A G AA W-3' ImImPyImPyPy-y-HpHpPyHpPyPy 1391) 5' -WG G A G AG W-3' ImImPyImPyIm-y-PyHpPyHpPyPy 1392) 5' -WG G A G AC W-3' ImImPyImPyPy-y-ImHpPyHpPyPy 1393) 5' -WG G A G GT W-3' ImImPyImImHp-y-PyPyPyHpPyPy 13 94 5' -WG G A G GA W-3 ' ImImPyImImPy-y-HpPyPyHppyPy ) 1395) 5' -WG G A G CT w-3' ImImPyImPyHp-y-PyImPyHpPyPy 1396) 5' -WG G A G CA W-3' ImImPyImPyPy-y-HpImPyHpPyPy 1397) 5' -WG G A G GG W-3' ImImPyImImIm-y-PyPyPyHppyPy 13 9 5' -WG G A G GC W-3 ' ImImPyImImPy-y- ImPyPyHpPyPy 8 ) 1399) 5' -WG G A G CG W-3' ImImPyImPyIm-y-PyImPyHpPyPy 1400) 5' -WG G A G CC W-3' ImImPyImPyPy-y-ImImPyHpPyPy 1401) 5' -WG G A C TT W-3' ImImPyPyHpHp-y-PyPyImHpPyPy 1402) 5' -WG G A C TA W-3' ImImPyPyHpPy-y-HpPyImHpPyPy 1403 5' -WG G A C TG W-3' ImImPyPyHpIm-y-PyPyImHpPyPy ) 1404) 5' -WG G A C TC W-3' ImImPyPyHpPy-y-ImPyImHpPyPy 1405) 5' -WG G A C AT W-3' ImImPyPyPyHp-y-PyHpImHpPyPy 1406) 5' -WG G A C AA W-3' ImImPyPyPyPy-y-HpHpImHpPyPy 1407) 5' -WG G A C AG W-3' ImImPyPyPyIm-y-PyHpImHpPyPy 1408} 5' -WG G A C AC W-3' ImImPyPyPyPy-y-ImHpImHpPyPy 1409} 5' -WG G A C GT W-3' ImImPyPyImHp-y-PypyImHpPyPy 1410 5' -WG G A C GA W-3 ' ImImPyPyImPy-y-HpPyImHpPyPy ) 1411) 5' -WG G A C CT W-3' ImImPyPyPyHp-y-PyImImHpPyPy 1412 5' -WG G A C CA W- 3 ImImPyPyPyPy-y-HpImImHpPypy ) ' 1413) 5' -WG G A C GG W-3' ImImPyPyImIm-y-PyPyImHpPyPy 1414) 5' -WG G A C GC W-3' ImImPyPyImPy-y-ImPyImHpPypy 1415) 5' -WG G A C CG W-3' ImImPyPyPyIm-y-PyImImHpPyPy 1416) 5' -WG G A C CC W-3' ImImPyPyPyPy-y-ImImImFippyPy TABLE
90:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGCWNNW-3' DNA aromatic amino acid sequence sequence 1417) 5' -W GG C T T T W-3' ImImPyHpHpHp-y-PyPyPyImPyPy 1418 5' -W GG C T T A W-3 ImImPyHpHpPy-y-HpPyPyImPyPy ) ' 1419) 5' -W GG C T T G W-3' ImImPyHpHpIm-y-PyPyPyImPyPy 1420) 5' -W GG C T T C W-3' ImImPyHpHpPy-y-ImPyPyImPyPy 1421) 5' -W GG C T A T W-3' ImImPyHpPyHp-y-PyHpPyImPyPy 1422) 5' -W GG C T A A W-3' ImImPyHpPyPy-y-HpHpPyImPyPy 1423) 5' -W GG C T A G W-3' ImImPyHpPyIm-y-PyHpPyImPyPy 1424) 5' -W GG C T A C W-3' ImImPyHpPyPy-y-ImHpPyImPyPy 1425) 5' -W GG C T G T W-3' ImImPyHpImHp-y-PyPyPyImPyPy 1426) 5' -W GG C T G A W-3' ImImPyHpImPy-y-HpPyPyImPyPy 1427) 5' -W GG C T G G W-3' ImImPyHpImIm-y-PyPyPyImPyPy 1428) 5' -W GG C T G C W-3' ImImPyHpImPy-y-ImPyPyImPyPy 1429) 5' -W GG C T C T W-3' ImImPyHpPyHp-y-PyImPyImPyPy 1430) 5' -W GG C T C A W-3' ImImPyHpPyPy-y-HpImPyImPyPy 143I) 5' -W GG C T C G W-3' ImImPyHpPyIm-y-PyImPyImPyPy 1432) 5' -W GG C T C C W-3' ImImPyHpPyPy-y-ImImPyImPyPy 1433) 5' -W GG C A T T W-3' ImImPyPyHpHp-y-PyPyHpImPyPy 1434) 5' -W GG C A T A W-3' ImImPyPyHpPy-y-HpPyHpImPyPy 1435) 5' -W GG C A T G W-3' ImImPyPyHpIm-y-PyPyHpImPyPy 1436) 5' -W GG C A T C W-3' ImImPyPyHpPy-y-ImPyHpImPyPy 1437) 5' -W GG C A A T W-3' ImImpyPyPyHp-y-PyHpHpImPyPy 1438) 5' -W GG C A A A W-3' ImImPyPyPyPy-y-HpHpHpImPyPy 1439) 5' -W GG C A A G W-3' ImImPyPyPyIm-y-PyHpHpImPyPy 1440) 5' -W GG C A A C W-3' ImImPyPyPyPy-y-ImHpHpImPyPy 1441) 5' -W GG C A G T W-3' ImImPyPyImHp-y-PyPyHpImPyPy 1442) 5' -W GG C A G A W-3' ImImPyPyImPy-y-HpPyHpImPyPy 1443) 5' -W GG C A G G W-3' ImImPyPyImIm-y-PyPyHpImPyPy 1444) 5' -W GG C A G C W-3' ImImPyPyimPy-y -ImPyHpImPyPy 1445) 5' -W GG C A C T W-3' ImImPyPyPyHp-y-PyImHpImPyPy 1446) 5' -W GG C A C A W-3' ImImPyPyPyPy-y-HpImHpImPyPy 1447) 5' -W GG C A C G W-3' ImImPyPyPyIm-y-PyImHpImPyPy 1448) 5' -W GG C A C C W-3' ImImPyPyPyPy-y-ImImHpImPyPy TABLE
91:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGGCSNNW-3' DNA aromatic amino acid sequence sequence 1449) 5' GG C G T T W-3' ImImPyImHpHp-y-PyPyPyImPyPy -W
1450) 5' GG C G T A W-3' ImImPyImHpPy-y-HpPyPyImPyPy -W
1451) 5' GG C G T G W-3' ImImPyImHpIm-y-PyPyPyImPyPy -W
1452) 5' GG C G T C W-3' ImImPyImHpPy-y-ImPyPyImPyPy -W
1453) 5' GG C G A T W-3' ImImPyImPyHp-y-PyHpPyImPyPy -W
1454) 5'-W GG C G A A W-3' ImImPyImPyPy-y-HpHpPyImPyPy 1455) 5' GG C G A G W-3' ImImPyImPyIm-y-PyHpPyImPyPy -W
1456) 5' GG C G A C W-3' ImImPyImPyPy-y-ImHpPyImPyPy -W
1457) 5'-W GG C G G T W-3' ImImPyImImHp-y-PyPyPyImPyPy 1458) 5' GG C G G A W-3' ImImPyImImPy-y-HpPyPyImPyPy -W
1459) 5' GG C G C T W-3' ImImPyImPyHp-y-PyImPyImPyPy -W
1460) 5' GG C G C A W-3' ImImPyImPyPy-y-HpImPyImPyPy -W
1461) 5' GG C C T T W-3' ImImPyPyHpHp-y-PyPyImImPyPy -W
1462) 5' GG C C T A W-3' ImImPyPyHpPy-y-HpPyImImPyPy -W
1463 5' GG C C T G W-3' ImImPyPyHpIm-y-PyPyImImPyPy ) -W
1464) 5' GG C C T C W-3' ImImPyPyHpPy-y-ImPyImImPyPy -W
1465) 5' GG C C A T W-3' ImImPyPyPyHp-y-PyHpImImPyPy -W
1466) 5' GG C C A A W-3' ImImPyPyPyPy-y-HpHpImImPyPy -W
1467) 5'-W GG C C A G W-3' ImImPyPyPyIm-y-PyHpImImPyPy 1468) 5' GG C C A C W-3' ImImPyPyPyPy-y-ImHpImImPyPy -W
1469) 5' GG C C G T W-3' ImImPyPyImHp-y-PyPyImImPyPy -W
1470) 5' GG C C G A W-3' ImImPyPyImPy-y-HpPyImImPyPy -W
1471) 5' GG C C C T W-3' ImImPyPyPyHp-y-PyImImImPyPy -W
1472) 5' GG C C C A W-3' ImImPyPyPyPy-y-HpImImImPyPy -W
G57) 5' GG C G G G W-3' ImImPyImImIm-y-PyPyPyImPyPy -W
G58) 5' GG C G G C W-3' ImImPyImImPy-y-ImPyPyImPyPy -W
G59) 5' GG C G C G W-3' ImImPyImPyIm-y-PyImPyImPyPy -W
G60) 5' GG C G C C W-3' ImImPyImPyPy-y-ImImPyImPyPy -W
G61) 5' GG C C G G W-3' ImImPyPyImIm-y-PyPyImImPyPy -W
G62) 5' GG C C G C W-3' ImImPyPyImPy-y-ImPyImImPyPy -W
G63) 5' GG C C C G W-3' ImImPyPyPyIm-y-PyImImImPyPy -W
G64) 5' GG C C C C W-3' ImImPyPyPyPy-y-ImImImImPyPy -W
WO 98!37067 PCT/US98/01714 TABLE
92:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCGWNNW-3' DNA aromatic amino acid sequence sequence 1473) 5' -W G C GT T T W-3' ImPyImHpHpHp-y-PyPyPyPyImPy .
1474) 5' -W G C GT T A W-3' ImPyImHpHpPy-y-HppypyPyImPy 1475) 5' -W G C GT T G W-3' ImPyImHpHpIm-y-PyPypypylmpy 1476) 5' -W G C GT T C W-3' ImPyImHpHpPy-y-ImPyPyPyImPy 1477) 5' -W G C GT A T W-3' ImPyImHpPyHp-y-PyHpPyPyImPy 1478) 5' -W G C GT A A W-3' ImPyImHpPyPy-y-HpHpPyPyImPy 1479) 5' -W G C GT A G W-3' ImPyImHpPyIm-y-PyHpPyPyImPy 1480) 5' -W G C GT A C W-3' ImPyImHpPyPy-y-ImHpPyPyImPy 1481} 5' -W G C GT G T W-3' ImPyImHpImHp-y-PyPyPypyImPy 1482) 5' -W G C GT G A W-3' ImPyImHpImPy-y-HpPyPypyImPy 1483) 5' -W G C GT G G W-3' ImPyImHpImIm-y-PypyPyPyImPy 1484) 5' -W G C GT G C W-3' ImPyImfipImPy-y-ImPyPyPyImPy 1485) 5' -W G C GT C T W-3' ImPyImHpPyHp-y-PyImPyPyImPy 1486 5' -W G C GT C A W-3' ImpyImHpPyPy-y-HpImPyPyImPy ) 1487) 5' -W G C GT C G W-3' ImPyImHpPyIm-y-PyImpyPyImPy 1488) 5' -W G C GT C C W-3' ImPyImHpPyPy-y-ImimPyPyImPy 1489) 5' -W G C GA T T W-3' ImPyImPyHpHp-y-PyPyHpPyImPy 1490) 5' -W G C GA T A W-3' ImPyImPyHpPy-y-HpPyHpPyImPy 1491) 5' -W G C GA T G W-3' ImPyImPyHpIm-y-PyPyHpPyImPy 1492) 5' -W G C GA T C W-3' ImPyImPyHpPy-y-ImPyHpPyImPy 1493) 5' -W G C GA A T W-3' ImPyImPyPyHp-y-pyHpHpPyImPy 1494) 5' -W G C GA A A W-3' ImPyImPyPypy-y-HpHpHpPyImPy 1495) 5' -W G C GA A G W-3' ImPyImpypylm-y-PyHpHpPyImPy 1496) 5' -W G C GA A C W-3' ImPyImPyPyPy-y-ImHpHppyImPy 1497) 5' -W G C GA G T W-3' ImpyImPyImHp-y-PypyHpPyImPy 1498) 5' -W G C GA G A W-3' ImPyImPyImpy-y-HpPyHpPyImPy 1499) 5' -W G C GA G G W-3' ImPyImPyImIm-y-PyPyHpPyImPy 1490) 5' -W G C GA G C W-3' ImPyImPyImpy-y-ImPyHpPyImPy 1501) 5' -W G C GA C T w-3' ImPyImPyPyHp-y-PyImHpPyImPy 1502) 5' -W G C GA C A W-3' ImPyImPyPyPy-y-HpImHpPyImPy _ 1503) 5' -W G C GA C G W-3' ImPyImPyPyIm-y-PyImHpPyImPy 1504) 5' -W G C GA C C W-3' ImPyImPyPyPy-y-ImImHpPyImPy TABLE
93:
I2-ring Hairpin Polyamides for recognition of 8-by 5'-WGCGSNNW-3' DNA aromatic amino acid sequence sequence 1505) 5' -WG C G G T T W-3' ImPyImImHpHp-y-PyPyPyPyImPy 1506) 5' -WG C G G T A W-3' ImPyImImHpPy-y-HpPyPyPyImPy 1507) 5' -WG C G G T G W-3' ImPyImImHpIm-y-PyPyPyPyImPy 1508) 5' -WG C G G T C W-3' ImPyImImHpPy-y-ImPyPyPyImPy 1509) 5' -WG C G G A T W-3' ImPyImImPyHp-y-PyHpPyPyImPy 1510) 5' -WG C G G A A W-3' ImPyImImPyPy-y-HpHpPyPyImPy 1511) 5' -WG C G G A G W-3' ImPyImImPyIm-y-PyHpPyPyImPy 1512) 5' -WG C G G A C W-3' ImPyImImPyPy-y-ImHpPyPyImPy 1513) 5' -WG C G G G T W-3' ImPyImImImHp-y-PyPyPyPyImPy 1514 5' -WG C G G G A W-3 ImPyImImImPy-y-HpPyPyPyImPy ) ' 1515) 5' -WG C G G C T W-3' ImPyImImPyHp-y-PyImPyPyImPy IS 1516) 5' -WG C G G C A W-3' ImPyImImPyPy-y-HpImPyPyImPy 1517) 5' -WG C G C T T W-3' ImPyImPyHpHp-y-PyPyImPyImPy 1518) 5' -WG C G C T A W-3' ImPyImPyHpPy-y-HpPyImPyImPy 1519) 5' -WG C G C T G W-3' ImPyImPyHpIm-y-PyPyImPyImPy 1520) 5' -WG C G C T C W-3' ImPyImPyHpPy-y-ImPyImPyImPy 1521) 5' -WG C G C A T W-3' ImPyImPyPyHp-y-PyHpImPyImPy 1522) 5' -WG C G C A A W-3' ImPyImPyPyPy-y-HpHpImPyImPy 1523) 5' -WG C G C A G W-3' ImPyImPyPyIm-y-PyHpImPyImPy 1524) 5' -WG C G C A C W-3' ImPyImPyPyPy-y-ImHpImPyImPy 1525) 5' -WG C G C G T W-3' ImPyImPyImHp-y-PyPyImPyImPy 1526) 5' -WG C G C G A W-3' ImPyImPyImPy-y-HpPyImPyImPy 1527) 5' -WG C G C C T W-3' ImPyImPyPyHp-y-PyImImPyImPy 1528) 5' -WG C G C C A W-3' ImPyImPyPyPy-y-HpImImPyImPy G65) 5' -WG C G G G G W-3' ImPyImImIrnIm-y-PyPyPyPyImPy G66) 5' -WG C G G G C W-3' ImPyImImImPy-y-ImPyPyPyImPy G67 ) 5' -WG C G G C G W-3 ImPyImImPyIm-y-PyImPyPyImPy ' G68) 5' -WG C G G C C W-3' ImPyImImPyPy-y-ImImPyPyImPy G69) 5' -WG C G C G G W-3' ImPyimPyImIm-y-PyPyImPyImPy G70) 5' -WG C G C G C W-3' ImPyImPyImPy-y-ImPyImPyImPy G71) 5' -WG C G C C G W-3' ImPyImPyPyIm-y-PyImImPyImPy G72) 5' -WG C G C C C W-3' ImPyImPyPyPy-y-ImImImPyImPy WO 98137067 , PCT/US98/01714 1A13L1;
94:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCTWNNW-3' DNA aromatic amino acid sequence sequence 1529) 5'-W G C TT T T W-3' ImPyHpHpHpHp-y-PypypypylmPy 1530) 5''-W G C TT T A W-3' ImPyHpHpHpPy-y-HppyPyPyImPy 1531) 5' G C TT T G W-3' ImPyHpHpHpIm-y-PypypypylmPy -W
1532) 5' G C TT T C W-3' ImPyHpHpHpPy-y-ImPyPyPyImPy -W
1533 5' G C TT A T W-3 ImPyHpHpPyHp-y-PyHpPyPyImPy ) -W ' 1534) 5'-W G C TT A A W-3' ImpyHpHpPyPy-y-HpHpPyPyImPy 1535) 5' G C TT A G W-3' ImPyHpHpPyIm-y-PyHpPyPyImPy -W
1536) 5'-W G C TT A C W-3' ImPyHpHpPyPy-y-ImHpPyPyImPy 1537) 5'-W G C TT G T W-3' ImPyHpHpImHp-y-PyPyPyPyImPy 1538) 5' G C TT G A W-3 ImPyHpHpImPy-y-HpPyPyPyImPy -W T
1539) 5'-W G C TT G G W-3' ImPyHpHpImIm-y-pypypypylmPy 1540) 5' G C TT G C W-3' ImPyHpHpImPy-y-ImPyPyPyImPy -W
154I) 5' G C TT C T W-3' ImPyHpHpPyHp-y-pyImPyPyImPy -W
1542) 5'-W G C TT C A W-3' ImPyHpHpPyPy-y-HpImPyPyImPy 1543) 5' G C TT C G W-3' ImPyHpHpPyIm-y-PyImPyPyImPy -W
1544) 5'-W G C TT C C W-3' ImPyHpHpPyPy-y-ImImPypyImPy 1545) 5' G C TA T T W-3' ImPyHpPyHpHp-y-PyPyHpPyImPy -W
1546) 5'-W G C TA T A W-3' ImPyHpPyHpPy-y-HpPyHpPyImPy 1547 5' G C TA T G W-3 ImPyHpPyHpim-y-PyPyHppyImPy ) -W ' 154 B 5' G C TA T C W-3 ImPyHpPyHpPy-y- ImPyHpPyImPy ) -W ' 1549) 5' G C TA A T W-3' ImpyHppyPyHp-y-PyHpHpPyImPy -W
1550 5' G C TA A A W-3 ImPyHpPyPyPy-y-HpHpHpPyImPy ) -W ' 1551) 5' G C TA A G W-3' ImPyHpPypyIm-y-PyHpHpPyImPy -W
1552) 5' G C TA A C W-3' ImPyHpPyPyPy-y-ImHpHpPyImPy -W
1553) 5' G C TA G T W-3' ImPyHpPyImHp-y-PyPyHpPyImPy -W
1554) 5'-W G C TA G A W-3' ImPyHpPyImPy-y-HpPyHpPyImPy 1555) 5'-W G C TA G G W-3' ImPyHpPyImIm-y-PyPyHpPyImPy 1556) 5'-W G C TA G C W-3' ImPyHpPyImPy-y-ImPyHpPyImPy 1557) 5'-W G C TA C T W-3' ImPyHpPyPyHp-y-PyImHpPyImPy 1558) 5' G C TA C A W-3' ImPyHpPyPyPy-y-HpImHpPyTmPy -W
1559) 5' G C TA C G W-3' ImPyHpPyPyIm-y-PyImHpPyImPy -W
1560) 5' G C TA C C W-3' ImPyHpPyPyPy-y-ImImHpPyImPy -W
TABLE 95: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCTSNNW-3' DNA sequence aromatic amino acid sequence 1561) 5'-W G C T G T T W-3' ImPyHpImHpHp-y-PyPyPyPyImPy 1562) 5'-W G C T G T A W-3' ImPyHpImHpPy-y-HpPyPyPyImPy 1563) 5'-W G C T G T G W-3' ImPyHpImHpIm-y-PyPyPyPyImPy 1564) 5'-W G C T G T C W-3' ImPyHpImHpPy-y-ImPyPyPyImPy 1565) 5' -W G C T G A T W-3' ImPyHpImPyHp-y-PyHpPyPyImPy 1566) 5'-W G C T G A A W-3' ImPyHpImPyPy-y-HpHpPyPyImPy 1567) 5'-W G C T G A G W-3' ImPyHpImPyIm-y-PyHpPyPyImPy 1568) 5' -W G C T G A C W-3' ImPyHpImPyPy-y-ImHpPyPyImPy 1569) 5'-W G C T G G T W-3' ImPyHpImImHp-y-PyPyPyPyImPy 1570) 5'-W G C T G G A W-3' ImPyHpImImPy-y-HpPyPyPyImPy 1571) 5'-W G C T G C T W-3' ImPyHpImPyHp-y-PyImPyPyImPy 1572) 5'-W G C T G C A W-3' ImPyHpImPyPy-y-HpImPyPyImPy 1573) 5'-W G C T G G G W-3' ImPyHpImImIm-y-PyPyPyPyImPy 1574) 5' -W G C T G G C. W-3' ImPyHpImImPy-y-ImPyPyPyImPy 1575) 5'-W G C T G C G W-3' ImPyHpImPyIm-y-PyImPyPyImPy 1576) 5'-W G C T G C C W-3' ImPyHpImPyPy-y-ImImPyPyImPy 1577) 5' -WG C TC T T W-3' ImPyHpPyHpHp-y-PyPyImPyImPy 1578) 5' -WG C TC T A W-3' ImPyHpPyHpPy-y-HpPyImPyImPy 1579) 5' -WG C TC T G W-3' ImPyHpPyHpIm-y-PyPyImPyImPy 1580) 5' -WG C TC T C W-3' ImPyHpPyHpPy-y-ImPyImPyImPy 1581) 5' -WG C TC A T W-3' ImPyHpPyPyHp-y-PyHpImPyImPy 1582) 5' -WG C TC A A W-3' ImPyHpPyPyPy-y-HpHpImPyImPy 1583) 5' -WG C TC A G W-3' ImPyHpPyPyIm-y-PyHpImPyImPy 1584) 5' -WG C TC A C W-3' ImPyHpPyPyPy-y-ImHpImPyImPy 1585) 5' -WG C TC G T W-3' ImPyHpPyImHp-y-PyPyImPyImPy 1586) 5' -WG C TC G A W-3' ImPyHpPyImPy-y-HpPyImPyImPy 1587) 5' -WG C TC C T W-3' ImPyHpPyPyHp-y-PyImImPyImPy 1588) 5' -WG C TC C A W-3' ImPyHpPyPyPy-y-HpImImPyImPy 1589) 5' -WG C TC G G W-3' ImPyHpPyImIm-y-PyPyImPyImPy 1590) 5' -WG C TC G C W-3' ImPyHpPyImPy-y-ImPyImPyImPy 1591) 5' -WG C TC C G W-3' ImPyHpPyPyIm-y-PyImImPyImPy 1592) 5' -WG C TC C C W-3' ImPyHpPyPyPy-y-ImImImPyImPy WO 98/37067 PCTlUS98/01714 TABLE
96:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCAWNNW-3' DNA aromatic amino acid sequence sequence 1593) 5'-W G C A TT T W-3' ImPyPyHpHpHp-y-pypypyHpImPy 1594) 5''-W G C A TT A W-3' ImPyPyHpHpPy-y-HpPyPyHpImPy 1595) 5' -W G C A TT G W-3' ImPyPyHpHpIm-y-PypypygplmPy 1596) 5' -W G C A TT C W-3' ImPyPyHpHpPy-y-ImPyPyHpImPy 1597) 5' -W G C A TA T W-3' ImPyPyHpPyHp-y-PyHpPyHpImPy 1598) 5' -W G C A TA A W-3' ImPyPyHpPyPy-y-HpHpPyHpImPy 1599) 5' -W G C A TA G W-3' ImPyPyHpPyIm-y-PyHpPyHpImPy 1600) 5' -W G C A TA C W-3' ImPyPyHpPyPy-y-ImHpPyHpImPy 1601) 5' -W G C A TG T W-3' ImPyPyHpImAp-y-PyPyPyHpImPy 1602) 5' -W G C A TG A W-3' ImPyPyHpImPy-y-HpPyPyHpImPy 1603) 5' -W G C A TG G W-3' ImPyPyHpImIm-y-PyPyPyHpImPy 1604) 5' -W G C A TG C W-3' ImPyPyHpImPy-y-ImPyPyHpImPy 1605) 5' -W G C A TC T W-3' ImPyPyHpPyHp-y-PyImPyHpImPy 1606) 5' -W G C A TC A W-3' ImPyPyHpPyPy-y-HpImPyHpImPy 1607) 5' -W G C A TC G W-3' ImPyPyHpPyIm-y-PyImPyHpImPy 1608) 5' -W G C A TC C W-3' ImPyPyHpPyPy-y-ImImPyHpImPy 1609) 5' -W G C A AT T W-3' ImPyPyPyHpHp-y-PyPyHpHpImPy 1610) 5' -W G C A AT A W-3' ImPyPyPyHpPy-y-HpPyHpHpimPy 1611) 5' -W G C A AT G W-3' ImPyPyPyHpIm-y-PyPyHpHpImPy 1612) 5' -W G C A AT C W-3' ImPyPyPyHpPy-y-ImPyHpHpImPy 1613) 5' -W G C A AA T W-3' ImPyPyPyPyHp-y-PyHpHpHpImPy 1614) 5' -W G C A AA A W-3' ImPyPyPyPyPy-y-HpHpHpFipImPy 1615) 5' -W G C A AA G W-3' ImPyPyPyPyIm-y-PyHpHpHpImPy 1616 5' -W G C A AA C W-3' ImPyPyPyPyPy-y-ImHpHpHpImPy ) 1617) 5' -W G C A AG T W-3' ImPyPyPyImHp-y-PypyHpHpImPy 1618) 5' -W G C A AG A W-3' ImPyPyPyImPy-y-HpPyHpHpImPy 1619) 5' -W G C A AG G W-3' ImPyPyPyImIm-y-PyPyFipHpImPy 1620) 5' -W G C A AG C W-3' ImPyPyPyImPy-y-ImPyHpHpImPy 1621) 5' -W G C A AC T W-3' ImPyPyPyPyHp-y-pyImHpHpImPy 1622) 5' -W G C A AC A W-3' ImPyPyPypypy-y-HpI~pHpImPy 1623) 5' -W G C A AC G W-3' ImPyPyPyPyIm-y-PyImHpHpImPy 1624) 5' -W G C A AC C W-3' ImPyPyPypyPy-y-ImImHpHpImPy TABLE
97:
12-ring Hairpin PoIyamides for recognition of 8-by 5'-WGCASNNW-3' DNA aromatic amino acid sequence sequence 1625) 5' -W G CA G T T W-3' ImPyPyImHpHp-y-PyPyPyHpImPy 1626) 5' ~-WG CA G T A W-3' ImPyPyImHpPy-y-HpPyPyHpItaPy 1627) 5' -W G CA G T G W-3' ImPyPyImHpIm-y-PyPyPyHpImPy 1628) 5' -W G CA G T C W-3' ImPyPyImHpPy-y-ImPyPyHpImPy 1629) 5' -W G CA G A T W-3' ImPyPyImPyHp-y-PyHpPyHpImPy 1630) 5' -W G CA G A A W-3' ImPyPyImPyPy-y-HpHpPyHpImPy 1631) 5' -W G CA G A G W-3' ImPyPyImPyIm-y-PyHpPyHpImPy 1632) 5' -W G CA G A C W-3' ImPyPyImPyPy-y-ImHpPyHpImPy 1633} 5' -W G CA G G T W-3' ImPyPyImImHp-y-PyPyPyHpImPy 1634) 5' -W G CA G G A W-3' ImPyPyImImPy-y-HpPyPyHpImPy 1635) 5' -W G CA G C T W-3' ImPyPyImPyHp-y-PyImPyHpImPy 1636) 5' -W G CA G C A W-3' ImPyPyImPyPy-y-HpImPyHpImPy 1637) 5' -W G CA G G G W-3' ImPyPyImImIm-y-PyPyPyHpImPy 1638} 5' -W G CA G G C W-3' ImPyPyImImPy-y-ImPyPyHpImPy 1639) 5' -W G CA G C G W-3' ImPyPyImPyIm-y-PyImPyHpImPy 1640) 5' -W G CA G C C W-3' ImPyPyImPyPy-y-ImImPyHpImPy 1641) 5' -W G CA C T T W-3' ImPyPyPyHpHp-y-PyPyImHpImPy 1642) 5' -W G CA C T A W-3' ImPyPyPyHpPy-y-HpPyImHpImPy 1643) 5' -W G CA C T G W-3' ImPyPyPyHpIm-y-PyPyImHp3mPy 1644) 5' -W G CA C T C W-3' ImPyPyPyHpPy-y-ImPyImHpImPy 1645) 5' -W G CA C A T W-3' ImPyPyPyPyHp-y-PyHpImHpImPy 1646) 5' -W G CA C A A W-3' ImPyPyPyPyPy-y-HpHpImHpImPy 1647) 5' -W G CA C A G W-3' ImPyPyPyPyIm-y-PyHpImHpImPy 1648) 5' -W G CA C A C W-3' ImPyPyPyPyPy-y-ImHpImHpImPy 1649) 5' -W G CA C G T W-3' ImPyPyPyImHp-y-PyPyImHpImPy 1650) 5' -W G CA C G A W-3' ImPyPyPyImPy-y-HpPyImHpImPy 1651) 5' -W G CA C C T W-3' ImPyPyPyPyHp-y-PyImImHpImPy 1652) 5' -W G CA C C A W-3' ImPyPyPyPyPy-y-HpImImHpImPy 1653) 5' -W G CA C G G W-3' ImPyPyPyImim-y-PyPyImHpImPy 1654) 5' -W G CA C G C W-3' ImPyPyPyImPy-y-ImPyImHpImPy 1655) 5' -W G CA C C G W-3' ImPyPyPyPyIm-y-PyImImHpImPy 1656) 5' -W G CA C C C W-3' ImPyPyPyPyPy-y-ImImImHpImPy 1'A13LE
98:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCCWNNW-3' DNA aromatic amino acid sequence sequence 1657) 5' -WG C CT T T W-3' ImPyPyHpHpHp-y-PyPypyImImPy 1658) 5' -WG C CT T A W-3' ImPyPyHpHpPy-y-HpPyPyImImPy 1659) 5' -WG C CT T G W-3' ImPyPyHpHpIm-y-PyPyPyImImPy 1660) 5' -WG C CT T C W-3' ImPyPyHpHpPy-y-ImPyPyImImPy 1661) 5' -WG C CT A T W-3' ImPyPyHpPyHp-y-PyHpPyImImPy 1662) 5' -WG C CT A A W-3' ImPyPyHpPyPy-y-HpHpPyImImPy 1663) 5' -WG C CT A G W-3' ImPypyHpPyIm-y-PyHpPyImImPy 1664) 5' -WG C CT A C W-3' ImPyPyHpPyPy-y-ImHppyImImPy 1665) 5' -WG C CT G T W-3' ImPyPyHpImHp-y-PyPyPyImImPy 1666) 5' -WG C CT G A W-3' ImPyPyHpImPy-y-HpPyPyImImPy 1667) 5' -WG C CT G G W-3' ImPyPyHpImIm-y-PyPyPyImImpy 1668) 5' -WG C CT G C W-3' ImPyPyHpImPy-y-ImPyPyImImPy 1669) 5' -WG C CT C T W-3' ImPyPyHpPyHp-y-PyImPyImImPy 1670) 5' -WG C CT C A W-3' ImPyPyHpPyPy-y-HpImPyImImPy 1671) 5' -WG C CT C G W-3' ImPyPyHpPyIm-y-PyImPyImImPy 1672) 5' -WG C CT C C W-3' ImPyPyHpPyPy-y-ImImPyImImPy 1673) 5' -WG C CA T T W-3' ImPyPyPyHpHp-y-PyPyHpImImPy 1674) 5' -WG C CA T A W-3' ImPyPyPyHpPy-y-HpPyHpImImPy 1675) 5' -WG C CA T G W-3' ImPyPyPyHpIm-y-PyPyHpImImPy 1676) 5' -WG C CA T C W-3' ImPyPyPyHpPy-y-ImPyHpImImPy 1677) 5' -WG C CA A T W-3' ImPyPyPyPyHp-y-PyHpHpImImPy 1678) 5' -WG C CA A A W-3' ImPyPyPypypy-y-HpHpHpImImPy 1679) 5' -WG C CA A G W-3' ImPyPyPyPyIm-y-PyApHpImImPy 1680) 5' -WG C CA A C W-3' ImPyPyPyPyPy-y-ImHpHpImImPy 1681) 5' -WG C CA G T W-3' ImPyPyPyImHp-y-pypyHpImImPy 1682) 5' -WG C CA G A W-3' ImPyPyPyImPy-y-HpPyHpImImPy 1683 ) 5' -WG C CA G G W-3' ImPyPyPyImIm-y-pypyHpImImPy 1684) 5' -WG C CA G C W-3' mPyPyPyImPy-y-ImPyHpImImPy I
1685) 5' -WG C CA C T W-3' ImPyPyPyPyHp-y-PyImHpImImPy 1686) 5' -WG C CA C A W-3' ImPyPyPyPyPy-y-HpImHpImImPy 1687) 5' -WG C CA C G W-3' ImPyPyPyPyIm-y-PyImHpImImPy 1688) 5' -WG C CA C C W-3' ImPyPyPyPyPy-y-ImImIipImImPy TABLE
99:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGCCSNNW-3' DNA aromatic amino acid sequence sequence 1689) 5' -WG C C G T T W-3' ImPyPyImHpHp-y-PyPyPyImImPy 1690) 5' -WG C C G T A W-3' ImPyPyImHpPy-y-HpPyPyImImPy 1691) 5' -WG C C G T G W-3' ImPyPyImHpIm-y-PyPyPyImImPy 1692) 5' -WG C C G T C W-3' ImPyPyImHpPy-y-ImPyPyImImPy 1693) 5' -WG C C G A T W-3' ImPyPyImPyHp-y-PyHpPyImImPy 1694) 5' -WG C C G A A W-3' ImPyPyImPyPy-y-HpHpPyImImPy 16 9 5 5' -WG C C G A G W-3 ImPyPyImPyIm-y-PyHpPyImImPy ) ' 1696) 5' -WG C C G A C W-3' ImPyPyImPyPy-y-ImHpPyImImPy 1697) 5' -WG C C G G T W-3' ImPyPyImImHp-y-PyPyPyImImPy 1698) 5' -WG C C G G A W-3' ImPyPyImImPy-y-HpPyPyImImPy 1699) 5' -WG C C G C T W-3' ImPyPyImPyHp-y-PyImPyImImPy 1700) 5' -WG C C G C A W-3' ImPyPyImPyPy-y-HpImPyImImPy 1701) 5' -WG C C C T T W-3' ImPyPyPyHpHp-y-PyPyImImImPy 1702) 5' -WG C C C T A W-3' ImPyPyPyHpPy-y-HpPyImImImPy 1703) 5' -WG C C C T G W-3' ImPyPyPyHpIm-y-PyPyImImImPy 1704) 5' -WG C C C T C W-3' ImPyPyPyHpPy-y-ImPyImImImPy 1705) 5' -WG C C C A T W-3' ImPyPyPyPyHp-y-PyHpImImImPy 1706) 5' -WG C C C A A W-3' ImPyPyPyPyPy-y-HpHpImImImPy 1707) 5' -WG C C C A G W-3' ImPyPyPyPyIm-y-PyHpImImImPy 1708) 5' -WG C C C A C W-3' ImPyPyPyPyPy-y-ImHpImImImPy 1709) 5' -WG C C C G T W-3' ImPyPyPyImHp-y-PyPyImImImPy 1710 ) 5' -WG C C C G A W-3 ImPyPyPyImPy-y-HpPyImImImPy ' 1711) 5' -WG C C C C T W-3' ImPyPyPyPyHp-y-PyImImImImPy 1712) 5' -WG C C C C A W-3' ImPyPyPyPyPy-y-HpImImImImPy G73) 5' -WG C C G G G W-3' ImPyPyImImIm-y-PyPyPyImImPy G74 ) 5' -WG C C G G C W- 3 ImPyPyImImPy-y- ImPyPyImImPy ' G75) 5' -WG C C G C G W-3' ImPyPyImPyIm-y-PyImPyImImPy G7 6 ) 5' -WG C C G C C W- 3 ImPyPyImPyPy-y-ImImPyImImPy ' G77) 5' -WG C C C G G W-3' ImPyPyPyImIm-y-PyPyImImImPy G7 8 ) 5' -WG C C C G C W- 3 ImPyPyPyImPy-y- ImPyImImImPy ' G7 9 ) 5' -WG C C C C G W- 3 ImPyPyPyPyIm-y-PyImImImImPy ' G80) 5' -WG C C C C C W-3' ImPyPyPyPyPy-y-ImImImImImPy WO 98/37067 PCTIUS98/Oi714 TABLE
100:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAGWNNW-3' DNA aromatic amino acid sequence sequence 1713) 5' -WG A G T T TW-3' ImPyImHpHpHp-y-PyPypypyHppy 1714) 5' -WG A G T T AW-3' ImPyImHpHpPy-y-HpPyPyPyHpPy 1715) 5' -WG A G T T GW-3' ImPyImHpHpIm-y-PyPyPyPyHpPy 1716) 5' -WG A G T T CW-3' ImPyImHpHpPy-y-ImPyPyPyHpPy 1717) 5' -WG A G T A TW-3' ImPyImHpPyHp-y-PyHpPyPyHpPy 1718) 5' -WG A G T A AW-3' ImPyImHpPyPy-y-HpHpPyPyHpPy 1719) 5' -WG A G T A GW-3' ImPyImHpPyIm-y-PyHpPyPyHpPy 17 2 0 5' -WG A G T A CW-3 ImPyImHpPyPy-y- ImHpPyPyFipPy ) ' 1721) 5' -WG A G T G TW-3' ImPyImHpImHp-y-PyPyPyPyHpPy 1722) 5' -WG A G T G AW-3' ImPyImHpImPy-y-HpPyPyPyHpPy 1723) 5' -WG A G T G GW-3' ImPyImHpImIm-y-PyPyPyPyHpPy 1724) 5' -WG A G T G CW-3' ImPyImHpImPy-y-ImPyPypyHpPy 1725) 5' -WG A G T C TW-3' ImPyImHpPyHp-y-PyImPyPyHpPy 1726) 5' -WG A G T C AW-3' ImPyImHpPyPy-y-HpImPyPyHpPy 1727) 5' -WG A G T C GW-3' ImPyImHpPyIm-y-PyImPyPyHpPy 1728) 5' -WG A G T C CW-3' ImPyImHpPyPy-y-ImImPyPyHpPy 1729) 5' -WG A G A T TW-3' ImPyImPyHpHp-y-PyPyHpPyHpPy 1730) 5' -WG A G A T AW-3' ImPyImPyHpPy-y-HpPyHpPyHpPy 1731) 5' -WG A G A T GW-3' ImPyImPyHpIm-y-PyPyHpPyHpPy 1732) 5' -WG A G A T CW-3' ImPyImPyHpPy-y-ImPyHpPyHpPy 1733) 5' -WG A G A A TW-3' ImPyImPyPyHp-y-PyHpHpPyHpPy 1734) 5' -WG A G A A AW-3' ImPyImPyPyPy-y-HpHpHpPyHpPy 1735) 5' -WG A G A A GW-3' ImPyImPyPyIm-y-PyHpHpPyHpPy 1736) 5' -WG A G A A CW-3' ImPyImPyPyPy-y-ImHpHpPyHpPy 1737) 5' -WG A G A G TW-3' ImPyImPyImHp-y-PyPyHpPyHpPy 1738) 5' -WG A G A G AW-3' ImPyImPyImPy-y-HpPyHpPyHpPy 1739) 5' -WG A G A G GW-3' ImPyImPyImIm-y-PyPyHpPyHpPy 1740) 5' -WG A G A G CW-3' ImPyImPyImPy-y-ImPyHpPyHpPy 1741) 5' -WG A G A C TW-3' ImPyImPyPyAp-y-PyImHpPyHpPy 1742) 5' -WG A G A C AW-3' ImPyImPyPyPy-y-HpImHpPyHpPy 1743) 5' -WG A G A C GW-3' ImPyImPyPyIm-y-PyImHpPyHpPy 1744) 5' -WG A G A C CW-3' ImPyImPyPyPy-y-ImImHpPyHpPy TABLE
101:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAGSNNW-3' DNA aromatic amino acid sequence sequence 1745) 5'-W G A GG T T W-3' ImpyImImHpHp-y-PyPypypyHpPy 1746) 5''-W G A GG T A W-3' ImPyImImHpPy-y-HpPyPyPyHpPy 1747) 5'-W G A GG T G W-3' ImPyImImHpIm-y-PyPyPypyHpPy 1748) 5'-W G A GG T C W-3' ImPyImImHpPy-y-ImPyPyPyHppy 1749) 5'-W G A GG A T W-3' ImPyImImPyHp-y-PyHpPyPyHpPy 1750) 5'-W G A GG A A W-3' ImPyImImPyPy-y-HpHpPyPyHpPy 1751) 5'-W G A GG A G W-3' ImPyImImPyIm-y-PyHpPyPyHpPy 1752) 5'-W G A GG A C W-3' ImPyImImPyPy-y-ImHpPyPyHpPy 1753} 5'-W G A GG G T W-3' ImPyImImImHp-y-PyPyPyPyHpPy 1754) 5'-W G A GG G A W-3' ImPyImImImPy-y-HpPyPyPyHpPy 1755} 5'-W G A GG C T W-3' ImPyImImPyHp-y-PyImPyPyHpPy 1756) 5'-W G A GG C A W-3' ImPyImImPyPy-y-HpImPyPyHpPy 1757) 5'-W G A GC T T W-3' ImPyImPyHpHp-y-PyPyImPyFipPy 1758) 5'-W G A GC T A W-3' ImPyImPyHpPy-y-HpPyImPyHpPy 1759) 5'-W G A GC T G W-3' ImPyImPyHpIm-y-PyPyImPyHpPy 1760) 5'-W G A GC T C W-3' ImPyImPyHpPy-y-ImPyImPyHpPy 1761} 5'-W G A GC A T W-3' ImPyImPyPyHp-y-PyHpImPyHpPy 1762) 5'-W G A GC A A W-3' ImPyImPyPyPy-y-HpHpImPyHpPy 1763) 5'-W G A GC A G W-3' ImPyImPyPyIm-y-PyHpImpyHpPy 1764) 5'-W G A GC A C W-3' ImPyImPyPyPy-y-ImHpImPyHpPy 1765) 5'-W G A GC G T W-3' ImPyImPyImHp-y-PyPyImPyHpPy 1766) 5'-W G A GC G A W-3' ImPyImPyImPy-y-HpPyImPyHpPy 1767) 5'-W G A GC C T W-3' ImpyImPyPyHp-y-PyImImPyHpPy 1768) 5'-W G A GC C A W-3' ImPyImPyPyPy-y-HpImImPyHpPy 1769) 5'-W G A GG G G W-3' ImPyImImImIm-y-PyPyPyPyHpPy 1770) 5'-W G A GG G C W-3' ImPyImImImPy-y-ImPyPyPyHpPy 1771) 5'-W G A GG C G W-3' ImPyImImPyIm-y-PyImPyPyHpPy 1772) 5'-W G A GG C C W-3' ImPyImImPyPy-y-ImImPyPyHpPy 1773) 5'-W G A GC G G W-3' ImPyImPyImIm-y-PyPyImPyHpPy 1774) 5'-W G A GC G C W-3' ImPyImPyImPy-y-ImPyImPyHppy 1775) 5'-W G A GC C G W-3' ImPyImPyPyIm-y-PyImImPyHpPy 1776) 5'-W G A GC C C W-3' ImPyImPyPyPy-y-ImImImPyHpPy WO 98/37067 , PCT/US98/01714 TABLE
102:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGATWNNW-3' DNA aromatic amino acid sequence sequence 1777) 5'-W G A T TT T W-3' ImPyHpHpHpHp-y-PyPyPyPyHpPy 1778) 5'~-W G A T TT A W-3' ImPyHpHpHppy-y-HpPyPyPyHpPy 1779) 5' G A T TT G W-3' ImPyHpHpHpIm-y-PyPyPyPyHpPy -W
1780) 5'-W G A T TT C W-3' ImPyHpHpHpPy-y-ImPyPyPyHpPy 1781) 5'-W G A T TA T W-3' ImPyHpHpPyHp-y-PyHpPyPyHpPy 1782) 5'-W G A T TA A W-3' ImPyHpHpPypy-y-HpHppypyHpPy 1783 ) 5'-W G A T TA G W-3 ImPyHpHpPyIm-y-PyApPyPyHpPy ' 1784) 5'-W G A T TA C W-3' ImPyHpHpPypy-y-I~ppypygppy 1785) 5'-W G A T TG T W-3' ImPyHpHpImHp-y-pypypypyHppy 1786) 5'-W G A T TG A W-3' ImPyHpHpImPy-y-HpPyPyPyHpPy 1787) 5'-W G A T TG G W-3' ImPyHpHpImIm-y-PyPypypygpPy 1788) 5'-W G A T TG C W-3' ImpyHpHpImPy-y-ImPyPypyHppy 1789) 5'-W G A T TC T W-3' ImPyHpHpPyHp-y-PyImPyPyHpPy 1790) 5'-W G A T TC A W-3' ImPyHpHpPyPy-y-HpImPyPyHpPy 1791) 5'-W G A T TC G W-3' ImPyHpHpPyIm-y-pyImPyPyHpPy 1792) 5'-W G A T TC C W-3' ImPyHpHpPyPy-y-ImImPyPyHpPy 1793) 5'-W G A T AT T W-3' ImPyHpPyHpHp-y-PypyHpPyHpPy 1794) 5'-W G A T AT A W-3' ImPyHpPyHpPy-y-HpPyHpPyHpPy 1795) 5'-W G A T AT G W-3' ImPyHpPyHpIm-y-PyPyHpPyHpPy 1796) 5'-W G A T AT C W-3' ImPyHpPyHpPy-y-ImPyHpPyHpPy 1797) 5'-W G A T AA T W-3' ImPyHpPyPyHp-y-PyHpHpPyHpPy 1798) 5'-W G A T AA A W-3' ImPyHpPyPyPy-y-HpHpHpPyHpPy 1799) 5'-W G A T AA G W-3' ImPylipPypyIm-y-PyHpHpPyHpPy 1800) 5'-W G A T AA C W-3' ImPyHpPyPyPy-y-ImHpHppyHpPy 1801) 5'-W G A T AG T W-3' ImPyHpPyImHp-y-pyPyHppyHpPy 1802) 5'-W G A T AG A W-3' ImPyHpPyImPy-y-HpPyHpPyHpPy 1803) 5'-W G A T AG G W-3' ImPyHpPyImIm-y-PyPyHpPyHpPy 1804) 5'-W G A T AG C W-3' ImPyHpPyImPy-y-ImPyHpPyHpPy 1805) 5'-W G A T AC T W-3' ImPyHpPyPyHp-y-PyImHpPyHpPy 1806) 5'-W G A T AC A W-3' ImPyHpPyPyPy-y-HpImHpPyHpPy _ 1807) 5'-W G A T AC G W-3' ImPyHpPyPyIm-y-PyImHpPyHpPy 1808) 5'-W G A T AC C W-3' ImPyHpPyPyPy-y-ImImHpPyHpPy TABLE
103:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGATSNNW-3' DNA aromatic amino acid sequence sequence 1809) 5' -WG A T G TT W-3' ImPyHpImHpHp-y-PyPyPyPyHpPy 1810) 5' -WG A T G TA W-3' ImPyHpImHpPy-y-HpPyPyPyHpPy 1811) 5' -WG A T G TG W-3' ImPyHpImHpIm-y-PyPyPyPyHpPy 1812) 5' -WG A T G TC W-3' ImPyHpImHpPy-y-ImPyPyPyHpPy 1813) 5' -WG A T G AT W-3' ImPyHpImPyHp-y-PyHpPyPyHpPy 1814) 5' -WG A T G AA W-3' ImPyHpImPyPy-y-HpHpPyPyHpPy 1815) 5' -WG A T G AG W-3' ImPyHpImPyIm-y-PyF-IpPyPyHpPy 1816) 5' -WG A T G AC W-3' ImPyHpImPyPy-y-ImHpPyPyHpPy 1817) 5' -WG A T G GT W-3' ImPyHpImImHp-y-PyPyPyPyHpPy 1818) 5' -WG A T G GA W-3' ImPyHpImImPy-y-HpPyPyPyHpPy 1819) 5' -WG A T G CT W-3' ImPyHpImPyHp-y-PyImPyPyHpPy 1820) 5' -WG A T G GA W-3' ImPyHpImPyPy-y-HpImPyPyHpPy 1821) 5' -WG A T G GG W-3' ImPyHpImImIm-y-PyPyPyPyHpPy 1822) 5' -WG A T G GC W-3' ImPyHpImImPy-y-ImPyPyPyHpPy 1823) 5' -WG A T G CG W-3' ImPyHpImPyIm-y-PyImPyPyHpPy 1824) 5' -WG A T G CC W-3' ImPyHpImPyPy-y-ImImPyPyHpPy 1825) 5' -WG A T C TT W-3' ImPyHpPyHpHp-y-PyPyImPyHpPy 1826) 5' -WG A T C TA W-3' ImPyHpPyHpPy-y-HpPyImPyHpPy 1827) 5' -WG A T C TG W-3' ImPyHpPyHpIm-y-PyPyImPyHpPy 1828) 5' -WG A T C TC W-3' ImPyHpPyHpPy-y-ImPyImPyHpPy 1829) 5' -WG A T C AT W-3' ImPyHpPyPyHp-y-PyHpImPyHpPy 1830) 5' -WG A T C AA W-3' ImPyHpPyPyPy-y-HpHpImPyHpPy 1831) 5' -WG A T C AG W-3' ImPyHpPyPyIm-y-PyHpImPyHpPy 1832) 5' -WG A T C AC W-3' ImPyHpPyPyPy-y-ImHpImPyHpPy 1833) 5' -WG A T C GT W-3' ImPyHpPyImHp-y-PyPyImPyHpPy 1834) 5' -WG A T C GA W-3' ImPyHpPyImPy-y-HpPyImPyHpPy 1835) 5' -WG A T C CT W-3' ImPyHpPyPyHp-y-PyImImPyHpPy 1836) 5' -WG A T C CA W-3' ImPyHpPyPyPy-y-HpImImPyHpPy 1837) 5' -WG A T C GG W-3' ImPyHpPyImIm-y-PyPyImPyHpPy 1838) 5' -WG A T C GC W-3' ImPyHpPyImPy-y-ImPyImPyHpPy 183 9 5' -WG A T C CG W-3' ImPyHpPyPyIm-y-PyImImPyHpPy ) 1840) 5' -WG A T C CC W-3' ImPyHpPyPyPy-y-ImImImPyHpPy TABLE
104:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGAAWNNW-3' DNA aromatic amino acid sequence sequence 184I) 5'-W G A AT T T W-3' ImPyPyHpHpHp-y-PypypyHpHpPy 1842) 5'-W G A AT T A W-3' ImPyPyHpHpPy-y-HpPyPyHpHpPy 1843) 5'-W G A AT T G W-3' ImPyPyHpHpIm-y-PyPypyHpHpPy 1844) 5'-W G A AT T C W-3' ImPyPyHpHpPy-y-ImPyPyHpHpPy 1845) 5'-W G A AT A T W-3' ImPyPyHpPyHp-y-PyHpPyHpHpPy 1846) 5'-W G A AT A A W-3' ImPyPyHpPyPy-y-HpHpPyHpHpPy 1847 ) 5'-W G A AT A G W-3 ImPyPyHpPyIm-y-PyHpPyHpHpPy ' 1848) 5'-W G A AT A C W-3' ImPyPyHpPyPy-y-ImHpPyHpHpPy 1849) 5'-W G A AT G T W-3' ImPyPyHpImHp-y-PypypyHpHpPy 1850) 5'-W G A AT G A W-3' ImPyPyHpImPy-y-HpPyPyHpHpPy 1851) 5'-W G A AT G G W-3' ImPyPyHpImIm-y-PyPyPyHpHppy 1852) 5'-W G A AT G C W-3' ImPypyHpImPy-y-ImPyPyHpHpPy 1853) 5'-W G A AT C T W-3' ImPyPyHpPyHp-y-PyImPyHpHpPy 1854) 5'-W G A AT C A W-3' ImPyPyHpPyPy-y-HpImPyHpHpPy 1855) 5'-W G A AT C G W-3' ImPyPyHpPyIm-y-PyImPyHpHpPy 1856) 5'-W G A AT C C W-3' ImPyPyHpPyPy-y-ImImPyHpHpPy 1857 ) 5'-W G A AA T T W-3' ImPyPyPyHpHp-y-PyPyHpHpHpPy 1858) 5'-W G A AA T A W-3' ImPyPyPyHpPy-y-HpPyHpHpHpPy 1869) 5'-W G A AA T G W-3' ImPyPyPyHpIm-y-PyPyHpHpHpPy 1860) 5'-W G A AA T C W-3' ImPyPyPyApPy-y-ImPyHpHpHpPy 1861) 5'-W G A AA A T W-3' ImPyPyPypyHp-y-PyHpHpHpHpPy 1862 ) 5'-W G A AA A A W-3 ImPyPyPyPyPy-y-HpHpHpHpHpPy ' 1863) 5'-W G A AA A G W-3' ImPyPyPyPyIm-y-PyHpHpHpHpPy 1864) 5'-W G A AA A C W-3' ImPyPyPyPyPy-y-ImHpHpHpHpPy 1865) 5'-W G A AA G T W-3' ImPyPyPyImHp-y-pyPyHpHpHpPy 1866) 5'-W G A AA G A W-3' ImPyPypyImPy-y-HpPyHpHpHpPy 1867) 5'-W G A AA G G W-3' ImPyPyPyImIm-y-PyPyHpHpHpPy 1868) 5'-W G A AA G C W-3' ImPyPyPyImPy-y-ImPyHpHpHpPy 1869) 5'-W G A AA C T W-3' ImPyPyPypyHp-y-PyImHpHpHpPy 1870) 5'-W G A AA C A W-3' ImPyPyPypypy-y-HpI,~pHpgpPy _ 1871) 5'-W G A AA C G W-3' ImPyPypypyIm-y-PyImHpHpHpPy 1872) 5'-W G A AA C C W-3' ImPyPyPypypy-y-ImImHpHpHpPy TABLE 105:
12-ring I airpin Polyamides for recognition of 8-by 5'-WGAASNNW-3' DNA sequence aromatic amino acid sequence 1873) 5'-W G A GT T W-3' ImPyPyImHpHp-y-PyPypygpgppy A
1874) 5'-W G A GT A W-3' ImPyPyImHpPy-y-HpPyPyHpHpPy A
1875) 5' -W G GT G W-3' ImPyPyImHpIm-y-PyPyPyHpHpPy A A
1876) 5' -W G GT C W-3' ImPyPyImHpPy-y-ImPyPyHpHpPy A A
1877) 5'-W G A GA T W-3' ImPyPyImPyHp-y-PyHpPyHpHpPy A
1878) 5'-W G A GA A W-3' ImPyPyImPyPy-y-HpHpPyHpHpPy A
1879) 5'-W G AA G A G W-3' ImPyPyImPyIm-y-pyHpPyHpHppy 1880) 5'-W G AA G A C W-3' ImPyPyImPypy-y-ImHppyHpHpPy 1881) 5'-W G AA G G T W-3' ImPyPyImImHp-y-PyPyPyHpHpPy 1882) 5'-W G AA G G A W-3' ImPyPyImImPy-y-HpPyPyHpHpPy 1883) 5'-W G AA G C T W-3' ImPyPyImPyHp-y-PyImPyHpHpPy 1884) 5'-W G AA G C A W-3' ImPyPyImPyPy-y-HpImpyHpHpPy 1885) 5'-W G A A G G G W-3' ImPyPyImImIm-y-PyPyPyHpHpPy 1886) 5' -W G A A G G C W-3' ImPyPyImImPy-y-ImpyPyHpHpPy 1887) 5'-W G A A G C G W-3' ImPyPyImPyIm-y-PyImPyHpHpPy 1888) 5'-W G A A G C C W-3' ImPyPyImPypy-y-ImImPyHpHpPy 1889) 5'-W G A A CT T W-3' ImPyPyPyHpHp-y-PyPyImHpHpPy 1890) 5'-W G A A CT A W-3' ImPyPyPyHpPy-y-HpPyImHpHpPy 1891) 5'-W G A A CT G W-3' ImPyPyPyHpIm-y-PyPyImHpHpPy 1892) 5'-W G A A CT C W-3' ImPyPyPyHpPy-y-ImPyImHpHpPy 1893) 5'-W G A A CA T W-3' ImPyPyPypyHp-y-PyHpImHpHpPy 1894) 5'-W G A A CA A W-3' ImPyPyPyPyPy-y-HpHpImHpHpPy 1895) 5'-W G A A CA G W-3' ImPyPyPyPyIm-y-PyHpImHpHpPy 1896) 5'-W G A A CA C W-3' ImPyPyPyPyPy-y-ImHpImHpHpPy 1897) 5'-W G A A CG T W-3' ImPyPyPyImHp-y-PyPyImHpHpPy 1898) 5'-W G A A CG A W-3' ImPyPyPyImPy-y-HpPyImHpHpPy 1899) 5'-W G A A CC T W-3' ImPyPyPyPyHp-y-PyImImHpHpPy 1900) 5'-W G A A CC A W-3' ImPyPyPyPyPy-y-HpImImHpHpPy 1901) 5'-W G A A CG G W-3' ImPyPyPyImIm-y-PyPyImHpHpPy 1902) 5'-W G A A CG C W-3' ImPyPyPyImPy-y-ImPyImHpHpPy 1903) 5'-W G A A CC G W-3' ImPyPyPyPyIm-y-PyImImHpHpPy 1904) 5'-W G A A CC C W-3' ImPyPyPyPyPy-y-ImImImHpHpPy WO g8I37067 PCT/US98/01714 TABLE
lOG:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGACWNNW-3' DNA aromatic amino acid sequence sequence 1905} 5'-W GA C T T T W-3' ImPyPyHpHpHp-y-PypypyImHpPy 1906) 5'-W GA C T T A W-3' ImPyPyHpHpPy-y-HppyPyImHpPy 1907) 5'-W GA C T T G W-3' ImPyPyHpHpIm-y-PypypyImHpPy 1908) 5'-W GA C T T C W-3' ImPyPyHpHpPy-y-ImPyPyImHpPy 1909) 5'-W GA C T A T W-3' ImpyPyHpPyHp-y-PyHppyImHpPy 1910) 5'-W GA C T A A W-3' ImPyPyHpPyPy-y-HpHpPyImHpPy 1911) 5'-W GA C T A G W-3' ImPyPyHpPyIm-y-PyHpPyImHpPy 1912) 5'-W GA C T A C W-3 ImPyPyHpPyPy-y-ImHpPyImHpPy T
1913) 5'-W GA C T G T W-3' ImPyPyHpImHp-y-PyPyPyImHpPy 1914) 5'-W GA C T G A W-3' ImPyPyHpImPy-y-HpPyPyImHpPy 1915) 5'-W GA C T G G W-3' TmPyPyHpImIm-y-PyPyPyImHpPy 1916) 5'-W GA C T G C W-3' ImPyPyHpImPy-y-ImPyPyImHpPy 1917) 5'-W GA C T C T W-3' ImPyPyHpPyHp-y-PyImPyImHpPy 1918) 5'-W GA C T C A W-3' ImpyPyHpPyPy-y-HpImPyImHpPy 1919) 5'-W GA C T C G W-3' ImPyPyHpPyIm-y-PyImPyImHppy 1920) 5'-W GA C T C C W-3' ImPyPyHpPyPy-y-ImImPyImHpPy 1921) 5'-W GA C A T T W-3' ImPyPyPyHpHp-y-PypyHpImHpPy 1922) 5'-W GA C A T A W-3' ImPyPyPyHpPy-y-HppyHpImHpPy 1923) 5'-W GA C A T G W-3' ImPyPyPyHpIm-y-PyPyHpImHpPy 1924) 5'-W GA C A T C W-3' ImPyPyPyHpPy-y-ImPyHpImHpPy 1925} 5'-W GA C A A T W-3' ImPyPyPyPyHp-y-PyHpHpImHpPy 1926) 5'-W GA C A A A W-3' ImPyPyPyPyPy-y-HpHpHpImHpPy 1927) 5'-W GA C A A G W-3' ImPyPyPyPyIm-y-PyHpHpImHpPy 1928) 5'-W GA C A A C W-3' ImPyPypyPyPy-y-ImHpHpImHpPy 1929) 5'-W GA C A G T W-3' ImPyPyPyImHp-y-PypyHpImHpPy 1930) 5'-W GA C A G A W-3' ImPyPyPyImPy-y-HpPyHpImHpPy 1931) 5'-W GA C A G G W-3' ImPyPyPyImIm-y-PypyHpImHpPy 1932) 5'-W GA C A G C W-3' ImPyPyPyImPy-y-ImPyHpImHpPy . 1933) 5'-W GA C A C T W-3' ImPyPyPyPyHp-y-PyImHpImHppy 1934) 5'-W GA C A C A W-3' ImPyPyPyPyPy-y-HpImHpImHpPy 1935) 5'-W GA C A C G W-3' ImPyPyPyPyIm-y-PyImHpImHpPy 1936) 5'-W GA C A C C W-3' ImPyPyPyPyPy-y-ImImHpImHpPy WO 98/37067 PCT/~7598/01714 TABLE
107:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGACSNNW-3' DNA aromatic amino acid sequence sequence 1937) 5' -WG A C G T T W-3' ImPyPyImHpHp-y-PyPyPyImHpPy 1938) 5' -WG A C G T A W-3' ImPyPyImHpPy-y-HpPyPyImHpPy 1939) 5' -WG A C G T G W-3' ImPyPyImHpIm-y-PyPyPyImHpPy 1940) 5' -WG A C G T C W-3' ImPyPyImHpPy-y-ImPyPyImHpPy 1941) 5' -WG A C G A T W-3' ImPyPyImPyHp-y-PyHpPyImHpPy 1942) 5' -WG A C G A A W-3' ImPyPyImPyPy-y-HpHpPyImHpPy 1943) 5' -WG A C G A G W-3' ImPyPyImPyIm-y-PyHpPyImHpPy 1944 5' -WG A C G A C W-3' ImPyPyImPyPy-y-ImHpPyImHpPy ) 1945) 5' -WG A C G G T W-3' ImPyPyImImHp-y-PyPyPyImHpPy 1946) 5' -WG A C G G A W-3' ImPyPyImImPy-y-HpPyPyImHpPy 1947) 5' -WG A C G C T W-3' ImPyPyImPyHp-y-PyImPyImHpPy 1948) 5' -WG A C G C A W-3' ImPyPyImPyPy-y-HpImPyImHpPy 1949) 5' -WG A C C T T W-3' ImPyPyPyHpHp-y-PyPyImImHpPy 1950) 5' -WG A C C T A W-3' ImPyPyPyHpPy-y-HpPyImImHpPy 1951) 5' -WG A C C T G W-3' ImPyPyPyHpIm-y-PyPyImImHpPy 1952) 5' -WG A C C T C W-3' ImPyPyPyHpPy-y-ImPyImImHpPy 1953) 5' -WG A C C A T W-3' ImPyPyPyPyHp-y-PyHpImImHpPy 1954) 5' -WG A C C A A W-3' ImPyPyPyPyPy-y-HpHpImImHpPy 1955) 5' -WG A C C A G W-3' ImPyPyPyPyIm-y-PyHpImImHpPy 1956) 5' -WG A C C A C W-3' ImPyPyPyPyPy-y-ImHpImImHpPy 1957) 5' -WG A C C G T W-3' ImPyPyPyImHp-y-PyPyImImHpPy 1958) 5' -WG A C C G A W-3' ImPyPyPyImPy-y-HpPyImImHpPy 1959) 5' -WG A C C C T W-3' ImPyPyPyPyHp-y-PyImImImHpPy 1960) 5' -WG A C C C A W-3' ImPyPyPyPyPy-y-HpImImImHpPy 1961) 5' -WG A C G G G W-3' ImPyPyImImIm-y-PyPyPyImHpPy 1962) 5' -WG A C G G C W-3' ImPyPyImImPy-y-ImPyPyImHpPy 1963) 5' -WG A C G C G W-3' ImPyPyImPyIm-y-PyImPyImHpPy 1964) 5' -WG A C G C C W-3' ImPyPyImPyPy-y-ImImPyImHpPy 1965) 5' -WG A C C G G W-3' ImPyPyPyImIm-y-PyPyImImHpPy 19 6 5' -WG A C C G C W- ImPyPyPyImPy-y- ImPyimImHpPy 6 ) 3 ' 1967) 5' -WG A C C C G W-3' ImPyPyPyPyIm-y-PyImImImHpPy 1968) 5' -WG A C C C C W-3' ImPyPyPyPyPy-y-ImImImImHpPy TABLE
108:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTGWNNW-3' DNA aromatic amino acid sequence sequence 1969) 5'-W GT G T T T W-3' ImHpImHpHpHp-y-PYPyPYPyPyPy 1970) 5'-W GT G T T A W-3' ImHpImHpHppy-y-HpPYPyPyPyPy 1971) 5'-W GT G T T G W-3' ImHpImHpHpIm-y-PyPypypypypy 1972) 5'-W GT G T T C W-3' ImHpImHpHpPy-y-ImPyPyPypypy 1973) 5'-W GT G T A T W-3' ImHpImHpPyHp-y-PyHpPyPyPYPy 1974) 5'-W GT G T A A W-3' ImHpImHpPYPy-y-HpHpPyPyPYpy 1975) 5'-W GT G T A G W-3' ImHpImHpPyIm-y-PyHpPyPyPyPy 1976) 5'-W GT G T A C W-3' ImHpImHpPyPy-y-ImHpPyPyPYPY
1977) 5'-W GT G T G T W-3' ImHpImHpImHp-y-PyPYPyPyPyPy 1978) 5'-W GT G T G A W-3' ImHpImHpImPy-y-HpPYPyPyPyPy 1979) 5'-W GT G T G G W-3' ImHpImHpImIm-y-PyPYPyPyPyPy 1980) 5'-W GT G T G C W-3' ImHpImHpImPy-y-ImPyPyPYPyPy 1981) 5'-W GT G T C T W-3' ImHpImHpPYHp-y-PyImPYPYPyPy 1982} 5'-W GT G T C A W-3' ImHpImHpPYPy-y-HpImPyPyPyPy 1983) 5'-W GT G T C G W-3' ImHpImHpPyIm-y-PyImPyPyPyPy 1984) 5'-W GT G T C C W-3' ImHpImHpPYPy-y-ImImPYPyPypy 1985) 5'-W GT G A T T W-3' ImHpImPYHpHp-y-PyPyHpPyPyPy 1986) 5'-W GT G A T A W-3' ImHpImPyHpPy-y-HpPYHpPyPyPy 1987) 5'-W GT G A T G W-3' ImHpImPyHpIm-y-PYPyHpPyPyPy 1988) 5'-W GT G A T C W-3' ImHpImPyHpPy-y-ImPYHpPyPyPy 1989) 5'-W GT G A A T W-3' ImHpImPyPyHp-y-PYHpHpPyPyPy 19 9 0 5'-W GT G A A A W- 3 ImHpImPyPyPy-y-HpHpHpPyPyPy ) ' 1991) 5'-W GT G A A G W-3' ImHpImPyPyIm-y-PyHpHpPYPyPy 1992) 5'-W GT G A A C W-3' ImHpImPyPyPy-y-ImHpHpPyPyPy 1993) 5'-W GT G A G T W-3' ImHpImPyImHp-y-PYPyHpPYPYPy 1994) 5'-W GT G A G A W-3' ImHpImPyImPy-y-HpPyHpPyPyPy 1995) 5'-W GT G A G G W-3' ImHpImPYImIm-y-PypyHpPyPyPy . 1996) 5'-W GT G A G C W-3' ImHpImPyImPy-y-ImPyHpPyPyPy 1997) 5'-W GT G A C T W-3' ImHpImPyPyHp-y-PYImHpPyPYPy 1998) 5'-W GT G A C A W-3' ImHpImPyPyPy-y-HpImHpPypyPy 1999) 5'-W GT G A C G W-3' ImHpImPYPYIm-y-pyImHpPYPYPy 2000) 5'-W GT G A C C W-3' ImHpImPyPyPy-y-ImImHpPyPYPy TABLE
109:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTGSNNW-3' DNA aromatic amino acid sequence sequence 2001) 5' -WG T G G T T W-3' ImHpImImHpHp-y-pypypypypypy 2002) 5' =WG T G G T A W-3' ImHpImImHpPy-y-HpPyPyPyPyPy 2003) 5' -WG T G G T G W-3' ImHpImImHpIm-y-PyPyPyPyPyPy 2004) 5' -WG T G G T C W-3' ImHpImImHpPy-y-ImPyPyPyPyPy 2005) 5' -WG T G G A T W-3' ImHpImImPyHp-y-PyHpPyPyPyPy 2006) 5' -WG T G G A A W-3' ImHpImImPyPy-y-HpHpPyPyPyPy 2007) 5' -WG T G G A G W-3' ImHpImImPyIm-y-PyHpPyPyPyPy 2008) 5' -WG T G G A C W-3' ImHpImImPyPy-y-ImHpPypyPyPy 2009) 5' -WG T G G G T W-3' ImHpImImImHp-y-PyPyPyPyPyPy 2 010 5' -WG T G G G A W- 3 ImHpImImImPy-y-HpPyPyPyPyPy ) ' 2011) 5' -WG T G G C T W-3' ImHpImImPyHp-y-pyImPyPyPyPy 2 012 5' -WG T G G C A W-3 ImHpImImPyPy-y-HpImPyPyPyPy ) ' 2013) 5' -WG T G C T T W-3' ImHpImPyHpHp-y-PyPyImPyPyPy 2014) 5' -WG T G C T A W-3' ImHpImPyHpPy-y-HpPyImPyPyPy 2015) 5' -WG T G C T G W-3' ImHpImPyHpIm-y-PyPyImPyPyPy 2016) 5' -WG T G C T C W-3' ImHpImPyHpPy-y-ImPyImPyPyPy 2017) 5' -WG T G C A T W-3' ImHpImPyPyHp-y-PyHpImPyPyPy 2018) 5' -WG T G C A A W-3' ImHpImPyPyPy-y-HpHpImPyPyPy 2019) 5' -WG T G C A G W-3' ImHpImPyPyIm-y-PyHpImPyPyPy 2020) 5' -WG T G C A C W-3' ImHpImPyPyPy-y-ImHpImPyPyPy 2021) 5' -WG T G C G T W-3' ImHpImPyImHp-y-PyPyImPyPyPy 2022) 5' -WG T G C G A W-3' ImHpImPyImPy-y-HpPyImPyPyPy 2023) 5' -WG T G C C T W-3' ImHpImPyPyHp-y-PyImImPyPyPy 2024) 5' -WG T G C C A W-3' ImHpImPyPyPy-y-HpImImPyPyPy 2025) 5' -WG T G G G G W-3' ImHpImImImIm-y-PyPyPyPyPyPy 2026) 5' -WG T G G G C W-3' ImHpImImImPy-y-ImPyPyPyPyPy 2027) 5' -WG T G G C G W-3' ImHpImImPyIm-y-PyImPyPyPyPy 2028) 5' -WG T G G C C W-3' ImHpImImPyPy-y-ImImPyPyPyPy 2029) 5' -WG T G C G G W-3' ImHpImPyImIm-y-PyPyImPyPyPy 2030) 5' -WG T G C G C W-3' ImHpImPyImPy-y-ImPyImPyPyPy 2031) 5' -WG T G C C G W-3' ImHpImPyPyIm-y-PyImImPyPyPy 2032) 5' -WG T G C C C W-3' ImHpImPyPyPy-y-ImImImPyPyPy t-At3Ll;
110:
12-ring Hairpin Polyamides for recogmt~on of 8-by 5'-WGTTWNNW-3' DNA aromatic amino acid sequence sequence 2033) 5'-W G T T W-3' ImHpHpHpHpHp-y-pypypypypypy T
T
T
2034) 5''-W G T T T A W-3' ImHpHpHpHpPy-y-HpPyPyPypypy T
2035) 5'-W GT T T T G W-3' ImHpHpHpHpIm-y-Pypypypypypy 2036) 5'-W GT T T T C W-3' ImHpHpHpHpPy-y-ImPYPYPYPYP
y 2037) 5' GT T T A T W-3' ImHpHplipPyHp-y-PYHpPYPYPyPy -W
2038) 5'-W GT T T A A W-3' ImHpHpHpPypy-Y-HpHpPyPyPypy 2039) 5' GT T T A G W-3' ImHpHpHpPyIm-Y-PyHpPyPyPypy -W
2040) 5'-W GT T T A C W-3' ImHpHpHpPYPy-y-ImHppyPYpypy 2041) 5' GT T T G T W-3' ImHpHpHpImHp-Y-PypypypyPYPy -W
2042) 5'-W GT T T G A W-3' ImHpHpHpImPy-y-HpPyPypypypy 2043) 5' GT T T G G W-3' ImHpHpHpImIm-y-pypypypypypy -W
2044) 5'-W GT T T G C W-3' ImHpHpHpImPy-y-ImPYPYPYPyPy 2045) 5' GT T T C T W-3' ImHplipHpPyHp-y-pyImPYPyPyPy -W
2046) 5'-W GT T T C A W-3' ImHpHpHpPyPy-Y-HpImPyPyPyPy 2047) 5'-W GT T T C G W-3' ImHpHpHpPyIm-y-PyImPYPYPYPy 2048) 5' GT T T C C W-3' ImHpHpHpPyPy-y-ImImPyPyPyPy -W
2049) 5'-W GT T A T T W-3' ImHpHpPyHpHp-Y-pypyHpPyPyPy 2050) 5' GT T A T A W-3' ImHpHpPyHpPy-Y-HpPyHppyPYPy -W
2051) 5' GT T A T G W-3' ImHpHpPyHpIm-y-PypyHppypypY
-W
2052) 5' GT T A T C W-3' ImHpHpPyHpPy-y-ImPyHpPYPyPy -W
2053) 5' GT T A A T W-3' ImApHppyPyHp-y-pyHpHpPyPyPy -W
2054) 5'-W GT T A A A W-3' ImHpHpPyPypy-y-HpHpHpPyPyPy 2055) 5'-W GT T A A G W-3' ImHpHpPyPyIm-y-PyHpHppyPyPy 2056) 5'-W GT T A A C W-3' ImHpHpPYPYPy-Y-ImHpHpPYPypy 2057) 5'-W GT T A G T W-3' ImHpHpPyImHp-y-pypygpPyPyPy 2058) 5'-W GT T A G A W-3' ImHpHpPyImPy-y-HpPyHpPyPypy 2059) 5'-W GT T A G G W-3' ImHpHpPyImIm-y-pypyHppypypy 2060) 5'-W GT T A G C W-3' ImHpHpPyImPy-y-ImPyHppypyPy 2061) 5' GT T A C T W-3' ImHpHpPyPyHp-y-Pyl~ppypyp~, -W
2062) 5'-W GT T A C A W-3' ImHpHpPyPyPy-y-HpImHpPYPypy 2063) 5'-W GT T A C G W-3' ImHpHpPyPYIm-y-Pyl~ppypypY
2064) 5' GT T A C C W-3' ImHpHpPyPyPy-Y-ImImHpPYPYpy -W
TABLE
111:
12-ring-I-lairpin Polyamides for recognition of 8-by 5'-WGTTSNNW-3' DNA aromatic amino acid sequence sequence 2065) 5' -WG T T G T TW-3' ImHpHpImHpHp-y-PyPyPyPyPyPy 2066) 5' -WG T T G T AW-3' ImHpHpImHpPy-y-HpPyPyPyPyPy 2067) 5' -WG T T G T GW-3' ImHpHpImHpIm-y-PyPyPyPyPyPy 2068) 5' -WG T T G T CW-3' ImHpHpImHpPy-y-ImPyPyPyPyPy 2069) 5' -WG T T G A TW-3' ImHpHpImPyHp-y-PyHpPyPyPyPy 2070) 5' -WG T T G A AW-3' ImHpHpImPyPy-y-HpHpPyPyPyPy 2071) 5' -WG T T G A GW-3' ImHpHpImPyIm-y-PyHpPyPyPyPy 2072) 5' -WG T T G A CW-3' ImHpHpImPyPy-y-ImHpPyPyPyPy 2073) 5' -WG T T G G TW-3' ImHpHpImImHp-y-PyPyPyPypypy 2074) 5' -WG T T G G AW-3' ImHpHpImImPy-y-HpPyPyPyPyPy 2075) 5' -WG T T G C TW-3' ImHpHpImPyHp-y-PyImPyPyPyPy 2076) 5' -WG T T G C AW-3' ImHpHpImPyPy-y-HpImPyPyPyPy 2077) 5' -WG T T G G GW-3' ImHpHpImImIm-y-PyPyPyPyPypy 2078) 5' -WG T T G G CW-3' ImHpHpImImPy-y-ImPyPyPyPyPy 2079) 5' -WG T T G C GW-3' ImHpHpImPyIm-y-PyImPyPyPyPy 2080) 5' -WG T T G C CW-3' ImHpHpImPyPy-y-ImImPyPyPyPy 2081) 5' -WG T T C T TW-3' ImlipHpPyHpHp-y-PyPyImPyPyPy 2082) 5' -WG T T C T AW-3' ImHpHpPyHpPy-y-HpPyImPyPyPy 2083) 5' -WG T T C T GW-3' ImHpHpPyHpIm-y-PyPyImPyPyPy 2084) 5' -WG T T C T CW-3' ImHpHpPyHpPy-y-ImPyImPyPyPy 2085) 5' -WG T T C A TW-3' ImHpHpPyPyHp-y-PyHpImPyPyPy 2086) 5' -WG T T C A AW-3' ImHpHpPyPyPy-y-HpHpImPyPyPy 2087) 5' -WG T T C A GW-3' ImHpHpPyPyIm-y-PyHpImPyPyPy 2088) 5' -WG T T C A CW-3' ImHpHpPyPyPy-y-ImHpImPyPyPy 2089) 5' -WG T T C G TW-3' ImHpHpPyImHp-y-PyPyImPyPyPy 2090) 5' -WG T T C G AW-3' ImHpHpPyImPy-y-HpPyImPyPyPy 2091) 5' -WG T T C C TW-3' ImHpHpPyPyFip-y-PyImImPyPyPy 2092) 5' -WG T T C C AW-3' ImHpHpPyPyPy-y-HpImImPyPyPy 2093) 5' -WG T T C G GW-3' ImHpHpPyImIm-y-PyPyImPyPyPy 2094) 5' -WG T T C G CW-3' ImHpHpPyImPy-y-ImPyImPyPyPy 2095) 5' -WG T T C C GW-3' ImHpHpPyPyIm-y-PyImImPyPyPy 2096) 5' -WG T T C C CW-3' ImHpHpPyPyPy-y-ImImImPyPyPy TABLE
I 12:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTAWNNW-3' DNA aromatic amino acid sequence sequence 2097) 5' -WG T AT T T W-3' ImHpPyHpHpHp-y-pypypyHppypy 2098) 5' -WG T AT T A W-3' ImHpPyHpHpPy-y-HpPyPyHpPyPy 2099) 5' -WG T AT T G W-3' ImHpPyApHpIm-y-PyPypyHpPyPy 2100) 5' -WG T AT T C W-3' ImHpPyHpHpPy-y-ImPyPyHpPyPy 2101) 5' -WG T AT A T W-3' ImHpPyHpPyHp-y-PyHpPyHppyPy 2102) 5' -WG T AT A A W-3' ImHpPyHpPyPy-y-HpHpPyHpPyPy 2103) 5' -WG T AT A G W-3' ImHpPyHpPyIm-y-PyHpPyHpPyPy 2104) 5' -WG T AT A C W-3' ImHpPyHpPyPy-y-ImHpPyHpPyPy 2105) 5' -WG T AT G T W-3' ImHpPyHpImHp-y-pypypyHppypy 2106) 5' -WG T AT G A W-3' ImHpPyHpImPy-y-HpPyPyHpPyPy 2107 5' -WG T AT G G W-3 ImHpPyHpImIm-y-PyPypyI-Ippypy ) ' 2108) 5' -WG T AT G C W-3' ImHpPyHpImPy-y-ImPyPyHpPypy 2109) 5' -WG T AT C T W-3' ImHpPyHpPyHp-y-PyImPyHpPyPy 2110) 5' -WG T AT C A W-3' ImHpPyHpPyPy-y-HpImPyHpPyPy 2111) 5' -WG T AT C G W-3' ImHpPyHpPyIm-y-PyImPyHpPyPy 2112) 5' -WG T AT C C W-3' ImHpPyHpPyPy-y-ImImPyHpPyPy 2113) 5' -WG T AA T T W-3' ImHpPyPyHpHp-y-PyPyHpHpPyPy 2114) 5' -WG T AA T A W-3' ImHpPyPyHpPy-y-HpPyHpHpPyPy 2115) 5' -WG T AA T G W-3' ImHpPyPyHpIm-y-PyPyHpHpPyPy 2116) 5' -WG T AA T C W-3' ImHpPyPyHpPy-y-ImPyHpHpPyPy 2117) 5' -WG T AA A T W-3' ImHpPyPyPyHp-y-PyHpApHpPyPy 2118 5' -WG T AA A A W-3 ImHpPyPyPyPy-y-HpHpHpHpPyPy ) ' 2119 5' -WG T AA A G W-3 ImHpPyPyPyIm-y-PyHpHpHpPyPy ) ' 2120) 5' -WG T AA A C W-3' ImHpPyPyPyPy-y-ImHpHpHpPyPy 2121) 5' -WG T AA G T W-3' ImHpPyPyImHp-y-PypyHpgpPypy 2122) 5' -WG T AA G A W-3' ImHpPyPyImPy-y-HppyHpHpPyPy 2123 5' -WG T AA G G W-3' ImHppyPyImIm-y-PyPyHpHpPyPy ) 2124) 5' -WG T AA G C W-3' ImHpPyPyImPy-y-ImPyHpHpPyPy 2125) 5' -WG T AA C T W-3' ImApPyPyPyHp-y-pyImHpHpPyPy 2126) 5' -WG T AA C A W-3' ImHpPyPyPyPy-y-HpImHpHpPyPy 2127) 5' -WG T AA C G W-3' ImHppyPyPyIm-y-PyImHpHpPyPy 2128) 5' -WG T AA C C W-3' ImHpPyPypyPy-y-ImImHpHpPyPy TABLE
1 I3:
I2-ring-Hairpin Polyamides for recognition of 8-by S'-WGTASNNW-3' DNA aromatic amino acid scquence sequence 2129) 5' -W GT AG T T W-3' ImHpPyImHpHp-y-PyPyPyHpPyPy 2130) 5''-W GT AG T A W-3' ImHpPyImHpPy-y-HpPyPyHpPyPy 2131) 5' -W GT AG T G W-3' ImHpPyImHpIm-y-PyPyPyHpPyPy 2132) 5' -W GT AG T C W-3' ImHpPyImHpPy-y-ImPyPyHpPyPy 2133) 5' -W GT AG A T W-3' ImHpPyImPyHp-y-PyHpPyHpPyPy 2134) 5' -W GT AG A A W-3' ImHpPyImPyPy-y-HpHpPyHpPyPy 2135} 5' -W GT AG A G W-3' ImHpPyImPyIm-y-PyHpPyHpPyPy 213 6 5' -W GT AG A C W-3 ImHpPyImPypy-y- ImHpPyHpPyPy ) ' 2137) 5' -W GT AG G T W-3' ImHpPyImImHp-y-PyPyPyHpPyPy 213 8 5' -W GT AG G A W-3 ImHpPyImImPy-y-HpPyPyHpPyPy ) ' 213 9 5' -W GT AG C T W-3 ImHpPyImPyHp-y-PyImPyHpPyPy ) ' 2140) 5' -W GT AG C A W-3' ImHpPyImPyPy-y-HpImPyHpPyPy 2141) 5' -W GT AG G G W-3' ImHpPyImImIm-y-PyPyPyHppyPy 2142) 5' -W GT AG G C W-3' ImHpPyImImPy-y-ImPyPyHpPyPy 2143 ) 5' -W GT AG C G W-3 ImHpPyImPyIm-y-PyImPyHpPyPy ' 2144) 5' -W GT AG C C W-3' ImHpPyImPyPy-y-ImImPyHpPyPy 2145) 5' -W GT AC T T W-3' ImHpPyPyHpHp-y-PyPyImHpPyPy 2146) 5' -W GT AC T A W-3' ImHpPyPyHpPy-y-HppyImHpPyPy 2147} 5' -W GT AC T G W-3' ImHpPyPyHpIm-y-PyPyImHpPyPy 2148) 5' -W GT AC T C W-3' ImHpPyPyHpPy-y-ImPyImHpPyPy 2149) 5' -W GT AC A T W-3' ImHpPyPyPyHp-y-PyHpImHpPyPy 2150) 5' -W GT AC A A W-3' ImHpPyPyPyPy-y-HpHpImHpPyPy 2151) 5' -W GT AC A G W-3' ImHpPyPyPyIm-y-PyHpImHpPyPy 2152) 5' -W GT AC A C W-3' ImHpPyPypyPy-y-ImHpImHpPyPy 2153) 5' -W GT AC G T W-3' ImHpPyPyImHp-y-PyPyImHpPyPy 2154) 5' -W GT AC G A W-3' ImHpPyPyImPy-y-HpPyImHpPyPy 2155) 5' -W GT AC C T W-3' ImHpPyPyPyHp-y-PyImImHpPyPy 2156) 5' -W GT AC C A W-3' ImHpPypyPyPy-y-HpImImHpPyPy 2157) 5' -W GT AC G G W-3' ImHpPyPyImIm-y-PyPyImHpPyPy 2158) 5' -W GT AC G C W-3' ImHpPyPyImPy-y-ImPyImHpPyPy 2159) 5' -W GT AC C G W-3' ImHpPyPyPyIm-y-PyImImHpPyPy 2160) 5' -W GT AC C C W-3' ImHpPyPyPyPy-y-ImImImHpPyPy _~.,.,,... _ , , , , .,.
WO 98/37067 , PCT/US98/01714 I
Al3Lt~
I
14:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTCWNNW-3' DNA aromatic amino acid sequence sequence 2161) 5'-W GT C T T T W-3' ImHpPyHpHpHp-y-Pypypylmpypy 2162) 5' GT C T T A W-3' ImHpPyHpHpPy-y-HpPyPyImPyPy -~n1 2163 ) 5' GT C T T G W-3 ImHpPyHpHpIm-y-PyPypyImPyPy -W ' 2164) 5'-W GT C T T C W-3' ImHpPYHpHpPy-y-ImPypyImPyPy 2165) 5'-W GT C T A T W-3' ImHpPyHpPyHp-y-PyHpPyImPyPy 2166) 5'-W GT C T A A W-3' ImHpPyHpPyPy-y-HpHpPyImpyPy 2167) 5'-W GT C T A G W-3' ImHppyHppYIm_Y_pYHppyImPyPy 2168) 5'-W GT C T A C W-3' ImHpPyHpPypy-y-ImHpPyImPyPy 2169) 5'-W GT C T G T W-3' ImHpPYHpImHp-y-PypypyImPyPy 2170) 5'-W GT C T G A W-3' ImHpPyHpImPy-y-HpPyPyImPyPy 2171) 5' GT C T G G W-3' ImHpPyHpImIm-y-PypypyzmPyPy -W
2172) 5' GT C T G C W-3' ImHpPyHpImPy-y-ImPyPyImPyPy -W
2173 ) 5' GT C T C T W-3' ImHpPyHpPyHp-y-PyImPyImPyPy -W
2174) 5' GT C T C A W-3' ImHpPyHpPYPy-y-HpImPyImPyPy -W
2175) 5' GT C T C G W-3' ImHppyHpPyIm-y-pyImPYImPyPy -W
2176) 5' GT C T C C W-3' ImHpPyHpPyPy-y-ImImPyImPyPy -W
2177 ) 5' GT C A T T W-3' ImHpPyPyHpHp-y-pypyHpImPYPy -W
2178) 5' GT C A T A W-3' ImHpPYPyHpPy-y-HpPYHpImPyPy -W
2179) 5' GT C A T G W-3' ImHpPyPyHpIm-y-PyPyHpImPyPy -W
2180) 5'-W GT C A T C W-3' ImHppypYHPPY_Y-ImPyHpImPyPy 2181) 5' GT C A A T W-3' ImHpPyPyPYHp-y-PyHpHpImPypy -W
2182) 5' GT C A A A W-3' ImHpPYPyPypy-Y-HpHpHpImPyPy -W
2183 ) 5' GT C A A G W-3' ImHpPyPyPyIm-Y-PyHpHpImPyPy -W
2184) 5' GT C A A C W-3' ImHpPyPypypy-Y-I~pHpImPyPy -W
2185) 5' GT C A G T W-3' ImHpPyPyImHp-y-PypyHpImPyPy -W
2186) 5'-W GT C A G A W-3' ImHppypylmpY_Y_HpPyHpImPyPy 2187) 5'-W GT C A G G W-3' ImHpPyPyImIm-y-PypygpImPyPy 2188) 5' GT C A G C W-3' ImHpPyPyImPy--W y -ImPyHpImPyPy 2189) 5'-W GT C A C T W-3' ImHpPyPyPyHp-Y-PyImHpImPyPy 2190) 5' GT C A C A W-3' ImHppypypypY_Y-HpImHpImpyPy -W
2191) 5' GT C A C G W-3' ImHpPypypylm-y-PyImHpImPyPy -W
2192) 5'-W GT C A C C W-3' ImHpPyPyPypy_y-ImImHpImPyPy WO 98/37067 , PCT/US98/01714 TABLE
115:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WGTCSNNW-3' DNA aromatic amino acid sequence sequence 2193) 5' -WG T C G TT W-3' ImHpPyImHpHp-y-PyPyPyImPyPy 2194) 5' -WG T C G TA W-3' ImHpPyImHpPy-y-HpPyPyImPyPy 2195) 5' -WG T C G TG W-3' ImHpPyImHpIm-y-PyPyPyImPyPy 2196) 5' -WG T C G TC W-3' ImHpPyImHpPy-y-ImPyPyImPyPy 2197) 5' -WG T C G AT W-3' ImHpPyImPyHp-y-PyHpPyImPyPy 2198) 5' -WG T C G AA W-3' ImHpPyImPyPy-y-HpHpPyImPyPy 2199) 5' -WG T C G AG W-3' ImHpPyImPyIm-y-PyHpPyImPyPy 2200) 5' -WG T C G AC W-3' ImHpPyImPyPy-y-ImHpPyImPyPy 2201) 5' -WG T C G GT W-3' ImHpPyImImHp-y-PyPyPyImPyPy 2202) 5' -WG T C G GA W-3' ImHpPyImImPy-y-HpPyPyImPyPy 2203) 5' -WG T C G CT W-3' ImHpPyImPyHp-y-PyImPyImPyPy 2204) 5' -WG T C G CA W-3' ImHpPyImPyPy-y-HpImPyImPyPy 2205) 5' -WG T C C TT W-3' ImHpPyPyHpHp-y-PyPyImImPyPy 2206) 5' -WG T C C.TA W-3' ImHpPyPyHpPy-y-HpPyImImPyPy 2207) 5' -WG T C C TG W-3' ImHpPyPyHpIm-y-PyPyImImPyPy 2208) 5' -WG T C C TC W-3' ImHpPyPyHpPy-y-ImPyImImPyPy 2209) 5' -WG T C C AT W-3' ImHpPyPyPyHp-y-PyHpImImPyPy 2210) 5' -WG T C C AA W-3' ImHpPyPyPyPy-y-HpHpImImPyPy 2211) 5' -WG T C C AG W-3' ImHpPyPyPyIm-y-PyHpImImPyPy 2212) 5' -WG T C C AC W-3' ImHpPyPyPyPy-y-ImHpImImPyPy 2213) 5' -WG T C C GT W-3' ImHpPyPyImHp-y-PyPyImImPyPy 2214) 5' -WG T C C GA W-3' ImHpPyPyImPy-y-HpPyImImPyPy 2215) 5' -WG T C C CT W-3' ImHpPyPyPyHp-y-PyImImImPyPy 2216) 5' -WG T C C CA W-3' ImHpPyPyPyPy-y-HpImImImPyPy 2217) 5' -WG T C G GG W-3' ImHpPyImImIm-y-PyPyPyImPyPy 2218) 5' -WG T C G GC W-3' ImHpPyImImPy-y-ImPyPyImPyPy 2219) 5' -WG T C G CG W-3' ImHpPyImPyIm-y-PyImPyImPyPy 2220) 5' -WG T C G CC W-3' ImHpPyImPyPy-y-ImImPyImPyPy 2221) 5' -WG T C C GG W-3' ImHpPyPyImIm-y-PyPyImImPyPy 2222) 5' -WG T C C GC W-3' ImHpPyPyImPy-y-ImPyImImPyPy 2223) 5' -WG T C C CG W-3' ImHpPyPyPyIm-y-PyImImImPyPy 2224) 5' -WG T C C CC W-3' ImHpPyPyPyPy-y-ImImImImPyPy TABLE 116:
12-ring Hairpin Polyamides for recognition of 8-by 5'WCGGWNNW-3' ' DNA aromatic amino acid sequence sequence 2225) 5'W C G G TT T W-3' PyImImHpHpHp-y-PyPypypypylm 2226) 5'W C G G TT A W-3' PyImImHpHpPy-y-HpPyPyPyPyim 2227 5' C G G TT G W-3' PyImImHpHpIm-y-PyPyPyPyPyIm ) W
2228) 5'W C G G TT C W-3' PyImImHpHpPy-y-ImPyPyPyPyIm 2229) 5'W C G G TA T W-3' PyImImHpPyHp-y-PyHpPyPyPyIm 223 0 5' C G G TA A W-3 ' PyImImHpPyPy-y-HpHpPyPyPyIm ) W
2231) 5'W C G G TA G W-3' PyImImHpPyIm-y-PyHpPyPyPyIm 2232) 5'W C G G TA C W-3' PyImImHpPyPy-y-ImHpPyPyPyIm 2233) 5'W C G G TG T W-3' PyImImHpImHp-y-PyPyPyPyPyIm 2234 5' C G G TG A W-3 ' PyImImHpImPy-y-HpPyPyPyPyIm ) W
2235) 5'W C G G TG G W-3' PyImImHpImIm-y-PyPyPypypyIm 2236) 5'W C G G TG C W-3' PyImImHpImPy-y-ImPyPyPyPyIm 2237) 5'W C G G TC T W-3' PyImImHpPyHp-y-PyImPyPyPyIm 223 8 5' C G G TC A W-3 ' PyImImHpPyPy-y-HpImPyPyPyIm ) W
223 9 5' C G G TC G W-3 ' PyImImHpPyIm-y-PyImPyPyPyIm ) W
2240) 5'W C G G TC C W-3' PyImImHpPyPy-y-ImImPyPyPyIm 2241) 5'W C G G AT T W-3' PyImImPyHpHp-y-PyPyHpPyPyIm 2242) 5'W C G G AT A W-3' PyImImPyHpPy-y-HpPyHpPyPyIm 2243 5' C G G AT G W-3 ' PyImImPyHpIm-y-PyPyHpPyPyIm ) W
2244) 5'W C G G AT C W-3' PyImImpyHpPy-y-ImPyHpPyPyIm 2245) 5'W C G G AA T W-3' PyImImPyPyHp-y-PyHpHpPyPyIm 2246) 5'W C G G AA A W-3' PyImImPyPyPy-y-HpHpHpPyPyIm 2247 5' C G G AA G W-3 ' PyImImPyPyIm-y-PyHpHpPyPyIm ) W
2248) 5'W C G G AA C W-3' PyImImPyPyPy-y-ImHpHpPyPyIm 2249) 5'W C G G AG T W-3' PyImImPyImHp-y-PyPyHpPyPyIm 2250) 5'W C G G AG A W-3' PyImImPyImPy-y-HpPyHpPyPyIm 2251) 5' C G G AG G W-3' PyImImPyImIm-y-PypyHpPyPyIm W
2252) 5'W C G G AG C W-3' PyImImPyImPy-y-ImPyHpPyPyIm 2253 5' C G G AC T W-3 ' PyImImPyPyHp-y-PyImHpPyPyIm ) W
2254) 5'W C G G AC A W-3' PyImImPyPyPy-y-HpImHpPyPyIm 2255) 5'W C G G AC G W-3' PyImImPyPyIm-y-PyImHpPyPyIm 2256) 5'W C G G AC C W-3' PyImImPyPyPy-y-ImImHpPyPyIm TABLE
117:
12-ring Hairpin Polyamides for recognition of 8-by 5'WCGGSNNW-3' DNA aromatic amino acid sequence sequence 2257) 5' W C G G GT T W-3' PyImImImHpHp-y-PyPyPyPyPyIm 2258) 5' W C G G GT A W-3' PyImImImHpPy-y-HpPyPyPyPyIm 2259) 5' W C G G GT G W-3' PyImImImHpIm-y-PyPyPyPyPyIm 2260) 5' W C G G GT C W-3' PyImImImHpPy-y-ImPyPyPyPyIm 2261) 5' W C G G GA T W-3' PyImImImPyHp-y-PyHpPyPyPyIm 2262) 5' W C G G GA A W-3' PyImImImPyPy-y-HpHpPyPyPyIm 2263) 5' W C G G GA G W-3' PyImImImPyIm-y-PyHpPyPyPyIm 2264) 5' W C G G GA C W-3' PyImImImPyPy-y-ImHpPyPyPyIm 2265) 5' W C G G GG T W-3' PyImImImImHp-y-PyPyPyPyPyIm 2266) 5' W C G G GG A W-3' PyImImImImPy-y-HpPyPyPyPyIm 2267) 5' W C G G GC T W-3' PyImImImPyHp-y-PyIircPyPyPyIm 226$) 5' W C G G GC A W-3' PyImImImPyPy-y-HpImPyPyPyIm 2269) 5' W C G G CT T W-3' PyImImPyHpHp-y-PyPyImPyPyIm 2270) 5' W C G G CT A W-3' PyImImPyHpPy-y-HpPyImPyPyIm 2271) 5' W C G G CT G W-3' PyImImPyHpIm-y-PyPyImPyPyIm 2272) 5' W C G G CT C W-3' PyImImPyHpPy-y-ImPyImPyPyIm 2273) 5' W C G G CA T W-3' PyImImPyPyHp-y-PyHpImPyPyIm 2274) 5' W C G G CA A W-3' PyImImPyPyPy-y-HpHpImPyPyIm 2275) 5' W C G G CA G W-3' PyImImPyPyIm-y-PyHpImPyPyIm 2276) 5' W C G G CA C W-3' PyImImPyPyPy-y-ImHpImPyPyIm 2277 5' W C G G CG T W-3 ' PyImImPyImHp-y-PyPyImPyPyIm ) 2278) 5' W C G G CG A W-3' PyImImPyImPy-y-HpPyImPyPyIm 227 9 5' W C G G CC T W-3 ' PyImImPyPyHp-y-PyImImPyPyIm ) 2280) 5' W C G G CC A W-3' PyImImPyPyPy-y-HpImImPyPyim G83) 5' W C G G GG G W-3' PyImImImImIm-y-PyPyPyPyPyIm G84) 5' W C G G GG C W-3' PyImImImImPy-y-ImPyPyPyPyIm G85) 5' W C G G GC G W-3' PyImImImPyIm-y-PyImPyPyPyIm G86 ) 5' W C G G GC C W-3 ' PyImImImPyPy-y-ImImPyPyPyIm G87 ) 5' W C G G CG G W-3 ' PyImImPyImIm-y-PyPyImPyPyIm G88) 5' W C G G CG C W-3' PyImImPyImPy-y-ImPyImPyPyIm G89) 5' W C G G CC G W-3' PyImImPyPyIm-y-PyImImPyPyIm G90) 5' W C G G CC C W-3' PyImImPyPyPy-y-ImImImPyPyIm WO 98/37067 . PCT/US98/01714 TABLE 12-ring 118: Hairpin Polyamides for recognition of 8-by 5'-WCGTWNNW-3' DNA aromatic amino acid sequence sequence 2281) 5'W C G T T T TW-3' PyImHpHpHpHp-y-PyPyPyPyPyIm 2282) 5'W C G T T T AW-3' PyImHpHpHpPy-y-HpPyPyPyPyIm 2283 ) 5' C G T T T GW-3 ' PyImHpHpHpIm-y-PyPyPyPyPyIm W
2284) 5'W C G T T T CW-3' PyImHpHpHpPy-y-ImPyPyPyPyIm 2285) 5'W C G T T A TW-3' PyImHpHpPyHp-y-PyHpPyPyPyIm 2286) 5'W C G T T A AW-3' PyImHpHpPyPy-y-HpHpPyPyPyIm 2287) 5'W C G T T A GW-3' PyImHpHpPyIm-y-PyHpPyPypyIm 2288) 5'W C G T T A CW-3' PyImHpHpPyPy-y-ImHpPyPyPyIm 2289) 5'W C G T T G TW-3' PyImHpHpImHp-y-PyPyPyPyPyIm 2290) 5'W C G T T G AW-3' PyImHpHpImPy-y-HpPypyPypylm 2291) 5'W C G T T G GW-3' PyImHpHpImIm-y-PyPyPyPyPyIm 2292) 5'W C G T T G CW-3' PyImHpHpImPy-y-ImPyPyPyPyIm 2293) 5'W C G T T C TW-3' PyImHpHpPyHp-y-PyTmPyPyPyIm 2294} 5'W C G T T C AW-3' PyImHpHpPyPy-y-HpImPyPyPyIm 2295) 5'W C G T T C GW-3' PyImHpHpPyIm-y-PyImPyPyPyIm 2296) 5'W C G T T C CW-3' PyImHpHpPyPy-y-ImImPyPyPyIm 2297) 5'W C G T A T TW-3' PyImHpPyHpHp-y-PyPyHpPyPyIm 2298) 5'W C G T A T AW-3' PyImHpPyHpPy-y-HpPyHpPyPyIm 2299) 5'W C G T A T GW-3' PyImHpPyHpIm-y-PyPyHpPyPyIm 2300} 5'W C G T A T CW-3' PyImHpPyHpPy-y-ImPyHpPyPyIm 2301) 5'W C G T A A TW-3' PyImHpPyPyHp-y-PyHpHpPyPyIm 2302) 5'W C G T A A AW-3' PyImHpPyPyPy-y-HpHpHpPyPyIm 2303) 5'W C G T A A GW-3' PyImHpPyPyim-y-PyHpHpPyPyim 2304) 5'W C G T A A CW-3' PyImHpPyPyPy-y-ImHpHpPyPyIm 2305) 5'W C G T A G TW-3' PyImHpPyImHp-y-PyPyHpPyPyIm 2306) 5'W C G T A G AW-3' PyImHpPyImPy-y-HpPyHpPyPyIm 2307) 5'W C G T A G GW-3' PyImHpPyImIm-y-PyPyHpPyPyIm 2308) 5'W C G T A G CW-3' PyImHpPyImPy-y-ImPyHpPyPyIm 2309) 5'W C G T A C TW-3' PyImHpPyPyHp-y-PyImHpPyPyIm 2310) 5'W C G T A C AW-3' PyImHpPyPyPy-y-HpImHpPyPyIm 2311) 5'W C G T A C GW-3' PyImHpPyPyIm-y-PyImHpPyPyIm 2312 ) 5' C G T A C CW-3 ' PyImHpPyPypy-y- ImImHpPyPyIm W
TABLE I 19: 12-ring-Hairpin Polyamides far recognition of 8-by 5'-WCGTSNNW-3' DNA sequence aromatic amino acid sequence 2313 ) 5' W C G T G T T W-3 ' PyImHpImHpHp-Y-PypypypypyIm 2314 ) 5' W C G T G T A W-3 ' PyImHpImHpPy-y-Hppypypypylm 2315) 5'W C G T G T G W-3' PyImHpImHpIm-y-PyPyPyPypyIm 2316 ) 5' W C G T G T C W-3 ' PyImHpImHpPy-y- ImPyPyPyPyIm 2317 ) 5' W C G T G A T W-3 ' PyImHpImPyHp-y-PyHpPyPyPyIm 2318) 5'W C G T G A A W-3' PyImHpImPyPy-y-HpHpPyPyPyIm 2319) 5'W C G T G A G W-3' PyImHpImPyIm-Y-PyHpPyPypyIm 2320) 5'W C G T G A C W-3' PyImHpImPyPy-y-ImHpPyPyPyIm 2321) 5'W C G T G G T W-3' PyImHpImImHp-y-pypypypypyim 2322) 5'W C G T G G A W-3' PyImHpImImPy-y-HPPyPyPyPyIm 2323) 5'W C G T G C T W-3' PyImHpImPyHp-y-pyImPyPyPyIm 2324) 5'W C G T G C A W-3' PyImHpImPyPy-y-HpImPyPyPyIm 2325) 5'W C G T G G G W-3' PyImHpImImIm-y-PyPyPyPyPyIm 2326) 5'W C G T G G C W-3' PyImApImImPy-y-ImPyPyPyPyIm 2327) 5'W C G T G C G W-3' PyImHpImPyIm-y-PyImPyPyPyIm 2328) 5'W C G T G C C W-3' PyImHpImPyPy-y-ImImPyPyPyIm 2329) 5'W C G T CT T W-3' PyImHpPyHpHp-y-PypyImPyPyIm 2330) 5' C G T CT A W-3' PyImHpPyHpPy-y-HpPyImPyPyIm W
2331) 5'W C G T CT G W-3' PyImHpPyI3pIm-y-PyPyImPyPyIm 2332) 5'W C G T CT C W-3' PyImHpPyHpPy-y-ImpyImPyPyIm 2333 ) 5' C G T CA T W-3' PyImHpPyPyHp-y-PyHpImPyPyIm W
2334 ) 5' C G T CA A W-3 ' PyImHpPyPyPy-y-HpHpImPyPyIm W
2335) 5'W C G T CA G W-3' PyImHppypylm-y-PyHpImPyPyIm 2336) 5'W C G T CA C W-3' PyImHpPyPyPy-y-ImHpImPyPyIm 2337 ) 5' C G T CG T W-3 ' PyImHpPyImHp-y-pypyImPyPyim W
2338) 5'W C G T CG A W-3' PyImHpPyImPy-y-HpPyImPyPyIm 2339) 5'W C G T CC T W-3' PyImHpPyPyHp-y-PyImImPyPyIm 2340) 5'W C G T CC A W-3' PyImHpPyPyPy-y-HpImImPyPyIm 2341) 5'W C G T CG G W-3' PyImHpPyImIm-y-pypyImPyPyIm 2342) 5'W C G T CG C W-3' PyImHpPyImPy-y-ImpyImPyPyIm 2343 ) 5' C G T CC G W-3 ' PyImHpPyPyIm-y-PyImImPyPyIm W
2 3 44 ) 5' C G T CC C W- 3 PyImHpPyPyPy-y- ImImImPyPyIm W ' 1A13LIr 120:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGAWNNW-3' DNA aromatic amino acid sequence sequence 2345) 5'W C GA T T T W-3' PyImPyHpHpHp-y-pypypyHppylm 2346) 5'W C GA T T A W-3' PyImPyHpHpPy-y-HpPyPyHpPyIm 2347) 5'W C GA T T G W-3' PyImpyHpHpIm-y-pyPypyHpPyIm 2348) 5'W C GA T T C W-3' PyImPyHpHpPy-y-ImPyPyHpPyIm 2349) 5'W C GA T A T W-3' PyImPyHpPyHp-y-PyHpPyHpPyIm 2350) 5'W C GA T A A W-3' pyImPyHpPyPy-y-HpHpPyHpPyIm 2351) 5'W C GA T A G W-3' PyImPyApPyIm-y-PyHpPyHpPyIm 2352) 5'W C GA T A C W-3' PyImPyHpPyPy-y-ImHpPyHpPyIm 2353) 5'W C GA T G T W-3' PyImPyHpImHp-y-Pypypygppylm 2354 ) 5' C GA T G A W-3 ' PyImPyHpImPy-y-HpPyPyHpPyIm W
2355) 5'W C GA T G G W-3' PyImPyHpImIm-y-PyPyPyHpPyIm 2356) 5'W C GA T G C W-3' PyImPyHpImPy-y-ImPyPyHpPyIm 2357) 5'W C GA T C T W-3' PyImPyHpPyHp-y-PyImPyHpPyIm 2358) 5'W C GA T C A W-3' PyImPyHpPyPy-y-HpImPyHpPyIm 2359) 5'W C GA T C G W-3' PyImPyHpPyIm-y-PyImPyHpPyIm 2360) 5'W C GA T C C W-3' PyImPyHpPyPy-y-ImImPyHpPyIm 2361) 5'W C GA A T T W-3' PyImPyPyHpHp-y-PypyHpHpPyIm 2362) 5'W C GA A T A W-3' PyImPyPyHpPy-y-HpPyHpHpPyIm 2363) 5'W C GA A T G W-3' PyImPyPyHpIm-y-PypyHpHpPyIm 2364) 5'W C GA A T C W-3' PyImPyPyHpPy-y-ImPyHpHpPyIm 2365) 5'W C GA A A T W-3' PyImPyPyPyHp-y-PyHpHpHpPyIm 2366) 5'W C GA A A A W-3' PyImPyPyPyPy-y-HpHpHpHpPyIm 2367) 5'W C GA A A G W-3' PyImPyPypylm-y-PyHpHpHpPyIm 2368) 5'W C GA A A C W-3' PyImPyPyPyPy-y-ImHpHpHpPyIm 2369) 5'W C GA A G T W-3' PyImPyPyImHp-y-PyPyHpHpPyIm 2370) 5'W C GA A G A W-3' PyImPyPyImPy-y-HpPyHpHpPyIm 2371) 5'W C GA A G G W-3' PyImPyPyImIm-y-PyPyHpHpPyIm 2372) 5'W C GA A G C W-3' yImPypyImPy-y-ImPyHpHpPyIm P
. 2373 ) 5' C GA A C T W-3 ' PyImPyPypyHp-y-PyImHpHpPyIm W
2374 ) 5' C GA A C A W-3' PyImPyPyPyPy-y-HpImHpHpPyIm W
2375) 5'W C GA A C G W-3' PyImPyPyPyIm-y-PyImHpHpPyIm 2376) 5'W C GA A C C W-3' PyImPyPyPyPy-y-ImImHpIipPyIm TABLE
121:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGASNNW-3' DNA aromatic amino acid sequence sequence 2377) 5'W C G A GT T W-3' PyImPyImHpHp-y-PyPyPyHpPyIm 2378) 5'W C G A GT A W-3' PyImPyImHpPy-y-HpPyPyHppyIm 2379) 5'W C G A GT G W-3' PyImPyImHpIm-y-PyPyPyHpPyIm 2380) 5'W C G A GT C W-3' PyImPyImHpPy-y-ImPyPyHpPyIm 2381) 5'W C G A GA T W-3' PyImPyImPyHp-y-PyHpPyHpPyIm 2382) 5'W C G A GA A W-3' PyImPyImPyPy-y-HpHpPyHpPyIm 2383) 5'W C G A GA G W-3' PyImPyImPyIm-y-PyHpPyHpPyIm 2384) 5'W C G A GA C W-3' PyImPyImPyPy-y-ImHpPyHpPyIm 2385) 5'W C G A GG T W-3' PyImPyImImHp-y-PyPyPyHpPyIm 2386) 5'W C G A GG A W-3' PyImPyImImPy-y-HpPyPyHpPyIm 2387) 5'W C G A GC T W-3' PyImPyImPyHp-y-PyImPyHpPyIm 2388) 5'W C G A GC A W-3' PyImPyImPyPy-y-HpImPyHpPyIm 2389) 5'W C G A GG G W-3' PyImPyImImIm-y-PyPyPyHpPyIm 2390) 5'W C G A GG C W-3' PyImPyImImPy-y-ImPyPyHpPyIm 2391) 5'W C G A GC G W-3' PyImPyImPyIm-y-PyImPyHpPyIm 2392) 5'W C G A GC C W-3' PyImPyImPyPy-y-ImImPyHpPyim 2393) 5'W C G A CT T W-3' PyImPyPyHpHp-y-PyPyImHpPyIm 2394) 5'W C G A CT A W-3' PyImPyPyHpPy-y-HpPyImHpPyIm 2395) 5'W C G A CT G W-3' PyImPyPyHpIm-y-PyPyImHpPyIm 2396) 5'W C G A CT C W-3' PyImPyPyHpPy-y-ImPyImHpPyIm 2397) 5'W C G A CA T W-3' PyImPyPyPyHp-y-PyHpImHpPyIm 2398) 5'W C G A CA A W-3' PyImPyPyPyPy-y-HpHpImHpPyIm 2399) 5'W C G A CA G W-3' PyImPyPyPyIm-y-PyHpImHpPyIm 2400) 5'W C G A CA C W-3' PyImPyPyPyPy-y-ImHpImHpPyIm 2401) 5'W C G A CG T W-3' PyImPyPyImHp-y-PyPyImHpPyIm 2402) 5'W C G A CG A W-3' PyImPyPyImPy-y-HpPyImHpPyIm 2403) 5'W C G A CC T W-3' PyImPyPyPyHp-y-PyImImHpPyIm 2404 5' C G A CC A W-3 PyImPyPyPyPy-y-HpImImHpPyIm ) W ' 2405) 5'W C G A CG G W-3' PyImPyPyImIm-y-PyPyImHpPyIm 2406) 5'W C G A CG C W-3' PyImPyPyImPy-y-ImPyImFFpPyIm 2407) 5'W C G A CC G W-3' PyImPyPyPyIm-y-PyImImHpPyIm 2408) 5'W C G A CC C W-3' PyImPyPyPyPy-y-ImImImHpPyIm TABLE 12-ring I22: Hairpin Polyamides for recognition of 8-by 5'-WCGCWNNW-3' DNA aromatic amino acid sequence sequence 2409) 5'W CG C T T T W-3' PyImPyHpHpHp-y-pypypyImPyIm 2410 ) 5' CG C T T A W-3 ' PyImPyHpHpPy-y-HpPyPyImPyIm TnT
2411) 5'W CG C T T G W-3' PyImPyHpHpIm-y-PypypyImPyIm 2412) 5'W CG C T T C W-3' PyImPyHpHpPy-y-ImPyPyImPyIm 2413 ) 5' CG C T A T W-3 ' PyImPyHpPyHp-y-PyHpPyImPyIm W
2414 ) 5' CG C T A A W-3 ' PyImPyHpPyPy-y-HpHpPyImPyIm W
2415 ) 5' CG C T A G W-3 T PyImPyHpPyIm-y-PyHpPyImPyIm W
2416) 5'W CG C T A C W-3' PyImPyHpPyPy-y-ImHpPyImPyIm 2417) 5'W CG C T G T W-3' PyImPyHpImHp-y-PyPypyImPyIm 2418 ) 5' CG C T G A W-3 ' PyImPyHpItttPy-y-HpPyPyImPyIm W
2419 ) 5' CG C T G G W-3' PyImPyHpImIm-y-PyPyPyImPyIm W
2420) 5'W CG C T G C W-3' PyImPyHpImPy-y-ImPyPyImPyIm 2421) 5'W CG C T C T W-3' PyImPyHpPyHp-y-PyImPyImPyIm 2422) 5'W CG C T C A W-3' PyImPyHpPyPy-y-HpImPyImPyIm 2423 ) 5' CG C T C G W-3' PyImPyHpPyIm-y-PyImPyImPyIm W
2424) 5'W CG C T C C W-3' PyImPyHpPyPy-y-ImImPyImPyIm 2425) 5'W CG C A T T W-3' PyImPyPyHpHp-y-pyPyHpimPyIm 2426 ) 5' CG C A T A W-3 ' PyImPyPyHppy-y-HpPyHpImPyIm W
2427 ) 5' CG C A T G W-3 ' PyImPypyHpIm-y-PyPyHpImPyIm W
2428) 5'W CG C A T C W-3' PyImPyPyHpPy-y-ImPyHpImPyIm 2429) 5'W CG C A A T W-3' PyImPyPyPyHp-y-PyHpHpImPyIm 2430) 5'W CG C A A A W-3' PyImPyPyPyPy-y-HpHpHpImPyIm 2431) 5'W CG C A A G W-3' PyImPyPyPyIm-y-PyHpHpImPyIm 2432) 5'W CG C A A C W-3' PyImPyPyPyPy-y-ImHpHpImPyIm 2433) 5'4JCG C A G T W-3' PyImPyPyImHp-y-PyPyHpImPyIm - 2434) 5'W CG C A G A W-3' PyImPyPyImPy-y-HpPyHpImPyIm 2435) 5'W CG C A G G W-3' PyImPyPyImIm-y-PyPyHpImPyIm 24 3 6 5' CG C A G C W-3 ' PyImPyPyImPy-y- ImPyHpImPyIm ) W
2437 ) 5' CG C A C T W-3' pyImPyPyPyHp-y-PyImHpImPyIm W
2438) 5'W CG C A C A W-3' PyImPyPyPyPy-y-HpImHpImPyIm _ 2439) 5'W CG C A C G W-3' PyImPyPyPyIm-y-PyImHpImPyIm 2440) 5'W CG C A C C W-3' PyImPyPyPyPy-y-ImImHpImPyim WO 9$/37067 PCT/US98/01714 TABLE 123:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCGCSNNW-3' DNA aromatic amino acid sequence sequence 2441) 5' W C GC GT T W-3' PyImPyImApHp-y-PyPyPyImPyIm 2442) 5' W C GC GT A W-3' PyImPyImHpPy-y-HpPyPyImPyIm 2443) 5' W C GC GT G W-3' PyImPyImHpIm-y-PyPyPyImPyIm 2444) 5' W C GC GT C W-3' PyImPyImHpPy-y-ImPyPyImPyIm 2445) 5' W C GC GA T W-3' PyImPyImPyHp-y-PyHpPyImPyIm 2446) 5' W C GC GA A W-3' PyImPyImPyPy-y-HpHpPyImPyim 2447) 5' W C GC GA G W-3' PyImPyImPyIm-y-PyHpPyImPyIm 2448) 5' W C GC GA C W-3' PyImPyImPyPy-y-ImHpPyImPyIm 2449) 5' W C GC GG T W-3' PyImPyImImHp-y-PyPyPyImPyim 2450) 5' W C GC GG A W-3' PyImPyImImPy-y-HpPyPyImPyIm 2451) 5' W C GC GC T W-3' PyImPyImPyHp-y-PyImPyImPyIm IS 2452) 5' W C GC GC A W-3' PyImPyImPyPy-y-HpImPyImPyIm 2453) 5' W C GC CT T W-3' PyImPyPyHpHp-y-PyPyImImPyIm 2454 5' W C GC CT A W-3 ' PyImPyPyHpPy-y-HpPyImImPyIm ) 2455) 5' W C GC CT G W-3' PyImPyPyHpIm-y-PyPyImImPyIm 2456 5' W C GC CT C W-3' PyImPyPyHpPy-y-ImPyImImPyIm ) 2457 5' W C GC CA T W-3' PyImPyPyPyHp-y-PyHpImImPyIm ) 2458) 5' W C GC CA A W-3' PyImPyPyPyPy-y-HpHpImImPyIm 2459) 5' W C GC CA G W-3' PyImPyPyPyIm-y-PyHpImImPyIm 2460) 5' W C GC CA C W-3' PyImPyPyPyPy-y-ImHpImImPyIm 2461) 5' W C GC CG T W-3' PyImPyPyImHp-y-PyPyImImPyIm 2462 5' W C GC CG A W-3' PyImPyPyImPy-y-HpPyImImPyIm ) 2463) 5' W C GC CC T W-3' PyImPyPyPyHp-y-PyImImImPyIm 2464) 5' W C GC CC A W-3' Py3mPyPyPyPy-y-HpImImImPyIm G91) 5' W C GC GG G W-3' PyImPyImImIm-y-PyPyPyImPyIm G92 ) 5' W C GC GG C W-3' PyImPyImImPy-y-ImPyPyImPyIm G93 ) 5' W C GC GC G W-3' PyImPyImPyIm-y-PyImPyImPyIm G94) 5' W C GC GC C W-3' PyImPyImPyPy-y-ImImPyImPyIm G95) 5' W C GC CG G W-3' PyImPyPyImIm-y-PyPyImImPyIm G96) 5' W C GC CG C W-3 ' PyImPyPyImPy-y-ImPyImImPyIm G97 ) 5' W C GC CC G W- 3 PyImPyPyPyIm-y-PyImImImPyIm ' G98) 5' W C GC CC C W-3' PyImPyPyPyPy-y-ImImImImPyIm TABLE
124:
12-ring Hairpin Polyamides for recognition of 8-by S'-WCCGWNNW-3' DNA aromatic amino acid sequence sequence 2465) 5'W C C G T T TW-3' PyPyImHpHpHp-y-PypypypyImIm S 2466) 5'W C C G T T AW-3' PyPyImHpHpPy-y-HpPyPypyImlm 2467) 5'W C C G T T GW-3' PyPyImHpHpIm-y-pyPypypylmlm 2468) 5'W C C G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyImIm 2469) 5'W C C G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyImIm 247 0 5' C C G T A AW-3 ' PyPyImHppyPy-y-HpHpPyPyImIm ) W
2471) 5'W C C G T A GW-3' PyPyImHpPyIm-y-PyHpPyPyImIm 2472) 5' C C G T A CW-3' PyPyImHpPyPy-y-ImHpPyPyImIm W
2473) 5'W C C G T G TW-3' PyPyImHpImHp_y-PyPypypylmlm 2474) 5'W C C G T G AW-3' PyPyImHpImPy-y-HpPyPyPyImIm 2475) 5'W C C G T G GW-3' PyPyImHpImIm-y-pyPypypylmlm 1S 2476) 5'W C C G T G CW-3' PyPyImHpImPy-y-ImpyPyPyImIm 2477 5' C C G T C TW-3 ' PyPyImHpPyHp-y-PyImPyPyImIm ) W
2478) 5'W C C G T C AW-3' PyPyImHpPyPy-y-HpImPyPyImIm 247 9 5' C C G T C GW-3 ' PyPyImHpPyIm-y-PyImPypyImlm ) W
2480) 5'W C C G T C CW-3' PyPyImHpPypy-y-ImImPyPyImIm 2481) 5'W C C G A T TW-3' PyPyImPyHpHp-y-PyPyHpPyImIm 2482) 5'W C C G A T AW-3' PyPyImPyHpPy-y-HpPyHppyImIm 2483) 5'W C C G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyImIm 2484) 5'W C C G A T CW-3' PyPyImPyHpPy-y-ImPyHpPyImIm 2485) 5'W C C G A A TW-3' PyPyImPyPyHp-y-PyHpHppyImlm 2S 2486) 5'W C C G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyImIm 2487) 5'W C C G A A GW-3' PyPyImPyPyIm-y-PyHpHpPyImIm 2488) 5'W C C G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyImIm 2489) 5'W C C G A G TW-3' PyPyImPyImHp-y-PyPyHpPyImIm 2490) 5'W C C G A G AW-3' PyPyImPyImPy-y-HppyHpPyImIm 2491) 5'W C C G A G GW-3' PyPyImPyImIm-y-PypyHpPyImIm 2492) 5'W C C G A G CW-3' PyPyImPyImPy-y-ImPyHpPyImIm 2493 5' C C G A C TW-3 ' PyPyImPypyHp-y-PyImHppyImIm ) W
24 94 5' C C G A C AW-3 ' PyPyImPyPyPy-y-HpImHpPyImIm ) W
_ 2495) 5'W C C G A C GW-3' PyPyImPyPyIm-y-PyImHpPyImIm 3S 2496) 5'W C C G A C CW-3' PyPyImPyPyPy-y-ImImHpPyImIm WO 98137067 , PCT/US98/01714 TABLE
125:
12-ring-Hairpin Polyamides for recognition of 8-by 5'-WCCGSNNW-3' DNA aromatic amino acid sequence sequence 2497) 5'W C C G G T TW-3' PyPyImImHpHp-y-PyPyPyPyImIm 2498} 5''W C C G G T AW-3' PyPyImImHpPy-y-HpPyPyPyImIm 2499) 5'W C C G G T GW-3' PyPyImImHpIm-y-PyPyPyPyImIm 2500) 5'W C C G G T CW-3' PyPyImImHpPy-y-ImPyPyPyImIm 2501) 5'W C C G G A TW-3' PyPyImImPyHp-y-PyHpPyPyImIm 2502) 5'W C C G G A AW-3' PyPyImImPyPy-y-HpHpPyPyImIm 2503 5' C C G G A GW-3 ' PyPyImImPyIm-y-PyHpPyPyImIm ) W
2504 5' C C G G A CW-3 ' PyPyImImPyPy-y-ImHpPyPyImIm ) W
2505) 5'W C C G G G TW-3' PyPyImImImHp-y-PyPyPyPyImIm 2506) 5'W C C G G G AW-3' PyPyImImImPy-y-HpPyPyPyImIm 2507) 5'W C C G G C TW-3' PyPyImImPyHp-y-PyImPyPyImIm 2508) 5'W C C G G C AW-3' PyPyImImPyPy-y-HpImPyPyImIm 2509) 5'W C C G C T TW-3' PyPyImPyHpHp-y-PyPyImPyImIm 2510 5' C C G C T AW-3' PyPyImPyHpPy-y-HpPyImPyImIm ) W
2511) 5'W C C G C T GW-3' PyPyImPyHpIm-y-PyPyImPyImIm 2512 5' C C G C T CW-3 ' PyPyImPyHpPy-y-ImPyImPyImIm ) W
2513 5' C C G C A TW-3' PyPyImPyPyHp-y-PyHpImPyImIm ) W
2514 5' C C G C A AW-3 ' PyPyImPyPyPy-y-HpHpImPyImIm ) W
2515 5' C C G C A GW-3 ' PyPyImPyPyIm-y-PyHpImPyImIm } W
2516) 5'W C C G C A CW-3' PyPyImPyPyPy-y-ImHpImPyImIm 2517 5' C C G C G TW-3 ' PyPyImPyImHp-y-PyPyImPyImIm ) W
2 518 5' C C G C G AW-3 ' PyPyImPyImPy-y-HpPyImPyImIm ) W
2519 5' C C G C C TW-3 ' PyPyImPyPyHp-y-PyImImPyImIm ) W
2520) 5'W C C G C C AW-3' PyPyImPyPyPy-y-HpImImPyImIm G99) 5'W C C G G G GW-3' PyPyImImImIm-y-PyPyPyPyImIm 6100) 5'W C C G G G CW-3' PyPyImImImPy-y-ImPyPyPyImIm 6101) 5'W C C G G C GW-3' PyPyImImPyIm-y-PyImPyPyImIm 6102) 5'W C C G G C CW-3' PyPyImImPyPy-y-ImImPyPyImIm 6103 5' C C G C G GW-3 ' PyPyImPyImIm-y-PyPyImPyImIm ) W
6104) 5'W C C G C G CW-3' PyPyImPyImPy-y-ImPyImPyImIm 6105) 5'W C C G C C GW-3' PyPyImPyPyIm-y-PyImImPyImIm 6106) 5'W C C G C C CW-3' PyPyImPyPyPy-y-ImImImPyImIm ~w_ ...~,.. . . , 1'A13LE
I26:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCTWNNW-3' DNA aromatic amino acid sequence sequence 2521) 5'W C C TT T T W-3' PyPyHpHpHpHp-y-PyPyPypyImIm 2522) 5'W C C TT T A W-3' PyPyHpHpHpPy-y-HpPyPyPyImIm 2523) 5'W C C TT T G W-3' PyPyHpHpHpIm-y-PyPyPyPyImIm 2524) 5'W C C TT T C W-3' PyPyHpHpHpPy-y-ImPyPypyImlm 2525) 5'W C C TT A T W-3' PyPyHpHpPyHp-y-PyHpPyPyImIm 2526) 5'W C C TT A A W-3' PyPyHpHpPyPy-y-HpHpPypyImIm 2527 ) 5' C C TT A G W-3' PyPyHpHpPyIm-y-PyHpPyPyImIm W
2528) 5'W C C TT A C W-3' PyPyHpHpPyPy-y-ImHppyPyImIm 2529) 5'W C C TT G T W-3' PyPyHpHpImHp-y-PyPyPyPyImIm 2530) 5'W C C TT G A W-3' PyPyHpHpImPy-y-HpPyPyPyImIm 2531) 5'W C C TT G G W-3' PyPyHpHpImIm-y-pypypypyImlm 2532) 5'W C C TT G C W-3' PyPyHpHpImPy-y-ImPyPyPyImIm 2533) 5'W C C TT C T W-3' PyPyHpHpPyHp-y-PyImPyPyImIm 2534 ) 5' C C TT C A W-3' PyPyHpHpPyPy-y-HpImPyPyImIm W
2535) 5'W C C TT C G W-3' PyPyHpI-ipPyIm-y-PyImPyPyImIm 2536) 5'W C C TT C C W-3' PypyHpHpPyPy-y-ImImPyPyImIm 2537) 5'W C C TA T T W-3' PyPyIipPyHpHp-y-PyPyHpPyImIm 2538) 5'W C C TA T A W-3' PyPyHpPyHpPy-y-HpPyHpPyImIm 2539) 5'W C C TA T G W-3' PyPyHpPyHpIm-y-PyPyHppyImlm 2540 ) 5' C C TA T C W-3 PyPyHpPyHpPy-y-ImPyHpPyImIm W ' 2541) 5'W C C TA A T W-3' PyPyHpPyPyHp-y-PyHpHpPyImIm 2542) 5'W C C TA A A W-3' PyPyHpPyPyPy-y-HpHplipPyImIm 2543) 5'W C C TA A G W-3' PyPyHpPyPyIm-y-PyHpHpPyImIm 2544) 5'W C C TA A C W-3' PyPyHpPyPyPy-y-ImHpHpPyImIm 2545) 5'W C C TA G T W-3' PyPyHpPyImHp-y-PyPyHpPyImIm 2546) 5'W C C TA G A W-3' PyPyHpPyImPy-y-HpPyHpPyImIm 2547 ) 5' C C TA G G W-3 PyPyHpPyImIm-y-PyPyHpPyImIm W ' 2548) 5'W C C TA G C W-3' PyPyHpPyImPy-y-ImPyFipPyImIm 2549) 5'W C C TA C T W-3' PypyHpPyPyHp-y-PyImHpPyImIm 2550) 5'W C C TA C A W-3' PyPyHpPyPyPy-y-HpImHpPyImIm 2551) 5'W C C TA C G W-3' PyPyHpPypyIm-y-PyImHpPyImIm 2552) 5'W C C TA C C W-3' PyPyHpPyPyPy-y-ImImHpPyImIm WO 98137067 , PCTIUS98/01714 TABLE
127:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCTSNNW-3' DNA aromatic amino acid sequence sequence 2553 5' C C T GT T W-3 ' PyPyHpImHpHp-y-PyPyPyPyImIm ) W
2554) 5'W C C T GT A W-3' PyPyHpImHpPy-y-HpPyPyPyImIm 2555) 5'W C C T GT G W-3' PyPyHpImFipIm-y-PyPyPyPyImIm 2556) 5'W C C T GT C W-3' PyPyHpImHpPy-y-ImPyPyPyImIm 2557 5' C C T GA T W-3 ' PyPyHpImPyHp-y-PyHpPyPyImIm ) W
2558) 5'W C C T GA A W-3' PyPyHpImPyPy-y-HpHpPyPyImIm 2559) 5'W C C T GA G W-3' PyPyHpImPyIm-y-PyHpPyPyImIm 2560) 5'W C C T GA C W-3' PyPyHpImPyPy-y-ImHpPyPyImIm 2561} 5'W C C T GG T W-3' PyPyHpImImHp-y-PyPyPypyImlm 2562) 5'W C C T GG A W-3' PyPyHpImImPy-y-HpPyPyPyImIm 2563) 5'W C C T GC T W-3' PyPyHpImPyHp-y-PyImPyPyImIm 2564) 5'W C C T GC A W-3' PyPyHpImPyPy-y-HpImPyPyImIm 2565) 5'W C C T GG G W-3' PypyHpImImIm-y-PyPyPyPyImIm 2566) 5'W C C T GG C W-3' PyPyHpImImPy-y-ImPyPyPyImIm 2567 5' C C T GC G W-3 ' PyPyHpImPyIm-y-PyImPyPyImIm ) W
2568) 5'W C C T GC C W-3' PyPyHpImPyPy-y-ImImPyPyImIm 2569) 5'W C C T CT T W-3' PyPyHpPyHpHp-y-PyPyImpyImlm 2570) 5'W C C T CT A W-3' PyPyHpPyHpPy-y-HpPyImPyImIm 2571) 5'W C C T CT G W-3' PyPyHpPyHpIm-y-PyPyImPyImIm 2572) 5'W C C T CT C W-3' PyPyHpPyHpPy-y-ImPyImPyImIm 2573) 5'W C C T CA T W-3' PyPyHpPyPyHp-y-PyHpImPyImIm 2574) 5'W C C T CA A W-3' PyPyHpPyPyPy-y-HpHpImPyImIm 2575) 5'W C C T CA G W-3' PyPyHpPyPyIm-y-PyHpImPyImIm 2 57 5' C C T CA C W-3 ' PyPyHpPyPyPy-y- ImHp ImPyImIm 6 } W
2577) 5'W C C T CG T W-3' PyPyHpPyImHp-y-PyPyImpyImIm 2578) 5'W C C T CG A W-3' PyPyHpPyImPy-y-HpPyImPyImIm 2579) 5'W C C T CC T W-3' PyPyHpPyPyF-Ip-y-PyImImPyImIm 2580) 5'W C C T CC A W-3' PypyHpPyPyPy-y-HpImImPyImIm 2581) 5'W C C T CG G W-3' PyPyHpPyImIm-y-PyPyImPyImIm 2582) 5'W C C T CG C W-3' PyPyHpPyImPy-y-ImPyImPyImIm 2583) 5'W C C T CC G W-3' PyPyHpPyPyIm-y-PyImImPyImIm 2584) 5'W C C T CC C W-3' PyPyHpPyPyPy-y-ImImImPyImIm 128:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCAWNNW-3' DNA aromatic amino acid sequence sequence 2585) 5'W CC A T T T W-3' PyPyPyHpHpHp-y-PyPypygpImIm 2586) 5'W CC A T T A W-3' PyPyPyHpHpPy-y-HpPyPyHpImIm 2587) 5'W CC A T T G W-3' PyPypyHpHpIm-y-PyPypyHpImIm 2588) 5'W CC A T T C W-3' PyPyPyHpHpPy-y-ImPyPyHpImIm 2589 ) 5' CC A T A T W-3' PyPyPyHpPyHp-y-PyHpPyHpImIm W
2590) 5'W CC A T A A W-3' PyPyPyHpPyPy-y-HpHpPyHpImIm 2591) 5'W CC A T A G W-3' PyPyPyHpPyIm-y-PyHpPyHpImIm 2592) 5'W CC A T A C W-3' PyPyPyHpPyPy-y-ImHpPyHpImIm 2593) 5'W C C A T G T W-3' PyPyPyHpImHp-y-PyPyPyHpImIm 2594) 5'W C C A T G A W-3' PyPyPyHpImPy-y-HpPyPyHpImIm 2595) 5'W C C A T G G W-3' PyPyPyHpImIm-y-PypypyHpImIm 2596) 5'W C C A T G C W-3' PyPyPyHpImPy-y-ImPyPyHpImIm 2597) 5'W C C A T C T W-3' PyPyPyHpPyHp-y-pyImPyHpImIm 2598) 5'W C C A T C A W-3' PyPyPyHpPypy-y-HpImPyHpImIm 2599) 5'W C C A T C G W-3' PyPyPyHpPyIm-y-PyImPyHpImIm 2600) 5'W C CA T C C W-3' PyPyPyHpPyPy-y-ImImPyHpImIm 2601) 5'W C CA A T T W-3' PyPyPyPyHpHp-y-PyPyHpHpImIm 2602) 5'W C CA A T A W-3' PyPyPyPyHpPy-y-HpPyHpHpImIm 2603) 5'W C CA A T G W-3' PyPyPyPyHpIm-y-PypyHpHpImIm 2604) 5'W C CA A T C W-3' PyPyPyPyHpPy-y-ImPyHpHpImIm 2605) 5'W C CA A A T W-3' PyPyPyPypyHp-y-pyHpHpHpImIm 2606) 5'W C CA A A A W-3' PyPyPyPyPyPy-y-HpHpHpHpImIm 2607) 5'W C CA A A G W-3' PyPyPypypyIm-y-PyHpHpHpImIm 2608) 5'W C CA A A C W-3' PyPyPyPyPyPy-y-ImHpHpHpImIm 2609) 5'W C CA A G T W-3' PyPyPyPyImHp-y-PyPyHpHpImIm 2610 ) 5' C CA A G A W-3 PyPyPyPyImPy-y-HpPyHpHpImIm W ' 2611) 5'W C CA A G G W-3' PyPyPyPyImIm-y-PyPyHpHpImIm 2 612 ) 5' C CA A G C W-3 yPyPyPyImPy-y- ImPyHpHpImIm W P ' 2613) 5'W C CA A C T W-3' PyPyPyPypyHp-y-PyImHpHpImIm 2 614 ) 5' C CA A C A W-3 PyPyPyPypypy-y-HpI~pHpImIm W ' _ 2615) 5'W C CA A C G W-3' pyPypypypylm-y-pyi~pHpimim 2616) 5'W C CA A C C W-3' PypyPypypypy-y-ImImHpHpImIm TABLE
129:
12-ring Hairpin Polyamides for recognition of 8-by S'-WCCASNNW-3' DNA aromatic amino acid sequence sequence 2617 ) 5' C CA GT T W-3 PyPyPyImHpHp-y-PyPyPyHpImIm W ' 2618) 5'~W C CA GT A W-3' PyPyPyImHpPy-y-HpPyPyHpImIm 2619) 5'W C CA GT G W-3' PyPyPyImHpIm-y-PyPyPyHpImIm 2620) 5'W C CA GT C W-3' PyPyPyImHpPy-y-ImPyPyHpImIm 2621) 5'W C CA GA T W-3' PyPypyImPyHp-y-PyHpPyHpImIm 2622) 5'W C CA GA A W-3' PyPypyImPyPy-y-HpHpPyHpImIm 2623) 5'W C CA GA G W-3' PyPyPyImPyIm-y-PyHpPyHpImIm 2624) 5'W C CA GA C W-3' PyPyPyImPyPy-y-ImHpPyHpImIm 2625) 5'W C CA GG T W-3' PyPyPyImImHp-y-PyPyPyHpImIm 2626) 5'W C CA GG A W-3' PyPyPyImImPy-y-HpPyPyHpImIm 2627) 5'W C CA GC T W-3' PyPyPyImPyHp-y-PyImPyHpImIm 2628) 5'W C CA GC A W-3' PyPyPyImPyPy-y-HpImPyHpImIm 2629) 5'W C CA GG G W-3' PyPyPyImImIm-y-PyPyPyHpImIm 2630) 5'W C CA GG C W-3' PyPyPyImImPy-y-ImPyPyHpImIm 2631) 5'W C CA GC G W-3' PyPyPyImPyIm-y-PyImPyHpImIm 2632) 5'W C CA GC C W-3' PyPyPyImPyPy-y-ImImPyHpImIm 2633) 5'W C CA CT T W-3' PyPyPyPyHpHp-y-PyPyImHpImIm 2634) 5'W C CA CT A W-3' PyPyPyPyHpPy-y-HpPyImHpImIm 2635) 5' C CA CT G W-3' PyPyPyPyHpIm-y-PyPyImHpImIm W
2636) 5'W C CA CT C W-3' PyPyPyPyHpPy-y-ImPyImHpImIm 2637) 5'W C CA CA T W-3' PyPyPyPyPyHp-y-PyHpImHpImIm 2638) 5'W C CA CA A W-3' PyPyPyPyPyPy-y-HpHpImHpImIm 2639) 5'W C CA CA G W-3' PyPyPyPyPyIm-y-PyHpImHpImIm 2640) 5'W C CA CA C W-3' PyPyPyPyPyPy-y-ImHpImHpImIm 2641) 5'W C CA CG T W-3' PyPyPyPyImHp-y-PyPyImHpImIm 2642) 5'W C CA CG A W-3' PyPyPyPyImPy-y-HpPyImHpImIm 2643) 5'W C CA CC T W-3' PyPyPyPyPyHp-y-PyImImHpImIm 2644) 5'W C CA CC A W-3' PyPyPyPyPyPy-y-HpImImHpImIm 2645) 5'W C CA CG G W-3' PyPyPyPyImIm-y-PyPyImHpImIm 2646) 5'W C CA CG C W-3' PyPyPyPyImPy-y-ImPyImHpImIm 2647) 5'W C CA CC G W-3' PyPyPyPyPyIm-y-PyImImHpImIm 2648) 5'W C CA CC C W-3' pypypyPyPyPy-y-ImImImHpImIm WO 98/37067 . PCT/US98/01714 'TABLE 130: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCCCWNNW-3' DNA sequence aromatic amino acid sequence 2649) 5'W C C C T T T W-3' PyPyPyHpHpHp-y-PyPypyImImIm 2650) 5'W C C C T T A W-3' PyPyPyHpHpPy-y-HpPyPyImImIm 2651) 5'W C C C T T G W-3' PyPyPyHpHpIm-y-PyPyPyImImIm 2652) 5'W C C C T T C W-3' PyPyPyHpHpPy-y-ImPyPyImImIm 2653) 5'W C C C T A T W-3' PyPyPyHpPyHp-y-PyHpPyImImIm 2654} 5'W C C C T A A W-3' PyPyPyHpPyPy-y-HgHpPyImImIm 2655) 5'W C C C T A G W-3' PyPyPyHpPyIm-y-PyHpPyImImIm 2656) 5'W C C C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImImIm 2657) 5'W C C C T G T W-3' PyPyPyHpImHp-y-PyPypyImImIm 2658) 5'W C C C T G A W-3' PyPyPyHpImPy-y-HpPyPyImImIm 2659) 5'W C C C TG G W-3' PyPypyHpImIm-y-PyPyPyImImIm 2660) 5'W C C C TG C W-3' PyPyPyHpImPy-y-ImPyPyImImIm 2661} 5'W C C C TC T W-3' PyPyPyHpPyHp-y-PyImPyImImIm 2662) 5'W C C C TC A W-3' PyPyPyHpPyPy-y-HpImPyImImIm 2663) 5'W C C C TC G W-3' PyPyPyHpPyIm-y-PyImPyImImIm 2664) 5'W C C C TC C W-3 T PyPyPyHpPyPy-y-ImImPyImImIm 2665) 5'W C C C AT T W-3' PyPyPyPyHpHp-y-PyPyHpImImIm 2666) 5'W C C C AT A W-3' PyPyPyPyHpPy-y-HpPyHpImImIm 2667} 5'W C C C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImImIm 2668) 5'W C C C AT C W-3' PyPyPyPyHpPy-y-ImPyHpImImIm 2669) 5'W C C C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImImIm 2670) 5'W C C C AA A W-3' PyPyPyPyPyPy-y-HpHpHpImImIm 2671) 5'W C C C AA G W-3' PyPyPyPyPyIm-y-PyHpHpImImIm 2 672 ) 5' W C C C A A C W-3 ' PyPyPyPyPyPy-y- ImHpHpImImIm 2673) 5'W C C C A G T W-3' PyPyPyPyImHp-y-PyPyHpImImim 2674) 5'W C C C A G A W-3' PyPyPyPyImPy-y-HpPyHpImImIm 2675) 5'W C C C A G G W-3' PyPyPyPyImIm-y-pyPyHpImImIm 2676) 5'W C C C A G C W-3' PyPypypylmpy-y-ImPyHpImImIm 2677) 5'W C C C A C T W-3' PyPyPyPyPyHp-y-PyImHpImImIm 2678) 5'W C C C A C A W-3' Pypypypypypy-y-HpImFipImImIm 2679) 5'W C C C A C G W-3' Pypypypypylm-y-pyImHpImImIm 2680) 5'W C C C A C C W-3' PyPyPyPyPyPy-y-ImImHpImImIm TABLE 131: 12-ring Hairpin Polyamides far recognition of 8-by 5'-WCCCSNNW-3' DNA sequence aromatic amino acid sequence 2681) 5'W C C C G T T W-3' PyPyPyImApHp-y-PyPyPyImImIm 2 6 82 ) 5' C C C G TA W-3 ' PyPypyImHppy-y-HpPyPyImImIm W' 2683) 5'W C C C G TG W-3' PyPyPyImHpIm-y-PyPyPyImImIm 2684) 5'W C C C G TC W-3' PyPyPyImHpPy-y-ImPyPyImImIm 2685) 5'W C C C G AT W-3' pyPyPyImPyHp-y-PyHpPyImImIm 2686) 5'W C C C G AA W-3' PyPyPyImPyPy-y-HpHpPyImImIm 2687) 5'W C C C G AG W-3' PyPyPyImPyIm-y-PyHpPyImImIm 2688) 5'W C C C G AC W-3' PyPyPyImPyPy-y-ImHpPyImImIm 2689) 5'W C C C G GT W-3' PyPyPyImImHp-y-PypypyzmImIm 2690) 5'W C C C G GA W-3' PyPypyImImPy-y-HpPyPyImImIm 2691) 5'W C C C G CT W-3' PyPyPyImPyHp-y-PyImPyImImIm 2692) 5'W C C C G CA W-3' PyPyPyImpypy_y-HpImPyImImIm 2693) 5'W C C C C TT W-3' PyPyPyPyHpHp-y-PyPyImIm3mIm 2694) 5'W C C C C TA W-3' PyPyPyPyFipPy-y-HpPyImImImIm 2695) 5'W C C C C TG W-3' PyPyPyPyHpIm-y-PyPyImImImIm 2696) 5'W C C C C TC W-3' pyPyPyPyIipPy-y-ImPyImImImIm 2697) 5'W C C C C AT W-3' PyPyPyPyPyHp-y-PyHpImImImIm 2698) 5' C C C C AA W-3' PyPyPyPyPyPy-y-HpHpImImImIm W
2699) 5'W C C C C AG W-3' PyPyPyPyPyIm-y-PyHpImImImIm 2690) 5'W C C C C AC W-3' PypypyPyPyPy-y-ImHpImImImIm 2701) 5'W C C C C GT W-3' PyPyPyPyImHp-y-PyPyImImImIm 2702) 5'W C C C C GA W-3' PyPyPyPyImPy-y-HpPyImImImIm 2703) 5'W C C C C C T W-3' PyPyPyPyPyHp-y-PyImImImImIm 2704) 5'W C C C C C A W-3' PyPyPyPyPypy-y-HpImImImImIm 6107 ) 5' W C C C G G G W-3' PyPyPyImImIm-y-PyPyPyImImIm 6108) 5'W C C C G G C W-3' PyPyPyImImPy-y-ImPyPyImImIm 6109) 5'W C C C G C G W-3' PyPyPyImPyIm-y-PyImPyImImIm 6110) 5'W C C C G C C W-3' PyPyPyImPyPy-y-ImImPyImImIm 6111) 5' W C C C C G G W-3' PypyPyPyImIm-y-PyPyImImImIm 6112 ) 5' W C C C C G C W-3 ' PyPyPyPyImPy-y- ImPyImImImIm 6113 ) 5' W C C C C C G W-3 ' PyPypypypylm-y-pyImImImImIm 6114) 5'W C C C C C C W-3' pypypypypypy-y-ImImImImImIm ,. , 1-Al3Lt; 132:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAGWNNW-3' DNA aromatic amino acid sequencc sequence ' 2705) 5'W C A G T T TW-3' PyPyImHpHpHp-y-pypypypyHplm ' 5 2706) 5'W C A G T T AW-3' PypyImHpHpPy-y-HpPyPyPyHpIm 270?) 5'W C A G T T GW-3' PyPyImHpHpIm-y-pypypypyHpIm 2708) 5'W C A G T T CW-3' PyPyImHpHpPy-y-ImPyPyPyHpIm 2709} 5'W C A G T A TW-3' PyPyImHpPyHp-y-PyHpPyPyHpIm 2700) 5'W C A G T A AW-3' PyPyImHpPyPy-y-HpHpPyPyFipIm 2711) 5' C A G T A GW-3 ' PyPyImHpPyIm-y-PyHpPyPyHpIm W
2712) 5'W C A G T A CW-3' PyPyImHpPyPy-y-ImHppyPyHpIm 2713) 5'W C A G T G TW-3' PyPyImHpImHp-y-PyPyPyPyHpIm 2714 5' C A G T G AW-3 ' PyPyImHpImPy-y-HpPyPyPyHpIm ) W
2715) 5'W C A G T G GW-3' PyPyImHpImIm-y-PypypypyHplm 2716) 5'W C A G T G CW-3' PyPyImHpImPy-y-ImPyPyPyHpIm 2717) 5'W C A G T C TW-3' PyPyImHpPyHp-y-PyImPyPyHpIm 2718) 5'W C A G T C AW-3' PyPyImHpPyPy-y-HpImPyPyHpIm 2719) 5'W C A G T C GW-3' PyPyImHpPyIm-y-PyImPyPyHpIm 2720) 5'W C A G T C CW-3' PyPyImHpPyPy-y-ImImPyPyHpIm 2721) 5'W C A G A T TW-3' PyPyImPyHpHp-y-PyPyHppyHplm 2722) 5'W C A G A T AW-3' PypyImPyHpPy-y-HpPyHpPyHpIm 2723) 5'W C A G A T GW-3' PyPyImPyHpIm-y-PyPyHpPyHpIm 2724) 5'W C A G A T CW-3' PyPyImPyHpPy-y- ImPyFipPyHpIm 2725) 5'W C A G A A TW-3' PyPyImPyPyHp-y-PyHpHpPyHpIm 2726) 5'W C A G A A AW-3' PyPyImPyPyPy-y-HpHpHpPyHpIm 2727) 5'W C A G A A GW-3' 'PyPyImPyPyIm-y-PyHpHpPyHpIm 2728) 5'W C A G A A CW-3' PyPyImPyPyPy-y-ImHpHpPyHpIm 2729) 5'W C A G A G TW-3' PyPyImPyImHp-y-pypyHpPyHpIm 2730) 5'W C A G A G AW-3' ' PyPyImPyImPy-y-HpPyHpPyHpIm 2731) 5'W C A G A G GW-3' PyPyImPyImIm-y-PyPyHpPyHpIm 2732) 5'W C A G A G CW-3' PyPyImPyImPy-y-ImPyHpPyHpIm 2733) 5'W C A G A C TW-3' PyPyImPyPyHp-y-PyImHpPyHpIm 2734) 5'W C A G A C AW-3' PyPyImPyPyPy-y-HpImHpPyHpIm 2735) 5'W C A G A C GW-3' PyPyImPyPyIm-y-pyImHpPyHpIm 2736) 5'W C A G A C CW-3' PyPyImPyPyPy-y-ImImHpPyHpIm TABLE 133: 12-ring Hairpin Polyamides for recognition of 8-by S'-WCAGSNNW-3' DNA sequence aromatic amino acid sequence 2737) 5'W C A G G T T W-3' PyPyImImHpHp-y-PyPyPyPyHpIm 2738) 5~'W C A G G T A W-3' PyPyImImHpPy-y-HpPyPyPyHpIm 2739) 5'W C A G G T G W-3' PyPyImImHpIm-y-PyPyPyPyHpIm 2740) 5'W C A G G T C W-3' PyPyImImHpPy-y-ImPyPyPyHpIm 2741) 5'W C A G G A T W-3' PyPyImImPyHp-y-PyHpPyPyHpIm 2742) 5'W C A G G A A W-3' PyPyImImPyPy-y-HpHpPyPyHpIm 2743) 5'W C A G G A G W-3' PyPyImImPyIm-y-PyHpPyPyHpIm 2744) 5'W C A G G A C W-3' PyPyImImPyPy-y-ImHpPyPyHpIm 2745) 5'W C A G G G T W-3' PyPyImImImHp-y-PyPyPyPyHpim 2746) 5'W C A G G G A W-3' PyPyImImImPy-y-HpPyPyPyHpIm 2747) 5'W C A G G C T W-3' PyPyImImPyHp-y-PyImPyPyHpIm 2748) 5'W CA G G C A W-3' PyPyImImPyPy-y-HpImPyPyHpIm 2749) 5'W CA G C T T W-3' PyPyImPyHpHp-y-PyPyImPyHpIm 2750} 5'W CA G C T A W-3' PyPyImPyHpPy-y-HpPyImPyHpIm 2751) 5'W CA G C T G W-3' PyPyImPyHpIm-y-PyPyImPyHpIm 2752) 5'W CA G C T C W-3' PyPyImPyHpPy-y-ImPyImPyHpIm 2753) 5'W CA G C A T W-3' PyPyImPyPyHp-y-PyHpImPyHpIm 2754) 5'W C A G C A A W-3' PyPyImPyPyPy-y-HpHpImPyHpIm 2755) 5'W C A G C A G W-3' PyPyImPyPyIm-y-PylipImPyHpIm 2756) 5'W C A G C A C W-3' PyPyImPyPyPy-y-ImHpImPyHpIm 2757} 5'W C A G C G T W-3' PyPyImPyImHp-y-PyPyImPyHpIm 2758} 5'W CA G C G A W-3' PyPyImPyImPy-y-HpPyImPyHpIm 2759) 5'W CA G C C T W-3' PyPyImPyPyHp-y-PyImImPyHpIm 2760) 5'W CA G C C A W-3' PyPyImPyPyPy-y-HpImImPyHpIm 2761) 5'W CA G G G G W-3' PyPyImImImIm-y-PyPyPyPyHpIm 2762) 5'W CA G G G C W-3' PyPyImImImPy-y-ImPyPyPyHpIm 2763) 5'W CA G G C G W-3' PyPyImImPyIm-y-PyImPyPyHpIm 2764) 5'W CA G G C C W-3' PyPyImImPyPy-y-ImImPyPyHpIm 2765) 5'W CA G C G G W-3' PyPyImPyImIm-y-PyPyImPyHpIm 2766) 5'W CA G C G C W-3' PyPyImPyImPy-y-ImPyImPyHpIm 2767) 5'W CA G C C G W-3' PyPyImPyPyim-y-PyImImPyHpIm 2768} 5'W CA G C C C W-3' PyPyImPyPyPy-y-ImImImPyHpIm TABLE 134:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCATWNNW-3 DNA sequence aromatic amino acid sequence 2769) 5'W C A T PyPyHpHpHpHp-y-pypypypyHpIm T T T W-3' 2770) .5'W C A T A W-3' PyPyHpHpHpPy-y-HpPyPypyHplm T T
2771) 5'W C A T T G W-3' PyPyHpHpHpIm-y-PypypypyHpim T
2772) 5'W C A T T C W-3' PyPyHpHpHpPy-y-ImPyPyPyHpIm T
2773) 5'W C A T A T W-3' PyPyHpHpPyHp-y-pyHppypyHpIm T
2774) 5'W C A T A A W-3' PyPyHpHpPyPy-y-HpHpPyPyHpIm T
2775} 5'W C A T A G W-3' PyPyHpHpPyIm-y-pygppypyHplm T
2776) 5'W C A T A C W-3' PyPyHpHpPyPy-y-ImHpPypygpIm T
2777) 5'W C A T G T W-3' PyPyHpHpImHp-y-PypypypyHplm T
2778) 5'W C A T G A W-3' PyPyHpHpImPy-y-HpPyPyPyHpIm T
2779) 5'W C A T G G W-3' PyPyHpHpImIm-y-pypypypyHpIm T
2780) 5'W C A T G C W-3' PyPyHpHpImPy-y-ImPyPyPyHpIm T
2781) 5'W C A T C T W-3' PyPyHpHpPyHp-y-PyImPyPyHpIm T
2782) 5'W C A T C A W-3' PyPyHpHpPyPy-y-HpImPyPyHpIm T
2783) 5'W C A T C G W-3' PyPyHpHpPyIm-y-pyImPyPyHpIm T
2784) 5'W C A T C C W-3' PyPyHpHpPyPy-y-ImImPyPyHpIm T
2785) 5'W C A T T T W-3' PyPyHpPyHpHp-y-PyPyHppyHpIm A
2786) 5'W C A T T A W-3' PyPyI-ippygpp~,_y-HpPyHpPyHpIm A
2787) 5'W C A T T G W-3' PyPyHpPyHpIm-y-pypyHppyHpIm A
2788) 5'W C A T T C W-3' PyPyHpPyHpPy-y-ImPyHpPyHpIm A
2789) 5'W C A T A T W-3' yPyHpPyPyHp-y-PyHpHpPyHpIm A P
2790) 5'W C A T A A W-3' PypyHpPyPypy-y-HpHpHpPyHpIm A
2791) 5'W C A T A G W-3' PypyHppypylm-y-PyHpHpPyHpIm A
2792) 5'W C A T A C W-3' PyPyHpPyPyPy-y-ImHpHpPyHpim A
2793) 5'W C A T G T W-3' pyPyHpPyImHp-y-pypygppyHpIm A
2794) 5'W C A T G A W-3' PyPyHpPyImPy-y-HpPyHpPyHpIm A
2795) 5'W C A T G G W-3' PyPyHpPyImIm-y-pypygppyHPIm A
2796) 5'W C A T G C W-3' PyPyHpPyImPy-y-ImPyHpPyHpIm A
2797) 5'W C A T C T W-3' PyPyHpPyPyHp-y-PyImHpPyHpIm A
2798) 5'W C A T C A W-3' PyPyHpPyPyPy-y-HpImHpPyHpIm A
2799) 5'W C A T C G W-3' PyPyHpPyPyIm-y-PyImHpPyHpIm A
2800) 5'W C A T C C W-3' PyPyHpPyPyPy-y-ImImHpPyHpIm A
TABLE 135: 12-ring Hanpm Polyamides for recogmt~on of 8-by 5'-WCATSNNW-3' DNA sequence aromatic amino acid sequence 2801) 5'W C PyPyHpImHpHp-y-pypypypyHprm A T G T T PyPyHpImHpPy-y-HpPyPyPyHpIm W-3' PyPyHpImHpIm-y-pypypypyHplm 2802) 5'W C PyPyHpImHppy-y-ImPyPypyHplm A T G T A PyPyHpImPyHp-y-pygppypyHplm W-3' PyPyHpImPyPy-y-HpHppypyHpIm 2803) 5'W C PyPyHpImPyIm-y-pyHppypyHpIm A T G T G PyPyHpImPyPy-y-ImHppypyHplm W-3' PypyHpImImHp_y-pypypypyHplm 2804) 5'W C PyPyHpImImPy-y-HppypypyHpIm A T G T C PypyHpImPyHp-y-pyImPyPyHpIm W-3' PyPyHpImpypy_y-HpImPyPyHpIm 2805) 5'W C PyPyHpImImIm-y-pypypypyHpim A T G A T PyPyHpImImPy-y-ImpypypyHpIm W-3' PyPyHpImPyIm-y-pylmpypyHpIm 2806) 5'W C PypyHpImPyPy-y-ImImPyPyHpIm A T G A A PyPyHppyHpHp-y-pypyimPyHpIm W-3' PyPyHpPyHpPy-y-HppyImPyHpIm 2807) 5'W PypyHpPyHpIm-y-PypyImPyHpIm C A T G A pyPyHpPyHpPy-y-ImPyImPyHpIm G W-3' PypyHpPypygp-y_pyHpImPyHpIm 2808) 5'W C PyPyHpPyPypy-y-HpHpImPyHpIm A T G A C PyPygppypylm-y_pyHpImPyHpIm W-3' PyPyHpPypypy-y-ImHpImPyHpIm 2809) 5'W C PypyHppyl~p-y-pypyImPyHpIm A T G G T PyPyHpPyImPy-y-HpPyImPyHpIm W-3' PyPyHpPypyHp-y-pyImImPyHpIm 2810) 5'W C PyPyHpPyPypy-y-HpImImPyHpIm A T G G A pypyHppyImIm-y-pypyImPyHpIm W-3' PyPyHppylmpy_y_ImpyImPyHpIm 2811) 5'W C PyPyHpPyPyIm-y-pyImImPyHpIm A T G C T PyPyHpPyPyPy-y-ImImImPyHpIm W-3' 2812) 5'W
C A T G C
A W-3' 2813) 5'W C
A T G G G
W-3' 2814) 5'W C
A T G G C
W-3' 2815) 5'W C
A T G C G
W-3' 2816) 5'W C
A T G C C
W-3' 2817) 5'W
C A T C T
T W-3' 2818) 5'W C
A T C T A
W-3' 2819) 5'W C
A T C T G
W-3' 2820) 5'W C
A T C T C
W-3' 2821) 5'W C
A T C A T
W-3' 2822) 5'W
C A T C A
A W-3' 2823) 5'W C
A T C A G
W-3' 2824) 5'W C
A T C A C
W-3' 2825) 5'W C
A T C G T
W-3' 2826) 5'W C
A T C G A
W-3' 2827) 5'W
C A T C C
T W-3' 2828) 5'W C
A T C C A
W-3' 2829) 5'W C
A T C G G
W-3' 2830) 5'W C
A T C G C
W-3' 2831) 5'W C
A T C C G
W-3' 2832) 5'W
C A T C C
C W-3' PCT1US98/Ol ? 14 TABLE
136:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAAWNNW-3' DNA aromatic amino acid sequence sequence ' 2833) 5'W C PyPYpyHpHpHp-y-pypypyHpHpim A
A
T
T
T
W-3' ' S 2834) 5'W C T A W-3' pypypyHpHppy_y_HppypyHpHpIm A
A
T
2835) 5'W C A T T G W-3' PyPyPyHpHpIm-y-PypypygpHplm A
2836) 5'W C A AT T C W-3' PYPypyHpHpPy-y-ImPyPyHpHpIm 2837) 5'W C A AT A T W-3' PyPyPyHppyHp-Y_pyHppyHpHpIm 2838) 5'W C A AT A A W-3' PYPyPyHpPYPy-y-HpHpPyHpHpIm 2839) 5'W C A AT A G W-3' PyPyPyHpPyIm-y-PyHpPYHpHpIm 2840) 5'W C A AT A C W-3' PyPyPYHpPYPy-Y-ImHppyHpHpIm 2841) 5'W C A AT G T W-3' PyPypyHpImHp-y-pypypygpHpIm 2842) 5'W C A AT G A W-3' PyPypyHpImPy-Y-HpPyPyHpHpIm 2843) 5'W C A AT G G W-3' PYPyPyHpImIm-Y-PypypYHpHpIm 1S 2844) 5'W C A AT G C W-3' PYPyPyHpImPy-y-ImPyPyHpHpIm 2845) 5'W C A AT C T W-3' PyPypyHpPYHp-y-PyImPyHpHpIm 2846) 5'W C A AT C A W-3' PyPyPyHpPyPy-y-HpImPyHpHpIm 2847) 5'W C A AT C G W-3' PyPypyHppYIm-y-PYImPyHpHpIm 2848) 5'W C A AT C C W-3' Pypypygppypy_Y_ImImPyHpHpIm 2849) 5'W C A AA T T W-3' PyPypypygpHp-y-PYPYHpHpHpIm 2850) 5'W C A AA T A W-3' PyPyPyPYHpPy-Y-HpPyHpHpHpim 2851) 5'W C A AA T G W-3' PyPyPypyHpIm-y-PYpyHpHpHpIm 2852) 5'W C A AA T C W-3' PyPyPyPyHpPy-y-ImPyHpHpHpIm 2853) 5'W C A AA A T W-3' PypypypypYHp_Y_pYHpHpHpHpIm 2854) 5'W C A AA A A W-3' PyPyPYPyPyPy-Y-HpHpHpHpHpIm 2855) 5'W C A AA A G W-3' PYPyPyPyPyIm-y-PyHpHpHpHpIm 2856) 5'W C A AA A C W-3' PYPypypypypy-y_ImHpHpHpHpIm 2857) 5'W C A AA G T W-3' PyPyPYPyImHp-Y-PypyHpHpHpIm 2858) 5'W C A AA G A W-3' Pypypypylmpy_y-HpPYHpHpHpIm 2859) 5'W C A AA G G W-3' PyPyPypyImlm-y-PYPYHpHpHpIm 2860 ) 5' C A AA G C W-3 ' PyPyPypyImpY_y_ ImPYHpHpHpIm W
2861) 5'W C A AA C T W-3' PYPyPyPyPyHp-Y-PyImHpHpHpIm 2862) 5'W C A AA C A W-3' PyPyPYpypypy-y-HpImHpHpHpIm 2863) 5'W C A AA C G W-3' PyPypypypYlm_y_pyImHpHpHpIm 3S 2864 ) 5' C A AA C C W-3 ' pypypypypypy-y_ ImImHpHpHpIm W
TABLE
137:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCAASNNW-3' DNA aromatic amino acid sequence sequence 2865) 5'W C A A GT T w-3' PyPyPyImHpHp-y-pypypyHpHpIm 2866) - C A A GT A W-3' PyPyPyImHpPy-y-HpPyPyHpHpIm 5' W
2867) 5'W C A A GT G W-3' PyPyPyImHpIm-y-PyPyPyHpHpIm 2868) 5'W C A A GT C W-3' PyPyPyImHpPy-y-ImPyPyHpHpIm 2869) 5'W C A A GA T W-3' PyPyPyImPyHp-y-PyHpPyHpHpIm 2870) 5'W C A A GA A W-3' PyPyPyImPyPy-y-HpHpPyHpHpIm 2871) 5'W C A A GA G W-3' PyPyPyImPyIm-y-PyHpPyHpHpIm 2872) 5'W C A A GA C W-3' PyPyPyImPyPy-y-ImHpPyHpHpIm 2873) 5'W C A A GG T W-3' PyPyPyImImHp-y-PyPyPyHpHpIm 2874) 5'W C A A GG A W-3' PyPyPyImImPy-y-HpPyPyHpHpIm 2875) 5'W C A A GC T W-3' PyPyPyImPyHp-y-PyImPyHpF3pIm 2876) 5'W C A A GC A W-3' PyPyPyImPyPy-y-HpImPyHpHpIm 2877) 5'W C A A GG G W-3' PyPyPyImImIm-y-PyPyPyHpHpIm 2878) 5'W C A A GG C W-3' PyPyPyImImPy-y-ImPyPyHpHpIm 2879) 5'W C A A GC G W-3' PyPyPyImPyIm-y-PyImPyHpHpIm 2880) 5'W C A A GC C W-3' PyPyPyImPyPy-y-ImImPyHpHpIm 2881) 5' C A A CT T W-3' PyPyPyPyHpllp-y-PyPyImHpHpIm W
2882) 5'W C A A CT A W-3' PyPyPyPyHpPy-y-HpPyImHpHpIm 2883) 5'W C A A CT G W-3' PyPyPyPyHpIm-y-PypyImHpHpIm 2884) 5'W C A A CT C W-3' PyPyPyPyHpPy-y-ImPyImHpHpIm 2885) 5'W C A A CA T W-3' PyPyPyPyPyHp-y-PyHpImHpHpIm 2886) 5'W C A A CA A W-3' PyPyPyPyPyPy-y-HpHpImHpHpIm 2887) 5'W C A A CA G W-3' PyPyPyPyPyIm-y-PyHpImHpHpIm 2888) 5'W C A A CA C W-3' pyPypypypypy-y-I~pImHpHpIm 2889) 5'W C A A CG T W-3' PyPyPyPyImHp-y-PyPyImHpfIpIm 2890) 5'W C A A CG A W-3' PyPyPyPyImPy-y-HpPyImHpHpIm 2891) 5'W C A A CC T W-3' PyPyPyPyPyHp-y-PyImImHpHpIm 2892) 5'W C A A CC A W-3' PyPyPyPyPyPy-y-HpImImHpHpIm 2893) 5'W C A A CG G W-3' PyPyPyPyImIm-y-PyPyImHpHpIm 2894) 5'W C A A CG C W-3' PypypypyImPy-y-ImPyImHpHpIm 2895) 5'W C A A CC G W-3' PyPyPyPyPyIm-y-PyImImHpHpIm 3$ 2896) 5'W C A A CC C W-3' PyPyPyPyPyPy-y-ImImImHpHpIm TABLE 138: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCACWNNW-3' DNA aromatic amino acid sequence sequence 2897) 5'W C A C TT T W-3' PyPyPyHpHpHp-y-PyPyPyImHpIm 2898) 5'W C A C TT A W-3' PYPYPYHPHPPY-y-HPPYPYI~PIm 2899) 5'W C A C TT G W-3' PyPyPyHpHpIm-y-PyPypyl~plm 2900) 5'W C A C TT C W-3' PYPYPyHpHppy_y-ImPYPyImHpIm 2901) 5'W C A C TA T W-3' PyPyPyHpPyHp-y-PyHpPyImHpIm 2902) 5'W C A C TA A W-3' PyPyPyHpPyPy-y-HpHpPyImHpIm 2903) 5'W C A C TA G W-3' PyPyPyHpPyIm-y-PyHpPyImHpIm 2904) 5'W C A C T A C W-3' PyPyPyHpPyPy-y-ImHpPyImHpIm 2905) 5'W C A C T G T W-3' PYpypygpl~p-y_pypypyl~plm 2906) 5'W C A C T G A W-3' PyPyPyHpImPy-y-HpPyPyImHpIm 2907) 5'W C A C T G G W-3' PyPyPyHpImIm-y-PypypyImHpIm 2908) 5'W C A C T G C W-3' PyPyPyHpImPy-y-ImPyPyImHpIm 2909) 5'W C A C T C T W-3' PyPyPyHpPyHp-y-PyImPyImHpIm 2910) 5'W C A C T C A W-3' PyPyPyHpPyPy-y-HpImPyImHpIm 2911) 5'W C A C TC G W-3' PyPyPyHpPyIm-y-PyImPyImHpIm 2912) 5'W C A C TC C W-3' PyPyPyHpPypy-y-ImImPyImHpIm 2913} 5'W C A C AT T W-3' PyPyPyPyHpHp-y-PypyHpImHpIm 2914) 5'W C A C AT A W-3' PyPyPyPyHpPy-y-HpPyHPImHpIm 2915) 5'W C A C AT G W-3' PyPyPyPyHpIm-y-PyPyHpImHpIm 2916) 5'W C A C AT C W-3' PyPyPypyHPPy-y-ImPyHpImHpIm 2917) 5'W C A C AA T W-3' PyPyPyPyPyHp-y-PyHpHpImHpIm 2918) 5'W C A C AA A W-3' PyPyPyPyPypy-y-HpHpHPImHpIm 2919) 5'W C A C AA G W-3' ~PyPyPyPyPyIm-y-PyHpHpImHpIm 2920) 5'W C A C AA C W-3' PyPyPyPyPypy-y-ImHpHpImHpIm 2921) 5'W C A C AG T W-3' PyPyPyPyImHp-y-PyPyHpImHpIm 2922) 5'W C A C AG A W-3' PyPyPyPyImPy-y-HpPyHpImHpIm 2923) 5'W C A C AG G W-3' PyPyPyPyImIm-y-PyPyHpImHpIm 2924) 5'W C A C AG C W-3' PyPyPyPyImPy-y-ImPyHPImHpIm - 2925) 5'W C A C AC T W-3' PypypypypyHp-y_pyl~pImHpIm 2926) 5'W C A C AC A W-3' PyPyPyPyPyPy-y-HpImHpImHpIm - 2927) 5'W C A C AC G W-3' PyPyPyPyPyIm-y-PyImHpImHpIm 2928) 5'W C A C AC C W-3' PyPyPyPyPyPy-y-ImImHpImHpIm TABLE
139:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCACSNNW-3' DNA aromatic amino acid sequence sequence 2929) 5'W C A CG T T W-3' PyPyPyImHpHp-y-PyPyPyImHpIm 2930) 5~'WC A CG T A W-3' PyPyPyImHpPy-y-HpPyPyImHpIm 2931) 5'W C A CG T G W-3' PyPyPyImHpIm-y-PyPyPyImHpIm 2932) 5'W C A CG T C W-3' PyPyPyImHpPy-y-ImPyPyImHpIm 2933) 5'W C A CG A T W-3' PyPyPyImPyHp-y-PyHpPyImHpIm 2934) 5'W C A CG A A W-3' PyPyPyImPyPy-y-HpHpPyImHpIm 2935) 5'W C A CG A G W-3' PyPyPyImPyIm-y-PyHpPyImHpIm 2936) 5'W C A CG A C W-3' PyPyPyImPyPy-y-ImHpPyImHpIm 2937) 5'W C A CG G T W-3' PyPyPyImImHp-y-PyPyPyImHpIm 2938) 5'W C A CG G A W-3' PyPyPyImImPy-y-HpPyPyImHpIm 2939) 5'W C A CG C T W-3' PyPyPyImPyHp-y-PyImPyImHpIm 2940) 5'W C A CG C A W-3' PyPyPyImPyPy-y-HpImPyImHpIm 2941) 5'W C A CC T T W-3' PyPyPyPyHpHp-y-PyPyImImI~ipIm 2942) 5'W C A CC T A W-3' PyPyPyPyHpPy-y-HpPyImImHpIm 2943) 5'W C A CC T G W-3' PyPyPyPyHpIm-y-PyPyImImHpIm 2944) 5'W C A CC T C W-3' PyPyPyPyHpPy-y-ImPyImImHpIm 2945) 5'W C A CC A T W-3' PyPyPyPyPyHp-y-PyHpImImHpIm 2946) 5'W C A CC A A W-3' PyPyPyPyPyPy-y-HpHpImImHpIm 2947) 5'W C A CC A G W-3' PyPyPyPyPyIm-y-PyHpImImHpIm 2948) 5'W C A CC A C W-3' PyPyPyPyPyPy-y-ImApImImHpIm 2949) 5'W C A CC G T W-3' PyPyPyPyImHp-y-PyPyImImHpIm 2950) 5'W C A CC G A W-3' PyPyPyPyImPy-y-HpPyImImHpIm 2951) 5'W C A CC C T W-3' ~PyPyPyPyPyHp-y-PyImImImHpim 2952) 5'W C A CC C A W-3' PyPyPyPyPyPy-y-HpImImImHpIm 2953) 5'W C A CG G G W-3' PyPyPyImImIm-y-PyPyPyImHpIm 2954) 5'W C A CG G C W-3' PyPyPyImImPy-y-ImPyPyImHPIm 2955) 5'W C A CG C G W-3' PyPyPyImPyIm-y-PyImPyImHpIm 2956) 5'W C A CG C C W-3' PyPyPyImPyPy-y-ImImPyImHpIm 2957) 5'W C A CC G G W-3' PyPyPyPyImIm-y-PyPyImImHpIm 2958) 5'W C A CC G C W-3' PyPyPyPyImPy-y-ImPyImImHpIm 2959) 5'W C A CC C G W-3' PyPyPyPyPyIm-y-PyImImImHpIm 2960) 5'W C A CC C C W-3' PyPyPyPyPyPy-y-ImImImImHpIm 1A13Lt; I2-ring 140: Hairpin Polyamides for recognition of 8-by 5'-WCTGWNNW-3' DNA aromatic amino acid sequence sequence ' 2961) 5'W C TG T T T W-3' PyHpImHpHpHp-y-PyPyPyPyPyIm 2962) ~5'W C TG T T A W-3' PyHpImHpHpPy-y-HpPyPyPyPyIm 2963) 5'W C TG T T G W-3' PyHpImHpHpIm-y-Pypypypypylm 2964) 5'W C TG T T C W-3' PyHpImHpHpPy-y-ImPyPyPyPyIm 2965) 5'W C TG T A T W-3' PyHpImHpPyHp-y-pyHpPyPyPyIm 2966) 5'W C TG T A A W-3' PyHpImHpPyPy-y-HpHpPyPypyIm 2967) 5'W C TG T A G W-3' PyHpImHpPyIm-y-PyHpPyPyPyIm 296$) 5'W C TG T A C W-3' PyHpImHpPyPy-y-ImHpPyPYPyIm 2969) 5'W C TG T G T W-3' PyHpImHpImHp-Y-PypypypyPyIm 2970) 5'W C TG T G A W-3' PyHpImHpImPy-y-HpPyPyPyPyIm 2971) 5'W C TG T G G W-3' PyHpImHpImIm-y-PypypypypyIm I5 2972) 5'W C TG T G C W-3' PyHpImHpImPy-y-ImPyPyPyPyIm 2973) 5'W C TG T C T W-3' PyHpImHpPyHp-y-PyImPyPyPyIm 2974) 5'W C TG T C A W-3' PyHpImHpPyPy-y-HpImPyPyPyIm 2975) 5'W C TG T C G W-3' PyHpImHpPyIm-y-PyImPyPyPyIm 2976) 5'W C TG T C C W-3' PyHpImHpPyPy-y-ImImPyPyPyIm 2977) 5'W C TG A T T W-3' PyHpImPyHpHp-y-pypyHpPyPyIm 2978) 5'W C TG A T A W-3' PyHpImPyHpPy-y-HpPyHpPyPyIm 2979) 5'W C TG A T G W-3' PyHpImPyHpIm-y-PyPyHpPyPyIm 2980) 5' C TG A T C W-3' PyHpImPyHpPy-y-ImPyHpPyPyIm W
2981) 5'W C TG A A T W-3' PyHpImPyPyHp-y-PyHpHpPyPyIm 2982) 5'W C TG A A A W-3' PyHpImPyPyPy-y-HpHpHpPyPyIm 2983) 5'W C TG A A G W-3' PyHpImPyPyIm-y-PyHpHpPyPyim 2984) 5'W T GA A C W-3' PyHpImPyPyPy-y-ImHpHpPyPyIm C
2985) 5'W T GA G T W-3' PyHpImPyImHp-y-PyPyHpPyPyIm C
2986) 5'W T GA G A W-3' PyHpImPyImPy-y-HpPyHpPyPyIm C
2 9 87 5' T GA G G W-3 ' PyHpImPyImIm-y-Pypygppypylm ) W
C
2988) 5'W T GA G C W-3' PyHpImPyImPy-y-ImPyHpPyPyIm C
2989) 5'W T GA C T W-3' PyHpImPyPyHp-y-PyImHpPyPyIm C
2990) 5'W T GA C A W-3' PyHpImPyPyPy-y-HpImHpPyPyIm C
2991) 5'W T GA C G W-3' PyHpImPyPyIm-y-PyImHpPyPyIm C
2992) 5'W T GA C C W-3' PyHpImPyPyPy-y-ImImHpPyPyIm C
TABLE 141:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTGSNNW-3' DNA aromatic amino acid sequence sequence 2993) 5'W C TG G T T W-3' PyHpIrnImHpHp-~-PyPyPyPyPyIm 2994) 5.'WC TG G T A W-3' PyHpImImHpPy-y-HpPyPyPyPyIm 2995) 5'W C TG G T G W-3' PyHpImImHpIm-y-PyPyPyPyPyIm 2996) 5'W C TG G T C W-3' PyHpImImHpPy-y-ImPyPyPyPyIm 2997) 5'W C TG G A T W-3' PyHpImImPyHp-'y-PyHpPyPyPyIm 2998) 5'W C TG G A A W-3' PyHpImImPyPy-~y-HpHpPyPyPyIm 2999) 5'W C TG G A G W-3' PyHpImImPyIm-'y-PyHpPyPyPyIm 3000) 5'W C TG G A C W-3' PyHpImImPyPy-y-ImHpPyPyPyIm 3001) 5'W C TG G G T W-3' PyHpImImImHp-y-PyPyPyPyPyIm 3002) 5'W C TG G G A W-3' PyHpIrnImImPy-y-HpPyPyPyPyim 3003) 5'W C TG G C T W-3' PyHpImImPyHp-y-PyImPyPyPyIm 3004) 5'W C TG G C A W-3' PyHpImImPyPy-y-HpImPyPyPyIm 3005) 5'W C TG C T T W-3' PyHpImPyHpHp-y-PyPyImPyPyIm 3006) 5'W C TG C T A W-3' PyHpImPyHpPy-~y-HpPyImPyPyIm 3007 ) 5' C TG C T G W-3' PyHpImPyHpIm-y-PyPyImPyPyIm W
3008) 5'W C TG C T C W-3' PyHpImPyFipPy-y-ImPyImPyPyIm 3009) 5'W C TG C A T W-3' PyHpImPyPyHp-y-PyHpImPyPyim 3 O 10 5' C TG C A A W-3 PyHpImPyPyPy-y-HpHpImPyPyIm ) W ' 3011) 5'W C TG C A G W-3' PyHpImPyPyIm-~y-PyHpImPyPyim 3012) 5'W C TG C A C W-3' PyHpImPyPyPy-~y-ImHpImPyPyIm 3013) 5'W C TG C G T W-3' PyHpImPyImHp-y-PyPyImPyPyIm 3 014 5' C TG C G A W-3 PyHpImPyImPy-'y-HpPyImPyPyIm ) W ' 3015) 5'W C TG C C T W-3' 'PyHpImPyPyHp-y-PyImImPyPyIm 3016) 5'W C TG C C A W-3' PyHpImPyPyPy-y-HpImImPyPyIm 3017) 5'W C TG G G G W-3' PyHpImImImIm-y-PyPyPyPyPyIm 3018) 5'W C TG G G C W-3' PyHpImImImPy-y-ImPyPyPyPyIm 3019) 5'W C TG G C G W-3' PyHpImImPyIm-y-PyImPyPyPyIm 3020) 5'W C TG G C C W-3' PyHpImImPyPy-y-ImImPyPyPyIm 3021) 5'W C TG C G G W-3' PyHpImPyImIm-y-PyPyImPyPyIm 3022) 5'W C TG C G C W-3' PyHpImPyImPy-y-ImPyImPyPyIm 3023) 5'W C TG C C G W-3' PyHpImPyPyIm-y-PyImImPyPyIm 3024) 5'W C TG C C C W-3' PyHpImPyPyPy-y-ImImImPyPyIm TABLE 142: r recognition of 8-by 5'-WCTTWNNW-3' 12-ring Hairpin Polyamides fo DNA sequence aromatic amino acid sequence 3025) 5'W C T T PyHpHpHpHpHp-y-pypypypypylm T T T W-3' ' 5 3026) ~ 5'W C T PyHpHpHpHpPy-y-HpPyPyPypylm T T T A
W-3' 3027) 5'W C T T PyHpHpHpHpIm-y-PyPypypypylm T T G W-3' 3 028 5' W C T PyHpHpHpHpPy-y-ImPyPypypylm ) T T T C
W-3 ' 3029) 5'W C T T A PyHpHpHpPyHp-y-pyHpPypypylm T T
W-3' 3030) 5'W C T T A A W-3' PyHpHpHpPyPy-y-Hpgppypypylm T
3031) 5'W C T T A G W-3' PyHpHpHpPyIm-y-PyI-lppypypylm T
3032) 5'W C T T A C W-3' PyHpHpHpPyPy-y-ImHPPYPYPyIm T
3033) 5'W C T T G T W-3' PyHpHpHpImHp-y-Pypypypypylm T
3034) 5'W C T T G A W-3' PyHpHpHpImPy-y-HpPYPYPYPyIm T
3035) 5'W C T T G G W-3' PyHpHpHpImIm-y-pypypypypylm T
3036) 5'W C T T G C W-3' PyHpHpHpImPy-y-ImPyPyPyPyIm T
3037) 5'W C T T C T W-3' PyHpHpHpPyHp-y-Pylmpypypylm T
3038) 5'W C T T C A W-3' PyHpHpHpPyPy-y-HpImPyPypylm T
3 03 5' W C T C G W- 3 ' PyHPHpHpPyIm-y-PyImPyPyPyIm 9 ) T T
3 04 5' W C T C C W-3 ' PyHpHpHpPyPy-y- ImImPyPyPyIm 0 ) T T
3041) 5'W C T T T T W-3' PyHpHpPyHpHp-y-PypyHpPyPyim A
3 042 5' W C T T A W-3 ' PyHpHpPyHpPy-y-HpPyHpPYPyIm ) T A
3043) 5'W C T T T G W-3' PyHpHpPyHpIm-y-pypygppypylm A
3044) 5'W C T T T C W-3' PyFipI-IpPyHpPy-y-ImPyHpPyPyIm A
3045) 5'W C T T A T W-3' A pYHPHPPYPYHP-Y-pYHPHPPYPYIm 3046) 5'W C T T A A W-3' PyHpHpPyPyPy-y-HpgpHPPyPyIm A
3047) 5'W C T T A G W-3' ' PyHpHpPyPyIm-y-pyHpHpPyPyIm A
3 04 5' W C T A C W-3 ' PyHpHpPyPyPy-y- ImHpHpPyPyIm 8 ) T A
3049) 5'W C T T G T W-3' PyHpHpPyImHp-y-PypyHpPypyIm A
3 050 5' W C T G A W-3 ' PyHpHpPyImPy-y-HpPyHpPypyIm ) T A
3051) 5'W C T T G G W-3' PyHpHpPyImIm-y-PypyHppypylm A
3052) 5'W C T T G C W-3' PyHpHpPyImPy-y-ImPyHPPYPyIm A
' 3053) 5'W C T T C T W-3' PyHpHpPyPyHp-y-pylmgppypy=m A
3054) 5'W C T T C A W-3' PyHpHppypypy-Y-HpImHpPyPyIm A
3055) 5'W C T T C G W-3' PyHpHpPyPyIm-y-pylmI-ippypylm A
3056) 5'W C T T C C W-3' PyHpHpPyPyPy-y-ImImHpPyPyIm A
TABLE
143:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTTSNNW-3' DNA aromatic amino acid sequence sequence 3057) 5'W C T TG T T W-3' PyHpHpImHpHp-y-PyPyPyPyPyIm 3058) 5'W C T TG T A W-3' PyHpHpImHpPy-y-HpPyPyPyPyIm 3059) 5'W C T TG T G W-3' PyHpHpImHpIm-y-PyPyPyPyPyIm 3060) 5'W C T TG T C W-3' PyHpHpImHpPy-y-ImPyPyPyPyIm 3061) 5' C T TG A T W-3' PyHpHpImPyHp-y-PyHpPyPyPyIm W
3062) 5'W C T TG A A W-3' PyHpHpImPyPy-y-HpHpPyPyPyIm 3063) 5'W C T TG A G W-3' PyHpHpImPyIm-y-PyHpPyPyPyIm 3064) 5'W C T TG A C W-3' PyHpHpImPyPy-y-ImHpPyPyPyIm 3065) 5'W C T TG G T W-3' PyHpHpImImHp-y-PyPyPyPyPyIm 3066) 5'W C T TG G A W-3' PyHpHpImImPy-y-HpPyPyPyPyIm 3067) 5'W C T TG C T W-3' PyHpHpImPyHp-y-PyImPyPyPyIm 3068) 5'W C T TG C A W-3' PyHpHpImPyPy-y-HpImPyPyPyIm 3069) 5'W C T TG G G W-3' PyHpHpImImIm-y-PyPyPyPyPyIm 3 07 0 5' C T TG G C W-3 ' PyHpHpImImPy-y- ImPyPyPyPyIm ) W
3071) 5'W C T TG C G W-3' PyHpHpImPyIm-y-PyImPyPyPyIm 3072) 5'W C T TG C C W-3' PyHpHpImPyPy-y-ImImPyPyPyIm 3073) 5'W C T TC T T W-3' PyHpHpPyHpHp-y-PyPyImPyPyIm 3 074 5' C T TC T A W-3 ' PyHpHpPyHpPy-y-HpPyImPyPyIm ) W
3 07 5 5' C T TC T G W-3 ' PyHpHpPyHpIm-y-PyPyImPyPyIm ) W
3076) 5'W C T TC T C W-3' PyHpHpPyHpPy-y-ImPyImPyPyIm 3077) 5'W C T TC A T W-3' PyHpHpPyPyHp-y-PyHpImPyPyIm 3 07 8 5' C T TC A A W-3 ' PyHpHpPyPyPy-y-HpHpImPyPyIm ) W
3079) 5'W C T TC A G W-3' 'PyHpFIpPyPyIm-y-PyHpImPyPyIm 3080) 5'W C T TC A C W-3' PyHpHpPyPyPy-y-ImHpImPyPyIm 3081) 5'W C T TC G T W-3' PyHpHpPyImHp-y-PyPyImPyPyIm 3 082 5' C T TC G A W-3 ' PyHpHpPyImPy-y-HpPyImPyPyIm ) W
3083) 5'W C T TC C T W-3' PyHpHpPyPyHp-y-PyImImPyPyIm 3084) 5'W C T TC C A W-3' PyHpHpPyPyPy-y-HpImImPyPyIm 3085) 5'W C T TC G G W-3' PyHpHpPyImIm-y-PyPyImPyPyIm 3086) 5'W C T TC G C W-3' PyHpHpPyImPy-y-ImPyImPyPyIm 3087) 5'W C T TC C G W-3' PyHpHpPyPyIm-y-PyImImPyPyIm 3088) 5'W C T TC C C W-3' PyHpHpPyPyPy-y-ImImImPyPyIm TABLE
144:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTAWNNW-3' DNA aromatic amino acid sequence sequence 3089) 5'W C T A TT T W-3' PyHpPyHpHpHp-y-PyPypyHpPyIm S 3090) 5'W C T A TT A W-3' PyHpPyHpHpPy-y-HpPyPyHpPyIm 3091) 5'W C T A TT G W-3' PyHpPyHpHpIm-y-Pypypygppylm 3092) 5'W C T A TT C W-3' PyHpPyHpHpPy-y-ImPyPyHpPyIm 3093) 5'W C T A TA T W-3' PyHpPyHpPyHp-y-pyHpPyHpPyIm 3 0 94 5' C T A TA A W-3 ' PyHpPyHpPyPy-y-HpHpPyHpPyIm ) W
3 095 5' C T A TA G W-3 ' PyHpPyHpPyIm-y-PyHpPyHpPyIm ) W
3096) 5'W C T A TA C W-3' pYHPPYHPPYPY-Y-ImHppyHppyIm 3097) 5'W C T A TG T W-3' PYHPPYHPImHp-y-PyPyPyHpPyim 3 098 5' C T A TG A W-3 ' PyHppyHpImPy-y-HpPyPyHpPyIm ) W
3099) 5'W C T A TG G W-3' PyHpPyHpImIm-y-Pypypygppylm 3100) 5'W C T A TG C W-3' PyHpPyHpImPy-y-ImPyPyHpPyIm 3101) 5'W C T A TC T W-3' PyHpPyHpPyHp-y-PyImPyHpPyIm 3102 5' C T A TC A W-3 ' PyHpPyHpPyPy-y-HpImPyHpPyIm ) W
3103 5' C T A TC G W-3 ' PyHppyHppylm-y_pyImPYHpPyIm ) W
3104 5' C T A TC C W-3' PyHpPyHpPyPy-y-ImImPyHpPyIm ) W
3105) 5'W C T A AT T W-3' PyHpPyPyHpHp-y-PypyHpHpPyIm 3106) 5'W C T A AT A W-3' PyHpPyPyHpPy-y-HpPyHpHpPyIm 3107) 5'W C T A AT G W-3' PyHpPyPyHpIm-y-PyPyHpHpPyIm 3108) 5'W C T A AT C W-3' PyHpPyPyHpPy-y-ImPyHpHpPyIm 3109) 5'W C T A AA T W-3' PyHpPyPyPyHp-y-PyHpHpHpPyIm 3110 5' C T A AA A W-3 ' PyHpPyPyPyPy-y-HpHpHpHpPyIm ) W
3111) 5'W C T A AA G W-3' PyHpPyPyPyIm-y-PyHpHpHpPyIm 3112) 5'W C T A AA C W-3' PyHpPyPyPyPy-y-ImHPHpHppyIm 3113 5' C T A AG T W-3 ' PyHpPyPyImHp-y-PyPyHpHpPyIm ) W
3114 5' C T A AG A W-3' PyHpPyPyImPy-y-HpPyHpHpPyIm ) W
3115) 5'W C T A AG G W-3' PyHpPyPyImIm-y-pyPyHpHpPyIm 3116) 5'W C T A AG C W-3' PYHPPYPYImPy-y-ImPyHpHpPyIm 3117 5' C T A AC T W-3 ' PyHpPyPyPyHp-y-PyImHpHpPyIm ) W
3118 5' C T A AC A W-3 ' PyHpPyPyPyPy-y-HpImHpHpPyIm ) W
3119 5' C T A AC G W-3 ' PyHpPyPyPyIm-y-PyImHpHpPyIm ) W
3120) 5'W C T A AC C W-3' PyHpPyPyPyPy-y-ImImHpHpPyIm TABLE
145:
I2-ring Hairpin Yolyamides for recognition of 8-by 5'-WCTASNNW-3' DNA aromatic amino acid sequence sequence 3121) 5'W C T A GT T W-3' PyHpPyImHpHp-y-PyPyPyHpPyIm 3122 ) ~5' C T A GT A W-3 PyHpPyImHpPy-y-HpPyPyHpPyIm W ' 3123 ) 5' C T A GT G W-3 PyHpPyImHpIm-y-PyPyPyHpPyIm W ' 3124) 5'W C T A GT C W-3' PyHpPyImHpPy-y-ImPyPyHpPyIm 3125 ) 5' C T A GA T W-3 PyHpPyImPyHp-y-PyHpPyHpPyIm W ' 3126) 5'W C T A GA A W-3' PyHpPyImPyPy-y-HpHpPyHpPyIm 3127 ) 5' C T A GA G W-3 PyHpPyImPyIm-y-PyHpPyHpPyIm W ' 3128 ) 5' C T A GA C W-3 PyHpPyImPyPy-y-ImHpPyHpPyIm W ' 3129) 5'W C T A GG T W-3' PyHpPyImImHp-y-PyPyPyHpPyIm 313 0 5' C T A GG A W- 3 PyHpPyImImPy-y-HpPyPyHpPyIm ) W ' 3131) 5'W C T A GC T W-3' PyHpPyImPyHp-y-PyImPyHpPyIm 3132 ) 5' C T A GC A W-3 PyHpPyImPyPy-y-HpImPyHpPyIm W ' 3133) 5'W C T A GG G W-3' PyHpPyImImIm-y-PyPyPyHpPyIm 3134) 5'W C T A GG C W-3' PyHpPyImImPy-y-ImPyPyHpPyIm 33.35) 5'W C T A GC G W-3' PyHpPyImPyIm-y-PyImPyHpPyIm 3136) 5'W C T A GC C W-3' PyHpPyImPyPy-y-ImImPyHpPyIm 3137 ) 5' C T A CT T W-3 PyHpPyPyHpHp-y-PyPyImHpPyIm W ' 313 8 5' C T A CT A W-3 PyHpPyPyHpPy-y-HpPyImHpPyIm ) W ' 3139) 5'W C T A CT G W-3' PyHpPyPyHpIm-y-PyPyImHpPyIm 3140 ) 5' C T A CT C W-3 PyHpPyPyHpPy-y- ImPyImHpPyIm W ' 3141) 5'W C T A CA T W-3' PyHpPyPyPyHp-y-PyHpImHpPyIm 3142) 5'W C T A CA A W-3' PyHpPyPyPyPy-y-HpHpImHpPyIm 3143 ) 5' C T A CA G W-3' ~ PyHpPyPyPyIm-y-PyHpImHpPyIm W
3144) 5'W C T A CA C W-3' PyHpPyPyPyPy-y-ImHpImHpPyIm 3145) 5'W C T A CG T W-3' PyHpPyPyImHp-y-PyPyImHpPyIm 3146) 5'W C T A CG A W-3' PyHpPyPyImPy-y-HpPyImHpPyIm 3147 ) 5' C T A CC T W-3' PyHpPyPyPyHp-y-PyImImHpPyIm W
3148) 5'W C T A CC A W-3' PyHpPyPyPyPy-y-HpImImHpPyIm 3149) 5'W C T A CG G W-3' PyHpPyPyImIm-y-PyPyImHpPyIm 3150) 5'W C T A CG C W-3' PyHpPyPyImPy-y-ImPyImHpPyIm 3151) 5'W C T A CC G W-3' PyHpPyPyPyIm-y-PyImImHpPyIm 3152) 5'W C T A CC C W-3' PyHpPyPyPyPy-y-ImImImHpPyIm TABLE 14b: 12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTCWNNW-3' DNA sequence aromatic amino acid sequence 3153) 5'W C T C T T T W-3' PyHpPyHpHpHp-y-PyPyPyImPyIm 3154 ) 5~' W C T C T T A W- 3 ' PyHpPyHpHpPy-y-HpPyPyImPyIm 3155 ) 5' C T CT T G W-3 ' PyHpPyHpHpIm-y-PyPyPyImPyTm W
3156) 5'W C T CT T C W-3' PyHpPyHpHpPy-y-ImPyPyImPyIm 3157 ) 5' C T CT A T W-3' PyHpPyHpPyHp-y-PyHpPyImPyIm W
3158) 5'W C T CT A A W-3' PyHpPyHpPyPy-y-HpHpPyImPyIm 3159) 5'W C T CT A G W-3' PyHpPyHpPyIm-y-PyHpPyImPyIm 3160) 5'W C T CT A C W-3' PyHpPyHpPyPy-y-ImHpPyImPyIm 3161) 5'W C T CT G T W-3' PyHpPyHpImHp-y-PyPyPyImPyIm 3162) 5'W C T CT G A W-3' PyHpPyHpImPy-y-HpPyPyImPyIm 3163) 5'W C T CT G G W-3' PyHpPyHpImIm-y-PyPyPyImPyIm 3164) 5'W C T CT G C W-3' PyHpPyHpImPy-y-ImPyPyImPyIm 3165 ) 5' C T CT C T W-3 ' PyHpPyHpPyHp-y-PyImPyImPyIm W
3166 ) 5' W C T C T C A W-3 ' PyHpPyHpPyPy-y-HpImPyImPyIm 3167 ) 5' W C T C T C G W-3' PyHpPyHpPyIm-y-PyImPyImPyIm 3168) 5'W C T C T C C W-3' PyHpPyHpPyPy-y-ImImPyImPyIm 3169) 5'W C T C A T T W-3' PyHpPyPyHpHp-y-PyPyHpImPyIm 3170) 5'W C T C A T A W-3' PyHpPyPyHpPy-y-HpPyHpImPyIm 3171) 5' W C T C A T G W-3' PyHpPyPyHpIm-y-PyPyHpImPyIm 3172) 5'W C T C A T C W-3' PyHpPyPyHpPy-y-ImPyHpImPyIm 3173) 5'W C T C A A T W-3' PyHpPyPyPyHp-y-PyHpHpImPyIm 3174 ) 5'W C T C AA A W-3' PyHpPyPyPyPy-y-HpHpHpImPyIm 3175) 5'W C T C AA G W-3' 'PyHpPyPyPyIm-y-PyHpHpImPyIm 317 6 ) 5'W C T C AA C W-3 ' PyHpPyPyPypy-y- ImHpHpImPyIm 3177) 5'W C T C AG T W-3' PyHpPyPyImHp-y-PyPyHpImPyIm 317 8 ) 5'W C T C AG A W-3 ' PyHpPyPyImPy-y-HpPyHpImPyIm 317 9 ) 5'W C T C AG G W-3 ' PyHpPyPyImIm-y-PyPyHpImPyIm 3180) 5'W C T C AG C W-3' PyHpPyPyImPy-y-ImPyHpImPyIm 3181) 5'W C T C AC T W-3' PyHpPyPyPyHp-y-PyImHpImPyIm 3182 ) 5'W C T C AC A W-3 ' PyHpPyPyPyPy-y-HpImHpImPyIm 3183 ) 5'W C T C AC G W-3 ' PyHpPyPyPyIm-y-PyImHpImPyIm 3184) 5'W C T C AC C W-3' PyHpPyPyPyPy-y-ImImHpImPyIm TABLE
147:
12-ring Hairpin Polyamides for recognition of 8-by 5'-WCTCSNNW-3' DNA aromatic amino acid sequence sequence 3185) 5'W C T C GT T W-3' PyHpPyImHpHp-y-PyPyPyImPyIm 3186) 5~'WC T C GT A W-3' PyHpPyImHpPy-y-HpPyPyImPyIm 3187 ) 5' C T C GT G W-3 ' PyHpPyImHpIm-y-PyPyPyImPyIm W
3188) 5'W C T C GT C W-3' PyHpPyImHpPy-y-ImPyPyImPyIm 3189 ) 5' C T C GA T W-3 ' PyHpPyImPyHp-y-PyHpPyImPyIm W
3190) 5'W C T C GA A W-3' PyHpPyImPyPy-y-HpHpPyImPyIm 3191) 5'W C T C GA G W-3' PyHpPyImPyIm-y-PyHpPyImPyIm 3192 ) 5' C T C GA C W-3 ' PyHpPyImPyPy-y- ImHpPyImPyIm W
3193 ) 5' C T C GG T W-3' PyHpPyImImHp-y-PyPyPyImPyIm W
3194 ) 5' C T C GG A W-3 ' PyHpPyImImPy-y-HpPyPyImPyIm W
3195) 5'W C T C GC T W-3' PyHpPyImPyHp-y-PyImPyImPyIm 3196) 5'W C T C GC A W-3' PyHpPyImPyPy-y-HpImPyImPyIm 3197 ) 5' C T C CT T W-3' PyHpPyPyHpHp-y-PyPyImImPyIm W
3198 ) 5' C T C CT A W-3' PyHpPyPyHpPy-y-HpPyImImPyIm W
3199 ) 5' C T C CT G W-3 ' PyHpPyPyHpIm-y-PyPyImImPyIm W
3200) 5'W C T C CT C W-3' PyHpPyPyHpPy-y-ImPyImImPyIm 3201) 5'W C T C CA T W-3' PyHpPyPyPyHp-y-PyHpImImPyIm 3202) 5'W C T C CA A W-3' PyHpPyPyPyPy-y-HpHpImImPyIm 3203 ) 5' C T C CA G W-3' PyHpPyPyPyIm-y-PyHpImImPyIm W
3204) 5'W C T C CA C W-3' PyHpPyPyPyPy-y-ImHpImImPyIm 3205) 5'W C T C CG T W-3' PyHpPyPyImHp-y-PyPyImImPyIm 3206 ) 5' C T C CG A W-3 ' PyHpPyPyImPy-y-HpPyImImPyIm W
3207) 5'W C T C CC T W-3' PyHpPyPyPyHp-y-PyImImImPy3m 3208) 5'W C T C CC A W-3' PyHpPyPyPyPy-y-HpImImImPyIm 3209) 5'W C T C GG G W-3' PyHpPyImImIm-y-PyPyPyImPyIm 3210) 5'W C T C GG C W-3' PyHpPyImImPy-y-ImPyPyImPyIm 3211) 5'W C T C GC G W-3' PyHpPyImPyIm-y-PyImPyImPyIm 3212) 5'W C T C GC C W-3' PyHpPyImPyPy-y-ImImPyImPyIm 3213 ) 5' C T C CG G W-3' PyHpPyPyImIm-y-PyPyImImPyIm W
3214) 5'W C T C CG C W-3' PyHpPyPyImPy-y-ImPyImImPyIm 3215) 5'W C T C CC G W-3' PyHpPyPyPyIm-y-PyImImImPyIm 3216) 5'W C T C CC C W-3' PyHpPyPyPyPy-y-ImImImImPyIm TABLE 148: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGGWNNW-3' -DNA aromatic amino acid sequence sequence ' 1233(3) 5' -W G G G T T T W-3' ImImIm-(3-HpHp-y-pypy-(3-pypypy S 1234(3) 5' -W G G G T T A W-3' ImImIm-(3-HpPy-Y-HpPy-(3-Pypypy 1235(3) 5' -W G G G T T G W-3' ImImIm-(3-HpIm-y-Pypy-~-pypypy ' 1236(3) 5' -W G G G T T C W-3' ImImIm-(3-HpPy-Y-ImPy-(3-Pypypy 1237(3) 5'-WG G G T AT W-3' ImImIm-J3-PyHp-Y-pyHp-(3-Pypypy 1238(3) 5'-WG G G T AA W-3' ImImIm-(3-PyPy-y-HpHp-(3-PyPypy 1239(3) 5'-WG G G T AG W-3' ImImIm-(3-Pylm-y-PyHp-(3-pypypy 12403) 5'-WG G G T AC W-3' ImImIm-(3-PyPy-y-ImHp-~3-pypypy 12413) 5'-WG G G T GT W-3' ImImIm-~-ImHp-y-pypy-~-pypypy 1242(3) 5'-WG G G T GA W-3' ImImIm-(3-ImPy-y-HpPy-~3-PyPypy 1243(3) 5'-WG G G T GG W-3' ImImIm-/3-Imlm-y-pypy-p-pypypy 12443) 5'-WG G G T GC W-3' ImImIm-~3-ImPy-Y-ImPy-[3-PyPyPy 1245(3) 5' -W G G G T C T W-3' ImImIm-~3-PyHp-Y-Pylm-~-Pypypy 12463) 5' -W G G G T C A W-3' ImImIm-(3-PyPy-y-Helm-~3-pypypy 12473) 5' -W G G G T C G W-3' ImImIm-~3-Pyim-Y-PyIm-(3-PyPyPy 12483) 5' -W G G G T C C W-3' ImImIm-(3-PyPy-y-ImIm-(3-PyPyPy 1249~i) 5' -WG G GA T T W-3' ImImIm-(3-HpHp-y-pypy-j3-pypypy 1250(3) 5' -WG G GA T A W-3' ImImIm-/3-HpPy-y-HpPy-p-pypypy 1251(3) 5' -WG G GA T G W-3' ImImIm-(3-HpIm-y-PyPy-~3-pypypy 1252(3) 5' -WG G GA T C W-3' ImImIm-(3-HpPy-y-ImPy-(3-Pypypy 12533) 5' -WG G GA A T W-3' ImImIm-(3-PyHp-y-PyHp-~3-Pypypy 1254(3) 5' -WG G GA A A W-3' ImImIm-~i-Pypy-y-HpHp-a_pypypy 1255(3) 5' -WG G GA A G W-3' ImImIm-(3-PyIm-y-pyHp-(3-PyPyPy 1256(3) 5' -WG G GA A C W-3' ImImIm-~3-PyPy-y-I~p_~_pypypy 1257(3) 5' -WG G GA G T W-3' ImImIm-(3-ImHp-Y-PyPY-~-pYPYPY
1258(3) 5' -WG G GA G A W-3' ImImIm-~3-ImPy-y-HpPy-(3-PyPyPy 1259(3) 5' -WG G GA G G W-3' ImImIm-(3-Im=m-y-pypy-~3-pypypy 1260~i) 5' -WG G GA G C W-3' ImImIm-(3-ImPy-y-ImPy-~3-PyPyPy 1261(3) 5' -WG G GA C T W-3' ImImIm-(3-PyHp-Y-pylm_~3_pypypy 12623) 5' -WG G GA C A W-3' ImImIm-(3-PyPy-y-Hplm-(3-PyPyPy 1263(3) 5' -WG G GA C G W-3' ImImIm-(3-P ylm-y-Pylm-p-Pypypy 1264(3) 5' -WG G GA C C W-3' ImImIm-(3-PyPy-y-Imlm-~3-Pypypy TABLE
149:
12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGGGSNNW-3' DNA aromatic amino acid sequence sequence 1265 (3)5' -WG G G G TT W-3' ImImImIm-(3-Hp-y-Py-~-PyPyPyPy 1266 (3)~ -WG G G G TA W-3' ImImImIm-~-Py-y-Hp-~i-PyPyPyPy 5' 1267 (3)5' -WG G G G TG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy 1268 (3)5' -WG G G G TC W-3' ImImImIm-(3-Py-y-Im-~i-PyPyPyPy 1269 ~3)5' -WG G G G AT W-3' ImImImIm-(3-Hp-y-Py-(3-PyPyPyPy 1270 (3)5' -WG G G G AA W-3' ImImImIm-(3-Py-y-Hp-~3-PyPyPyPy 1271 (3)5' -WG G G G AG W-3' ImImImIm-(3-Im-y-Py-(3-PyPyPyPy 1272 ~)5' -WG G G G AC W-3' ImImImIm-(3-Py-y-Im-(3-PyPyPyPy 1275 (3)5' -WG G G G CT W-3' ImImImIm-(3-Hp-y-PyImPy-(3-PyPy 1276 (3)5' -WG G G G CA W-3' ImImImIm-(3-Py-y-HpImPy-~i-PyPy 1277 (3)5' -WG G G C TT W-3' ImImIm-(3-HpHp-y-PyPyIm-(3-PyPy 1278 ~3)5' -WG G G C TA W-3' ImImIm-~3-HpPy-y-HpPyIm-(3-PyPy 1279 (3)5' -WG G G C TG W-3' ImImIm-~3-HpIm-y-PyPyIm-~3-PyPy 1280 (3)5' -WG G G C TC W-3' ImImIm-(3-HpPy-y-ImPyIm-p-PyPy 1281 (3)5' -WG G G C AT W-3' ImImIm-(3-PyHp-y-PyHpIm-(3-PyPy 1282 (3)5' -WG G G C AA W-3' ImImIm-(3-PyPy-y-HpHpIm-p-PyPy 1283 (3)5' -WG G G C AG W-3' ImImIm-(3-PyIm-y-PyHpIm-(3-PyPy 1284 (3)5' -WG G G C AC W-3' ImImIm-(3-PyPy-y-ImHpIm-(3-PyPy 1285 (3)5' -WG G G C GT W-3' ImImIm-(3-ImHp-y-PyPyIm-(3-PyPy 1286 ~3)5' -WG G G C GA W-3' ImImIm-(3-ImPy-y-HpPyIm-(3-PyPy 1287 (3)5' -WG G G C CT W-3' ImImIm-(3-PyHp-y-PyImIm-~3-PyPy 2S 1288 (3)5' -WG G G C CA W-3' ImImIm-~i-PyPy-y-HpImIm-J3-PyPy G52 5' -WG G G G CC W-3' ImImImIm-~3-Py-y-ImImPy-~3-PyPy (3) G53 5' -WG G G C GG W-3' ImImIm-(3-ImIm-y-PyPyIm-(3-PyPy (3) G54 5' -WG G G C GC W-3' ImImIm-~3-ImPy-y-ImPyIm-(3-PyPy (3) G55 5' -WG G G C CG W-3' ImImIm--Pylm-y-Pylmim-~3-PyPy ~3) G56 5' -WG G G C CC W-3' ImImIm--PyPy-y-ImImIm-(3-PyPy (3) TABLE -Hairpin 150: Polyamides 12-ring for (3 recognition of 8-by S'-WGGTWNNW-3' .
DNA aromatic amino acid sequence sequence 1289(3) 5' -W G GT T T T W-3' ImIm-(3-HpHpHp-y-pypypy-~3-pypy 12903} 5' -W G GT T T A W-3' ImIm-(3-HpHpPy-y-HpPyPy-(3-PyPy S 1291} ~ -W G GT T T G W-3' ImIm-~3-HpHpIm-y-Pypypy-(3-pypy 5' 1292(3) 5' -W G GT T T C W-3' ImIm-(3-HpHpPy-y-ImPypy-~i-Pypy 1293(3) 5' -W G GT T A T W-3' ImIm-G3-HpPyHp-y-pyHpPy-~3-pyPy 12943} 5' -W G GT T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-~3-PyPy 1295(3) 5' -W G GT T A G W-3' Imlm-(3-HpPyIm-y-PyHpPy-(3-PyPy 12963) 5' -W G GT T A C W-3' ImIm-~I-HpPypy-y-ImHppy_~_pyp~, 12973) 5' -W G GT T G T W-3' Imam-~3-HpImHp-y-pypypy-(3-pypy 12983) 5' -W G GT T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-PyPy 12993) 5' -W G GT T G G W-3' ImIm-~-HpImIm-y-PyPyPy-~3-Pypy 1300) 5' -W G GT T G C W-3' ImIm-(3-HpImPy-y-ImPyPy-(3-PYPy 1301(3) 5' -W G GT T C T W-3' Imam-p-HpPyHp-y-PyImPy-p-pypy 1302(3) 5' -W G GT T C A W-3' ImIm-~-HpPyPy-y-HpImPy-(3-PYPy 1303(3) 5' -W G GT T C G W-3' ImIm-p-HpPyIm-y-PyImPy-~3-PyPy 1304(3) 5' -W G GT T C C W-3' ImIm-(3-HpPyPy-y-ImImPy-(3-PyPy 1305(3) 5' -W G GT A T T W-3' Imlm-(3-PYHpHp-y-PyPYHp-~3-PyPy 1306~i) 5' -W G GT A T A W-3' ImIm-~3-PyHpPy-y-HpPyHp-(3-PyPy 13073) 5' -W G GT A T G W-3' ImIm-~3-PyHpIm-y-PyPyHp-(3-PyPy 13083) 5' -W G GT A T C W-3' Imam-(3-PyHpPy-y-ImPyHp-p-pyPy 1309(3) 5' -W G GT A A T W-3' ImIm-p-PyPyHp-y-PyHpHp-(3-PyPy 1310(3) 5' -W G GT A A A W-3' ImIm-p-PyPyPy-y-HpHpHp-/3-PyPy 2S 1311(3) 5' -W G GT A A G W-3' ImIm-~i-PyPyIm-y-PyHpHp--Pypy 1312(3) 5' -W G GT A A C W-3' ImIm-(3-PyPYPy-y-ImHpHp-~3-PyPy 1313(3) 5' -W G GT A G T W-3' Imlm-[3-PyImHp-y-PypyHp-(3-PYPy 13143) 5' -W G GT A G A W-3' Imlm-~i-pyImPy-y-HpPyHp-(3-pypy 1315(3) 5' -W G GT A G G W-3' Imlm-(3-PyImIm-y-PyPYHp-(3-PyPy 1316(3} 5' -W G GT A G C W-3' Imlm-~i-PyImPy-y-ImPyHp-(3-PyPy 1317~i) 5' -W G GT A C T W-3' ImIm-(3-PyPyHp-y-PyImHp-p-pypy 1318(3) 5' -W G GT A C A W-3' ImIm-(3-PyPyPy-y-HpImHp-p-PyPy 1319~i) 5' -W G GT A C G W-3' ImIm-(3-PyPyIm-y-PyImHp-~3-Pypy 1320(3) 5' -W G GT A C C W-3' ImIm-(3-PyPYPy-y-ImImHp-p-PyPy TABLE 151: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGTSNNW-3' DNA sequence aromatic amino acid sequence 1321(3) 5' -W G G T G T T W-3' ImIm-(i-ImHpHp-y-PyPyPy-(3-PyPy 1322(3) 5' -W G G T G T A W-3' Imlm-J3-ImHpPy-y-HpPyPy-~3-PyPy 1323(3) 5' -W G G T G T G W-3' ImIm-(3-ImHpIm-y-PyPyPy-p-PyPy 1324(3) 5' -W G G T G T C W-3' ImIm-(3-ImHpPy-y-ImPyPy-(3-PyPy 1325(3) 5' -W G G T G A T W-3' Imlm-(3-ImPyHp-y-PyHpPy-~3-PyPy 1326(3) 5' -WG G T G AA W-3' ImIm-(3-ImPyPy-y-HpHpPy-(3-PyPy 1327(3) 5' -WG G T G AG W-3' ImIm-~i-ImPyIm-y-PyHpPy-(3-PyPy 1328(3) 5' -WG G T G AC W-3' ImIm-(3-ImPyPy-y-ImHpPy-J3-Pypy 1329(3) 5' -WG G T G GT W-3' ImIm-(3-ImImHp-y-PyPyPy-(3-PyPy 1330(3) 5' -WG G T G GA W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy 1331(3) 5' -WG G T G CT W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy 1332(3) 5' -WG G T G CA W-3' ImIm-(3-ImPyPy-y-HpImPy-~3-PyPy 1333(3) 5' -WG G T G GG W-3' Imlm-(3-ImImIm-y-PypyPy-(3-PyPy 1334(3) 5' -W G G T G G C W-3' Imam-(3-ImImPy-y-ImPyPy-~i-PyPy 13353) 5' -W G G T G C G W-3' ImIm-p-ImPyIm-y-PyImPy-(3-PyPy 1336(3) 5' -W G G T G C C W-3' ImIm-(3-ImPyPy-y-ImImPy-~-PyPy 1337) 5' -W G G T C T T W-3' ImIm-~3-PyHpHp-y-PyPyIm-(3-PyPy 13383) 5' -W G G T C T A W-3' ImIm-(3-PyHpPy-y-HpPyIm-(3-PyPy 1339(3) 5' -W G G T C T G W-3' ImIm-~i-PyHpIm-y-PyPyIm-(3-PyPy 13403) 5' -W G G T C T C W-3' ImIm-(3-PyHpPy-y-ImPyIm-~3-PyPy 13413) 5' -W G G T C A T W-3' ImIm-~i-PyPyHp-y-PyHpIm-(3-PyPy 13423) 5' -W G G T C A A W-3' Imlm-(3-PyPyPy-y-HpHpIm-(3-PyPy 1343(3) 5' -W G G T C A G W-3' ImIm-(3-PyPyIm-y-PyFipIm-(3-PyPy 13440 5' -W G G T C A C W-3' ImIm-~i-PyPyPy-y-imHpIm-(3-PyPy 1345(3) 5' -W G G T C G T W-3' ImIm-(3-PyImHp-y-PyPyIm-(3-PyPy 1346(3) 5' -W G G T C G A W-3' Imlm-(3-PyImPy-y-HpPyIm-(3-PyPy 13470 5' -W G G T C C T W-3' Imlm-(3-PyPyHp-y-PyImIm-~3-PyPy 1348(3) 5' -W G G T C C A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy 1349~i) 5' -W G G T C G G W-3' Imlm-(3-PyImIm-y-PyPyIm-~3-PyPy 1350(3) 5' -W G G T C G C W-3' Imlm-(3-PyImPy-y-ImPyIm-(3-PyPy 1351(3) 5' -W G G T C C G W-3' ImIm-(3-PyPyIm-y-PyImIm-(3-PyPy 1352ø) 5' -W G G T C C C W-3' Imlm-~3-PyPyPy-y-ImImIm-~i-PyPy TABLE 152: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGAVVNNW-3' -DNA sequence aromatic amino acid sequence 1353(3) 5' -W G T T T W-3' ImIm-~3-HpHpHp-y-pypypy-(3-pypy G A
1354(3) '5'-W G T T A W-3' ImIm-~3-HpHpPy-y-HpPyPy-(3-PyPy G A
1355(3) 5' -W G T T G W-3' ImIm-(3-HpHp3m-y-PypyPy-~3-PyPy G A
1356(3) 5' -W G T T C W-3' ImIm-~-HpHpPy-y-ImPyPy-[3-PyPy G A
1357(3) 5' -W G T A T W-3' ImIm-(3-HpPyHp-y-PyHpPy-~-pypy G A
13583) 5'-W G T A A W-3' ImIm-(3-HpPyPy-y-HpHpPy-(3-PyPy G A
13593) 5'-W G GA T A G W-3' ImIm-(3-HpPyIm-y-PyHpPy-(3-PyPy 1360(3) 5'-W G GA T A C W-3' ImIm-~3-HppyPy-y-ImHppy_~3_pypy 1361(3) 5'-W G GA T G T W-3' ImIm-~3-HpImHp-y-pypypy_~_pypy 1362(3) 5'-W G GA T G A W-3' ImIm-(3-HpImPy-y-HpPyPy-(3-pypy 1363(3) 5'-W G GA T G G W-3' Imlm-~3-HpImIm-y-PyPyPy-(3-PyPy 1364(3) 5'-W G GA T G C W-3' Imlm-~3-HpImPy-y-ImPyPy-(3-PyPy 1365(3) 5'-W G GA T C T W-3' ImIm-R-HpPyHp-y-PyImPy-(3-PyPy 13663) 5'-W G GA T C A W-3' ImIm-(3-HpPyPy-y-HpImPy-(3-PyPy 13673) 5'-W G GA T C G W-3' ImIm-(3-HpPyIm-y-PyIrr~Py-(3-PyPy 1368(3) 5'-W G GA T C C W-3' ImIm-(3-HpPyPy-y-ImImpy-(3-Pypy 1369(3) 5'-W G GA A T T W-3' Imlm-p-PyHpHp-y-PypyHp-(3-PyPy 1370(3) 5'-W G GA A T A W-3' ImIm-(3-PyHpPy-y-HpPyHp-/3-PyPy 1371(3) 5'-W G GA A T G W-3' ImIm-J3-PyHpIm-y-PyPyHp-(3-PyPy 1372(3) 5'-W G GA A T C W-3' Imlm-~3-pyHpPy-y-ImPyHp-j3-PyPy 13733) 5'-W G GA A A T W-3' ImIm-(3-PyPyHp-y-pyHpHp-~i-Pypy 1374(3) 5'-W G GA A A A w-3' ImIm-(3-PyPyPy-y-HpHpHp-(3-PyPy 13753) 5'-W G GA A A G W-3' Imlm-(3-PyPyIm-y-PyHpHp-~3-PyPy 1376(3) 5'-W G GA A A C W-3' ImIm-~i-Pypypy-y-I~pHp_(3_pyp~, 13773) 5'-W G GA A G T W-3' Imam-a-pyImHp-y-PypyHp-~3-PyPy 13783) 5'-W G GA A G A W-3' ImIm-~3-pyImPy-y-HpPyHp-~3-PyPy 1379(3) 5'-W G GA A G G W-3' Imlm-(3-PyImIm-y-PypyHp-~3-Pypy 1380(3) 5'-W G GA A G C W-3' Imlm-(3-PyImPy-y-ImPyHp-~3-PyPy 1381~i) 5'-W G GA A C T W-3' ImIm-~3-PyPyHp-y-PyImHp-(3-PyPy 1382~i) 5'-W G GA A C A W-3' Imlm_(3_pypypy_y_Hp=~p-(3-pypy 1383(3) 5'-W G GA A C G W-3' ImIm-(3-PyPyim-y-pyImHp-(3-PyPy 13843) 5'-W G GA A C C W-3' ImIm-(3-PypyPy-y-ImImHp-~3-Pypy WO 98/370b7 PCT/US98/01714 TABLE
153:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGASNNW-3' DNA aromatic amino acid sequence sequence 1385(3) 5' -WG G A GT T W-3' ImIm-~i-ImHpHp-y-PyPyPy-~3-PYPy 13863) ' -WG G A GT A W-3' ImIm-~i-ImHpPy-y-HpPyPy-~3-PyPy 5' 1387(3) 5' -WG G A GT G W-3' Imlm-~3-ImHpIm-y-PyPyPy-~3-PyPy 1388(3) 5' -WG G A GT C W-3' ImIm-~i-ImHpPy-y-ImPyPy-~3-PyPy 1389(3) 5' -WG G A GA T W-3' ImIm-~3-TmPyHp-y-PyHpPy-(3-PyPy 1390(3) 5' -WG G A GA A W-3' ImIm-~i-ImPyPy-y-HpHpPy-(3-PyPy 13913) 5' -WG G A GA G W-3' ImIm-~3-ImPyIm-y-PyHpPy-(3-PyPy 1392(3) 5' -WG G A GA C W-3' ImIm-(3-ImPyPy-y-ImHpPy-(3-PyPy 13933) 5' -WG G A GG T W-3' ImIm-(3-ImImHp-y-PyPyPy-[3-PyPy 13943) 5' -WG G A GG A W-3' ImIm-(3-ImImPy-y-HpPyPy-(3-PyPy 1395(3) 5' -WG G A GC T W-3' ImIm-(3-ImPyHp-y-PyImPy-(3-PyPy 13963) 5' -WG G A GC A W-3' Imlm-(3-ImPyPy-y-HpImPy-(3-PyPy 1397(3) 5' -WG G A GG G W-3' Imlm-(3-ImImIm-y-PyPyPy-(3-PyPy 1398(3) 5' -WG G A GG C W-3' ImIm-/3-ImImPy-y-ImPYPy-(3-PyPy 1399(3) 5' -WG G A GC G W-3' ImIm-(3-ImPyIm-y-PyImPy-(3-PyPy 1400(3) 5' -WG G A GC C W-3' ImIm-~-ImPyPy-y-ImImPy-(3-PyPy 1401~i) 5' -WG G A CT T W-3' Imlm-(3-PyHpHp-y-PYPyIm-/3-PyPy 1402(3) 5' -WG G A CT A W-3' ImIm-(3-PyHpPy-y-HpPyIm-R-PyPy 1403(3) 5' -WG G A CT G W-3' ImIm-(3-PyHpIm-y-PyPy3m-~3-PyPy 14043) 5' -WG G A CT C W-3' ImIm-~-PyHpPy-y-ImPyIm-(3-PyPy 14053) 5' -WG G A CA T W-3' ImIm-~3-PyPyHp-y-PyHpIm-(3-PyPy 1406~i) 5' -WG G A CA A W-3' ImIm-(3-PyPyPy-y-HpHpIm-p-PyPy 1407(3) 5' -WG G A CA G W-3' ~ImIm-(3-PyPyIm-y-PyHpIm--PyPy 1408(3) 5' -WG G A CA C W-3' ImIm-(i-PyPyPy-y-ImHpIm-(i-PyPy 1409~i) 5' -WG G A CG T W-3' ImIm-(i-PyImHp-y-PyPyIm-(3-PyPy 1410(3) 5' -WG G A CG A W-3' Imlm-(3-PyImPy-y-HpPyIm-~-PyPy 1411) 5' -WG G A CC T W-3' ImIm-~3-PyPyHp-y-PyImIm-(3-PyPy 1412(3) 5' -WG G A CC A W-3' ImIm-(3-PyPyPy-y-HpImIm-(3-PyPy 1413(3) 5' -WG G A CG G W-3' ImIm-~3-PyImIm-y-PyPYIm-~i-PyPy 1414(3) 5' -WG G A CG C W-3' Imam-~3-PyImPy-y-ImPyIm-p-PyPy 1415p) 5' -WG G A CC G W-3' ImIm-~i-PyPyIm-y-PyImIm-(3-PyPy 1416(3) 5' -WG G A CC C W-3' Imlm-(3-PyPyPy-y-ImImIm-~i-PyPy _~__... _.._ ? , . , TABLE 154:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGGCWNNW-3' -DNA sequence aromatic amino acid sequence 1417(3) ImImPy-~3-HpHp-y-PyPy-(3-ImPyPy 5' -W
G G C
T T T
W-3' 1418(3) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-/3-ImPyPy C T
1419(3) 5' -W G G T G W-3' ImImPy-~3-HpIm-y-Pypy-(3-Impypy C T
14200 5' -W G G T C W-3' ImImPy-~-HpPy-y-ImPy-(3-ImPypy C T
14213) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pygp-~-ImPyPy C T
1422(3) 5' -W G G A A W-3' ImImPy-(3-Pypy-y-HpHp_~3-ImPyPy C T
1423(3) 5' -W G G A G W-3' ImImPy-(3-Pylm-y-pygp-~3-ImPyPy C T
1424(3) 5' -W G G A C W-3' C T ImImPy-(3-PyPy-y-ImHp-~i-ImPyPy 1425(3) 5' -W G G G T W-3' C T ImImPy-(3-ImHp-y-PyPy-(3-ImPyPy 1426) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-~-ImPyPy C T
1427(3) 5' -W G G G G W-3' ImImPy-(3-ImIm-y-Pypy-~-ImPyPy C T
1428(3) 5' -W G G G C W-3' ImImPy-(3-ImPy-y-ImPy-/3-ImPyPy C T
1429(3) 5' -W G G C T W-3' ImImPy-(3-PyHp-y-pyIm-(3-ImPyPy C T
1430(3) 5' -W G G C A W-3' ImImPy-~3-pypy-y-HpIm-J3-ImPyPy C T
1431(3) 5' -W G G C G W-3' ImImPy-~3-pylm-y-pylm_(~_ImPyPy C T
14323) 5' -W G G C C W-3' ImImPy-(3-pypy-y-Imlm-(3-ImPyPy C T
14330 5' -W G G T T W-3' ImImPy-(3-HpHp-y-Pypy-~3-ImPyPy C A
1434~i) 5' -W G G T A W-3' ImImPy-(3-HpPy-y-HpPy-(3-ImPyPy C A
14353) 5' -W G G T G W-3' ImImPy-(3-Hplm-y-Pypy-~3-ImPyPy C A
14363) 5' -W G G T C W-3' C A ImImPy-~i-HpPy-y-ImPy-(3-ImPyPy 1437(3) 5' -W G G A T W-3' ImImPy-(3-PyHp-y-pyHp-(3-ImPyPy C A
1438~i) 5' -W G G A A W-3' ImImPy-(3-PyPy-y-HpHp-(3-ImPyPy C A
1439(3) 5' -W G G A G W-3' Imlmpy-a-pyim-y-pyHp-(3-ImPyPy C A
1440(3) 5' -W G G A C W-3' C A ImImPy-(3-PyPy-y-ImHp-~3-ImPyPy 14413) 5' -W G G G T W-3' C A ImImPy-~3-ImHp-y-PyPy-(3-ImPyPy 14423) 5' -W G G G A W-3' ImImPy-~3-ImPy-y-HpPy-(3-ImPyPy C A
1443(3) 5' -W G G G G W-3' ImImPy-p-Imlm-y-PyPy-R-ImPyPy C A
1444(3) 5'-W G G G C W-3' ImImPy-~3-ImPy-y-Impy-(3-ImPyPy C A
1445(3) 5' -W G G C T W-3' ImImPy-(3-pyHp-y-pylm-~i-ImPyPy C A
1446(3) 5' -W G G C A W-3' ImImPy-(3-PyPy-y-Hplm-(3-ImPyPy C A
1447(3) 5' -W G G C G W-3' ImImPy-(3-Pylm-y-Pylm-/3-ImPyPy C A
14483) 5' -W G G C C W-3' ImImPy-(3-pypy-y-ImIm-/3-ImPypy C A
TABLE
155:
12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGGCSNNW-3' -DNA aromatic amino acid sequence sequence 1449R) 5'-W G GC G T T W-3' ImIm-(3-ImHpHp-y-PyPy-~3-ImPyPy 14503) ~5'-W G GC G T A W-3' Imlm-~3-ImHpPy-y-HpPy-(3-ImPyPy 1451(3) 5'-W G GC G T G W-3' ImIm-(3-ImHpIm-y-PyPy-(3-ImPyPy 1452(3) 5'-W G GC G T C W-3' Imlm-(3-ImHpPy-y-ImPy-(3-ImPyPy 14530 5'-W G GC G A T W-3' ImIm-(3-ImPyHp-y-PyHp-(3-ImPyPy 1454(3) 5'-W G GC G A A W-3' ImIm-(3-ImPyPy-y-HpHp-~3-ImPyPy 14553) 5'-W G GC G A G W-3' Imlm-~-ImPyIm-y-PyHp-(3-ImPyPy 1456(3) 5'-W G GC G A C W-3' ImIm-(3-ImPyPy-y-ImHp-(3-ImPyPy 1457~i) 5'-W G GC G G T W-3 Imlm-(3-ImImHp-y-PyPy-(3-ImPyPy 14583) 5'-W G GC G G A W-3' ImIm-~-ImImPy-y-HpPy-~-ImPyPy 1459(3) 5'-W G GC G C T W-3' ImIm-(3-ImPyHp-y-PyIm-(3-ImPyPy 1460(3) 5'-W G GC G C A W-3' Imlm-(3-ImPyPy-y-HpIm-(3-ImPyPy 14613) 5'-W G GC C T T W-3' Imlm-p-PyHpHp-y-Py-(3-ImImPyPy 1462(3) 5'-W G GC C T A W-3' ImIm-~3-PyHpPy-y-Hp-~-ImImPyPy 14633) 5'-W G GC C T G W-3' ImIm-/3-PyHpIm-y-Py-~i-ImImPyPy 1464(3) 5'-W G GC C T C W-3' Imlm-(3-PyHpPy-y-Im-(3-ImImPyPy 1465~i) 5'-W G GC C A T W-3' ImIm-(3-PyPyHp-y-Py-p-ImImPyPy .
1466(3) 5'-W G GC C A A W-3' ImIm-[3-PyPyPy-y-Hp-/3-ImImPyPy 1467(3) 5'-W G GC C A G W-3' ImIm-(3-PyPyIm-y-Py-(3-ImImPyPy 14683) 5'-W G GC C A C W-3' ImIm-p-PyPyPy-y-Im-(3-ImImPyPy 1469p) 5'-W G GC C G T W-3' Imlm-(3-PyImHp-y-Py-(3-ImImPyPy 1470(3) 5'-W G GC C G A W-3' Imlm-(3-PyImPy-y-Hp-~3-ImImPyPy 14713) 5'-W G GC C C T W-3' ' ImIm-J3-PyPyHp-y-PyImImIm-(3-Py 1472(3) 5'-W G GC C C A W-3' Imlm-~3-PyPyPy-y-HpImImIm-(3-Py G57(3) 5'-W G GC G G G W-3' Imlm-(3-ImImIm-y-PyPy-(3-ImPyPy G58(3) 5'-W G GC G G C W-3' Imlm-J3-ImImPy-y-ImPy-(3-ImPyPy G59~) 5'-W G GC G C G W-3' ImIm-~3-ImPyIm-y-PyIm-~3-ImPyPy G60(3) 5'-W G GC G C C W-3' ImIm-(3-ImPyPy-y-ImIm-(3-ImPyPy G6l~i) 5'-W G GC C G G W-3' ImIm-(3-PyImIm-y-Py-(3-ImImPyPy G62~3) 5'-W G GC C G C W-3' ImIm-(3-PyImPy-y-Im-(3-ImImPyPy G63(3) 5'-W G GC C C G W-3' ImIm-(3-PyPyIm-y-PyImImIm-(3-Py G64(3) 5'-W G GC C C C W-3' ImIm-(3-PyPyPy-y-ImImImIm-(3-Py TABLE 156:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCGWNNW-3' .
DNA aromatic amino acid sequence sequence 1473(3) 5'-WG C G T TT W-3' ImPyIm-(3-HpHp-y-PyPyPy-(3-ImPy 1474(3) ~5'-WG C G T TA W-3' ImPyIm-(3-HpPy-y-Hppypy-~3_Impy 1475(3) 5'-WG C G T TG W-3' ImPyIm-(3-Hplm-y-PyPyPy-~3-ImPy 1476(3) 5'-WG C G T TC W-3' ImPyIm-(3-HpPy-y-ImPyPy-(3-ImPy 1477(3) 5'-WG C G T AT W-3' ImPyIm-~-PyHp-y-pyHpPy-(3-ImPy 1478) 5'-WG C G T AA W-3' ImPyIm-~3-PyPy-y-HpHpPy-(3-ImPy 1479(3) 5'-WG C G T AG W-3' ImPyIm-(3-PyIm-y-pyHppy-(3-ImPy 14803) 5'-WG C G T AC W-3' ImPyIm-(3-PyPy-y-ImHpPy-(3-ImPy 1481(3) 5'-WG C G T GT W-3' ImPyIm-(3-ImHp-y-pypypy-~3-ImPy 14823) 5'-WG C G T GA W-3' ImPyIm-(3-ImPy-y-HpPyPy-p-ImPy 1483(3) 5'-WG C G T GG W-3' ImPyIm-(3-ImIm-y-Pypypy-(3-ImPy 14843) 5'-WG C G T GC W-3' ImPyIm-~3-ImPy-y-ImPyPy-j~-ImPy 1485(3) 5'-WG C G T CT W-3' ImPyIm-(3-PyHp-Y-PyImPy-(3-ImPy 1486(3) 5'-WG C G T CA W-3' ImPyIm-~3-PyPy-y-HpImPy-(3-ImPy 1487(3) 5'-WG C G T CG W-3' ImPyIm-(3-Pylm-y-PyImPy-~3-Irr~Py 1488(3) 5'-WG C G T CC W-3' ImPyIm-(3-PyPy-y-ImImPy-~i-ImPy 14893) 5'-WG C G A TT W-3' ImPyIm-~-HpHp-Y-PypyHp-/3-ImPy 1490(3) 5'-WG C G A TA W-3' ImPyIm-~-HpPy-y-HpPyHp-(3-ImPy 1491(3) 5'-WG C G A TG W-3' ImPyIm-(3-HpIm-y-PyPyHp-(3-ImPy 1492(3) 5'-WG C G A TC W-3' ImPyIm-(3-HpPy-y-ImPyHp-~-ImPy 1493(3) 5'-WG C G A AT W-3' ImPyIm-~3-PyHp-y-pyHpHp-(3-ImPy 14940 5'-WG C G A AA W-3' ImPyIm-(3-pyPy-y-HpHpHp-(3-ImPy 1495(3) 5'-WG C G A AG W-3' ImPyIm-(3-PyIm-y-PyHpHp-~3-ImPy 1496(3) 5'-WG C G A AC W-3' ImPyIm-(3-Pypy-y-ImHpHp-~3-ImPy 1497(3) 5'-WG C G A GT W-3' ImPyIm-~-ImHp-y-PyPyHp-(3-ImPy 1498(3) 5'-WG C G A GA W-3' ImPyIm-(3-ImPy-y-HpPyHp-(3-ImPy 1499(3) 5'-WG C G A GG W-3' ImPyIm-(3-Imlm-y-PyPyHp-p-ImPy 1490(3) 5'-WG C G A GC W-3' ImPyIm-/3-ImPy-y-ImPyHp-(3-ImPy 1501(3) 5'-WG C G A CT W-3' ImPyIm-(3-PyHp-y-PyImHp-(3-ImPy 1502(3) 5'-WG C G A CA W-3' ImPyIm-~3-PyPy-Y-HpImHp-p-ImPy 1503(3) 5'-WG C G A CG W-3' ImPyIm-(3-PyIm-y-pyImHp-a-ImPy 1504(3) 5'-WG C G A CC W-3' ImPyIm-p-PyPy-y-ImImHp-p-ImPy TABLE
157:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCGSNNW-3' -DNA aromatic amino acid sequence sequence 15053) 5'-W G C G GT T W-3' Im-(3-ImImHpHp-y-PyPyPy-(3-ImPy 1506(3) 5'-W G C G GT A W-3' Im-(3-ImImHpPy-y-HpPyPy-(3-ImPy 1507(3) 5'-W G C G GT G W-3' Im-(3-ImImHpIm-y-PyPyPy-(3-ImPy 1508(3) 5'-W G C G GT C W-3' Im-(3-ImImHpPy-y-ImPyPy-(3-ImPy 1509(3) 5'-W G C G GA T W-3' Im-(3-ImImPyHp-y-PyHpPy-(3-ImPy 1510(3) 5'-W G C G GA A W-3' Im-(3-ImImPyPy-y-HpHpPy-(3-Impy 1511~i) 5'-W G C G GA G W-3' Im-(3-ImImPyIm-y-PyHpPy-(3-ImPy 1512(3) 5'-W G C G GA C W-3' Im-(3-ImImPyPy-y-ImHpPy-(3-ImPy 1513(3) 5'-W G C G GG T W-3' Im-~3-ImImImHp-y-PyPyPy-p-ImPy 153-4(3) 5'-W G C G GG A W-3' Im-~3-ImImImPy-y-HpPyPy-(3-ImPy 1515(3) 5'-W G C G GC T W-3' Im-p-ImImPyHp-y-PyImPy-(3-ImPy 1516(3) 5'-W G C G GC A W-3' Im-~-ImImPyPy-y-HpImPy-~3-ImPy 1517(3) 5'-W G C G CT T W-3' ImPyIm-(3-HpHp-y-PyPyIm-~i-ImPy 1518(3) 5'-W G C G CT A W-3' ImPyIm-(3-HpPy-y-HpPyIm-~3-ImPy 1519(3) 5'-W G C G CT G W-3' ImPyIm-a-HpIm-y-PyPyIm-(3-ImPy 1520(3) 5'-W G C G CT C W-3' ImPyIm-(3-HpPy-y-ImPyIm-(3-ImPy 15213) 5'-W G C G CA T W-3' ImPyIm-(3-PyAp-y-PyHpIm-(3-ImPy 1522(3) 5'-W G C G CA A W-3' ImPyIm-(3-PyPy-y-HpHpIm-(3-ImPy 1523(3) 5'-W G C G CA G W-3' ImPyIm-(3-PyIm-y-PyHpIm-(3-ImPy 1524(3) 5'-W G C G CA C W-3' ImPyIm-~3-PyPy-y-ImHpIm-(3-ImPy 1525(3) 5'-W G C G CG T W-3' ImPyIm-(3-ImHp-y-PyPyIm-~3-ImPy 15263) 5'-W G C G CG A W-3' ImPyim-(3-ImPy-y-HpPyIm-(3-ImPy 1527) 5'-W G C G CC T W-3' ImPyIm-~i-PyHp-y-PyImIm-(3-ImPy 1528(3) 5'-W G C G CC A W-3' ImPyIm-~-PyPy-y-HpImIm-(3-ImPy G65~) 5'-W G C G GG G W-3' Im-~i-ImImImIm-y-PyPyPy-~i-ImPy G66~3) 5'-W G C G GG C W-3' Im-p-ImImImPy-y-ImPyPy-(3-ImPy G67(3) 5'-W G C G GC G W-3' Im-(3-ImImPyIm-y-PyImPy-/3-ImPy G68(3) 5'-W G C G GC C W-3' Im-(3-ImImPyPy-y-ImImPy-p-ImPy G69(3) 5'-W G C G CG G W-3' ImPyIm-(3-ImIm-y-PyPyIm-(3-ImPy G70~3) 5'-W G C G CG C W-3' ImPyIm-(3-ImPy-y-ImPyIm-~3-ImPy G71(3) 5'-W G C G CC G W-3' ImPyIm-~i-PyIm-y-PyImIm-p-ImPy G72(3) 5'-W G C G CC C W-3' ImPyIm-(3-PyPy-y-ImImIm-(3-ImPy ,, TABLE 158:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGCTWNNW-3' -DNA aromatic amino acid sequence sequence ' 1529(3) 5' G C T T T TW-3' ImPy-~3-HpHpHp-y-Pypypy_~3-ImPy -W
15303) - G C T T T AW-3' ImPy-~i-HpHpPy-y-HpPyPy-~3-ImPy 5' -W
1531(3) 5' G C T T T GW-3' ImPy-(3-HpHpIm-y-Pypypy-a-ImPy -W
15323) 5' G C T T T CW-3' ImPy-(3-HpHpPy-y-ImPyPy-(3-ImPy -W
15333) 5' G C T T A TW-3' ImPy-~3-HpPyHp-y-pyHpPy-~i-ImPy -W
1534(3) 5' G C T T A AW-3' ImPy-~3-HpPyPy-y-HpHpPy-(3-ImPy -W
15353) 5' G C T T A GW-3' ImPy-(3-HpPyIm-y-PyHpPy-(3-ImPy -W
1536~i) 5'-W G C T T A CW-3' ImPy-~;-Hppypy_y_I~ppy-~_Impy 15373) 5' G C T T G TW-3' ImPy-(1-HpImHp-y-PyPypy-(3-ImPy -W
1538(3) 5' G C T T G AW-3' ImPy-/3-HpImPy-y-HpPyPy-~i-ImPy -W
1539(3) 5' G C T T G GW-3' ImPy-~-HpImIm-y-Pypypy-(3-Impy -W
1540p) 5' G C T T G CW-3' ImPy-a-HpImPy-y-ImPyPy-~3-ImPy -W
1541(3) 5' G C T T C TW-3' ImPy-(3-HppyHp-y-pyImPy-~3-ImPy -W
1542~i) 5' G C T T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-~-ImPy -W
15433) 5' G C T T C GW-3' ImPy-~3-HpPyIm-y-pyImPy-p-ImPy -W
15443) 5' G C T T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-(3-ImPy -W
1545(3) 5' G C T A T TW-3' ImPy-(1-pyHpHp-y-pypyHp-(3-ImPy -W
15463) 5' G C T A T AW-3' Impy-(3-PyHppy-y-HppyHp-~i-ImPy -W
1547(3) 5' G C T A T GW-3' ImPy-(3-PyHpIm-y-pypyHp-~3-ImPy -W
1548(3) 5' G C T A T CW-3' ImPy-(3-PyHpPy-y-ImPyHp-p-ImPy -W
1549~i) 5' G C T A A TW-3' ImPy-(3-PyPyHp-y-pyHpHp-~i-ImPy -W
1550p) 5' G C T A A AW-3' ImPy-(3-PyPyPy-y-HpHpHp_~3-ImPy -W
1551(3) 5' G C T A A GW-3' ImPy-~-Pypylm-y_pyHpHp-(3-ImPy -W
1552(3) 5' G C T A A CW-3' ImPy-p-Pypypy-y-I~pHp-(3-ImPy -W
1553(3) 5' G C T A G TW-3' ImPy-~-PyImHp-y-PypyHp-(3-ImPy -W
1554(3) 5' G C T A G AW-3' ImPy-p-PyImPy-y-HpPyHp-/3-ImPy -W
1555(3) 5' G C T A G GW-3' Impy-(3-PyImIm-y-pypyHp-(3-ImPy -W
1556(3) 5' G C T A G CW-3' ImPy-~3-PyImPy-y-ImPyHp-(3-ImPy -W
I557(3) 5' G C T A C TW-3' ImPy-(3-PyPyHp-y-PyImHp-p-ImPy -W
15583) 5' G C T A C AW-3' ImPy-(3-Pypypy-Y_Hpl~p_~3_ImPy -W
1559(3) 5' G C T A C GW-3' ImPy-R-Pypylm-Y-PyImHp-/3-ImPy -W
1560~i) 5' G C T A C CW-3' Impy-~i-pypypy-y-ImImHp-(3-ImPy -W
TABLE
159:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCTSNNW-3' DNA aromatic amino acid sequence sequence 15613) 5'-W G C TG T T W-3' ImPy-j3-ImHpHp-y-PyPyPy-(3-ImPy 1562(3) 5'-W G C TG T A W-3' ImPy-~3-ImHpPy-y-HpPyPy-(3-ImPy 1563(3) 5'-W G C TG T G W-3' ImPy-(3-ImHpIm-y-PyPyPy-(3-ImPy 1564(3) 5'-W G C TG T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy 1565(3) 5'-W G C TG A T W-3' ImPy-(3-ImPyHp-y-PyHppy-(3-ImPy 1566(3) 5'-W G C TG A A W-3' Impy-(3-ImPyPy-y-HpHpPy-(3-ImPy 1567(3) 5'-W G C TG A G W-3' ImPy-p-ImPyIm-y-PyHpPy-p-ImPy 1568(3) 5'-W G C TG A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-(3-ImPy 1569(3) 5'-W G C TG G T W-3' ImPy-~3-ImImHp-y-PyPyPy-(3-ImPy 1570(3) 5'-W G C TG G A W-3' ImPy-(3-ImImPy-y-HpPyPy-(3-ImPy 15713) 5'-W G C TG C T W-3' ImPy-(3-ImPyHp-y-PyImPy-(3-ImPy 1572(3) 5'-W G C TG C A W-3' ImPy-~-ImPyPy-y-HpImPy-(3-ImPy 1573~i) 5'-W G C TG G G W-3' ImPy~-(3-ImImIm-y-PyPyPy-(3-ImPy 1574(3) 5'-W G C TG G C W-3' ImPy-[3-ImImPy-y-ImPyPy-p-ImPy 1575(3) 5'-W G C TG C G W-3' ImPy-(3-ImPyIm-y-PyImPy-(3-ImPy 15760 5'-W G C TG C C W-3' ImPy-(3-ImPyPy-y-ImImPy-(3-ImPy 1577(3) 5'-W G C TC T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-ImPy 1578(3) 5'-W G C TC T A W-3' ImPy-(3-PyHpPy-y-HpPyIm-(3-ImPy 1579(3) 5'-W G C TC T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-/3-ImPy 1580(3) 5'-W G C TC T C W-3' ImPy-(3-PyHpPy-y-ImPyIm-(3-ImPy 1581(3) 5'-W G C TC A T W-3' ImPy-(3-PyPyHp-y-PyHpIm-/3-ImPy 1582(3) 5'-W G C TC A A W-3 ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy T
1583(3) 5'-W G C TC A G W-3' 'Impy-J3-Pypylm-y-PyHpIm-(3-ImPy 1584(3) 5'-W G C TC A C W-3' ImPy-~3-PyPyPy-y-ImHpIm-(3-ImPy 15853) 5'-W G C TC G T W-3' ImPy-(3-PyImHp-y-PypyIm-~-ImPy 1586(3) 5'-W G C TC G A W-3' ImPy-(3-PyImPy-y-HpPyIm-~i-ImPy 1587(3) 5'-W G C TC C T W-3' ImPy-(3-PyPyHp-y-PyImIm-(3-ImPy 1588(3) 5'-W G C TC C A W-3' ImPy-~3-PyPyPy-y-HpImIm-(3-ImPy 1589~i) 5'-W G C TC G G W-3' ImPy-(3-PyImIm-y-PyPyIm-(3-ImPy 1590~i) 5'-W G C TC G C W-3' ImPy-~3-PyImPy-y-ImPyIm-(3-ImPy 15913) 5'-W G C TC C G W-3' ImPy-p-PyPyIm-y-PyImIm-(3-ImPy 1592(3) 5'-W G C TC C C W-3' ImPy-p-PyPyPy-y-ImImIm-p-ImPy ,..
TABLE 160: 12-ring ~i-Hairpin Polyamides for recognition of 8-by 5'-WGCAWNNW-3' DNA sequence aromatic amino acid sequence 1593(3) 5' -W G C A T T T W-3' ImPy-~-HpHpHp-y-Pypypy-(3-ImPy 1594(3) 5' -W G C A T T A W-3' ImPy-~3-HpHpPy-y-HpPyPy-p-ImPy 1595(3) 5' -W G C A T T G W-3' ImPy-~i-HpHpIm-y-pypypy-(3-ImPy 1596(3) 5' -W G C A T T C W-3' ImPy-~3-HpHpPy-y-ImPyPy-(3-ImPy 1597) 5'-WG C A T A TW-3' ImPy-(3-HpPyHp-y-PyHpPy-~3-ImPy 1598(3) 5'-WG C A T A AW-3' ImPy-(~-HpPyPy-y-HpHpPy-(3-ImPy 1599(3) 5'-WG C A T A GW-3' ImPy-~3-HpPyIm-y-PyHpPy-~3-ImPy 1600(3) 5'-WG C A T A CW-3' ImPy-~3-HpPyPy-y-ImHpPy-p-ImPy 1601(3) 5'-WG C A T G TW-3' ImPy-p-HpImHp-y-PyPyPy-(3-ImPy 1602~i) 5'-WG C A T G AW-3' ImPy-(3-HpImPy-y-HpPyPy-(3-ImPy 1603(3) 5'-WG C A T G GW-3' ImPy-~3-HpImIm-y-Pypypy-(3-ImPy IS 16043) 5'-WG C A T G CW-3' ImPy-~-HpImPy-y-ImPyPy-(3-ImPy 1605(3) 5'-WG C A T C TW-3' ImPy-~i-HpPyHp-y-pylmPy-(3-ImPy 1606(3) 5'-WG C A T C AW-3' ImPy-(3-HpPyPy-y-HpImPy-(3-ImPy 16073) 5'-WG C A T C GW-3' ImPy-(3-HpPyIm-y-PyImPy-~-ImPy 1608(3) 5'-WG C A T C CW-3' ImPy-~3-HpPyPy-y-ImImPy-~3-ImPy 1609~i) 5'-WG C A A T TW-3' ImPy-~-PyHpHp-y-PypyHp-(3-ImPy 16103) 5'-WG C A A T AW-3' ImPy-~3-pyHpPy-y-HpPyHp-~-ImPy 16113) 5'-WG C A A T GW-3' ImPy-(3-PyHpIm-y-PypyHp-p-ImPy 1612(3) 5'-WG C A A T CW-3' ImPy-~3-PyHpPy-y-ImPyHp-p-ImPy 1613(3) 5'-WG C A A A TW-3' ImPy-(3-PypyHp-y-pyHpHp-(3-ImPy 1614(3) 5'-WG C A A A AW-3' Impy-(3-PyPyPy-y-HpHpHp-(3-Impy 1615(3) 5'-WG C A A A GW-3' ~ImPy-~3-pypylm-y-PyHpHp-~3-ImPy 16163) 5'-WG C A A A CW-3' ImPy-R-PyPypy-y-I~pHp-~3-ImPy 1617(3) 5'-WG C A A G TW-3' ImPy-(3-pyl~p_y-pypyHp-~-ImPy 16183) 5'-WG C A A G AW-3' ImPy-(3-PyImPy-y-HpPyHp-(3-ImPy 1619(3) 5'-WG C A A G GW-3' ImPy-(3-PyImIm-y-PypyHp-~i-ImPy 1620(3) 5'-WG C A A G CW-3' ImPy-J3-PyImPy-y-ImPyHp-(3-ImPy 16213) 5'-WG C A A C TW-3' ImPy-(3-pypyHp-Y-pYI~Pv-ImPy 1622(3) 5'-WG C A A C AW-3' ImPy-~3-Pypypy-y-Hpl~p_~3_ImPy 1623(3) 5'-WG C A A C GW-3' ImPy-(3-PyPyIm-y-py=mt-tp_~3_ImPy 1624(3) 5'-WG C A A C CW-3' ImPy-~3-pypypy-y_ImImHp-~3-ImPy WO 98/37067 PCTIi1S98/01714 TABLE 161:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGCASNNW-3' -DNA aromatic amino acid sequence sequence 1625(3) 5' -WG C A G TT W-3' ImPy-(3-ImHpHp-y-PyPyPy-~3-ImPy 1626~i) ~ -WG C A G TA W-3' ImPy-[3-ImHpPy-y-HpPyPy-p-ImPy 5' 1627(3) 5' -WG C A G TG W-3' ImPy-(3-ImHpIm-y-PyPyPy-/3-ImPy 1628(3) 5' -WG C A G TC W-3' ImPy-(3-ImHpPy-y-ImPyPy-(3-ImPy 1629(3) 5' -WG C A G AT W-3' ImPy-p-ImPyHp-y-PyHpPy-~-ImPy 1630(3) 5' -WG C A G AA W-3' ImPy-(3-ImPyPy-y-HpHpPy-~i-ImPy 1631(3) 5' -WG C A G AG W-3' ImPy-~i-ImPyIm-y-PyHpPy-(i-ImPy 1632(3) 5' -WG C A G AC W-3' ImPy-[3-ImPyPy-y-ImHpPy-(3-ImPy 16333) 5' -WG C A G GT W-3' ImPy-(3-ImImHp-y-PyPyPy-(3-ImPy 16343) 5' -WG C A G GA W-3' ImPy-p-ImImPy-y-HpPyPy-(3-ImPy 1635(3) 5' -WG C A G CT W-3' ImPy-~3-ImPyHp-y-PyImPy-~3-ImPy 1636(3) 5' -WG C A G CA W-3' ImPy-(3-ImPyPy-y-HpImPy-(3-ImPy 1637) 5' -WG C A G GG W-3' ImPy-(3-ImImIm-y-PyPyPy-~i-ImPy 1638(3) 5' -WG C A G GC W-3' ImPy-~3-ImImPy-y-ImPyPy-~3-ImPy 1639(3) 5' -WG C A G CG W-3' ImPy-J3-ImPyIm-y-PyImPy-~i-ImPy 1640(3) 5' -WG C A G CC W-3' ImPy-~i-ImPyPy-y-ImImPy-(3-ImPy 1641(3) 5' -WG C A C TT W-3' ImPy-(3-PyHpHp-y-PyPyIm-[3-ImPy 1642(3) 5' -WG C A C TA W-3' ImPy-(3-PyHpPy-y-HpPyIm-~3-ImPy 16433) 5' -WG C A C TG W-3' ImPy-(3-PyHpIm-y-PyPyIm-(3-ImPy 1644(3) 5' -WG C A C TC W-3' ImPy-~3-PyHpPy-y-ImPyIm-(3-ImPy 1645(3) 5' -WG C A C AT W-3' ImPy-~-PyPyHp-y-PyHpIm-(3-ImPy 16463) 5' -WG C A C AA W-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-ImPy 1647(3) 5' -WG C A C AG W-3' ImPy-(3-PyPyIm-y-PyHpIm-(3-ImPy 1648(3) 5' -WG C A C AC W-3' ImPy-(3-PyPyPy-y-ImHpIm-(3-ImPy 1649(3) 5' -WG C A C GT W-3' ImPy-(3-PyImHp-y-PyPyIm-~3-ImPy 1650~i) 5' -WG C A C GA W-3' ImPy-(3-PyImPy-y-HpPyIm-(3-ImPy 1651~i) 5' -WG C A C CT W-3' ImPy-~3-PyPyHp-y-PyImIm-(3-ImPy 1652(3) 5' -WG C A C CA W-3' ImPy-(3-PyPyPy-y-HpImIm-(3-ImPy 1653(3) 5' -WG C A C GG W-3' ImPy-(3-PyImIm-y-PyPyIm-p-ImPy 1654(3) 5' -WG C A C GC W-3' ImPy-f3-PyImPy-y-ImPyIm-(3-ImPy 1655(3) 5' -WG C A C CG W-3' ImPy-(3-PyPyIm-y-PyImIm-(3-ImPy 1656~i) 5' -WG C A C CC W-3' ImPy-p-PyPyPy-y-ImImIm-(3-ImPy TABLE 162: 12-ring ~3-Hairpin Polyamides for recognition of 8-by S'-WGCCWNNW-3' -DI'TA sequence aromatic amino acid sequence ' 1657R) 5' -W G T T T W-3' ImPyPy-~-HpHp-y-pypy-(3-ImImPy C C
1658(3) 5' -W G T T A W-3' ImPyPy-(3-HpPy-y-HpPy-~3-ImImPy C C
16593) 5' -W G T T G W-3' ImPyPy-(3-HpIm-y-PyPy-(3-ImImPy C C
1660~i) 5' -W G T T C W-3' ImPyPy-/~-HpPy-y-ImPy-(3-ImImPy C C
1661(3) 5' -W G T A T W-3' C C ImPyPy-(3-PyHp-y-PyHp-(3-ImImPy 1662(3) 5'-WG C C T A A W-3' ImPyPy-~3-pypy-y-HpHp-(3-ImImPy IO 1663(3) 5'-WG C C T A G W-3' ImPyPy-(3-pylm-y-pyHp-(3-ImImPy 1664(3) 5'-WG C C T A C W-3' ImPyPy-~-pypy-y-I~p-~3-ImImPy 16653) 5'-WG C C T G T W-3' ImpyPy-~-ImHp-y-pypy_~3_ImImPy 16663) 5'-WG C C T G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImImPy 1667(3) 5'-WG C C T G G W-3' ImPyPy-(3-Imlm-y-pypy-~3-ImImPy 1668(3) 5'-WG C C T G C W-3' ImPyPy-J3-Impy-y-Impy-(3-Imlmpy 1669(3) 5'-WG C C T C T W-3' ImPyPy-(3-PyHp-y-pyIm-(3-ImImPy 1670(3) 5'-WG C C T C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy 1671(3) 5'-WG C C T C G W-3' ImPyPy-~3-pylm-y-PyIm-(3-ImImPy 1672(3) 5'-WG C C T C C W-3' ImPypy-~-PyPy-y-Imlm-(3-ImImpy 16733) 5'-WG C C A T T W-3' ImPyPy-~3-HpHp-y-pypy_~-ImImPy 1674(3) 5'-WG C C A T A W-3' ImPyPy-(3-HpPy-y-HpPy-(i-ImImPy 1675(3) 5'-WG C C A T G W-3' ImPyPy-p-HpIm-y-pypy-~-ImImPy 1676(3) 5'-WG C C A T C W-3' ImPyPy-(3-HpPy-y-ImPy-~3-ImImPy 1677(3) 5'-WG C C A A T W-3' ImPyPy-~3-PyHp-y-PyHp-(3-ImImPy 1678(3) 5'-WG C C A A A W-3' ImPyPy-R-Pypy-y-HpHp-(3-ImImPy 16793) 5'-WG C C A A G W-3' ImPyPy-~3-PyIm-y-pyHp-~i-ImImPy 1680(3) 5'-WG C C A A C W-3' ImPyPy-(3-pypy-y-I~p-a-ImImPy 1681(3) 5'-WG C C A G T W-3' ImPyPy-~i-ImHp-y-PyPy-p-ImImPy 1682(3) 5'-WG C C A G A W-3' ImPyPy-(3-ImPy-y-HpPy-~3-ImImPy 1683~i) 5'-WG C C A G G W-3' ImPyPy-~3-Imim-y-Pypy-(3-ImImPy 1684(3) 5'-WG C C A G C W-3' ImPyPy-j3-ImPy-y-ImPy-~3-ImImPy 16853) 5'-WG C C A C T W-3' ImPyPy-(3-PyHp-y-Pylm-(3-ImImPy 1686(3) 5'-WG C C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-~3-ImImPy 1687(3) 5'-WG C C A C G W-3' ImPyPy-(3-Pylm-y-PyIm-~3-ImImPy 1688~i) 5'-WG C C A C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImImPy TABLE 163:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGCCSNNW-3' DNA aromatic amino acid sequence sequence 1689(3) 5'-WG C C G T TW-3' ImPy-(3-ImHpHp-y-PyPy-~3-ImImPy 16903) ~5'-WG C C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImImPy 1691(3) 5'-WG C C G T GW-3' ImPy-(3-ImHpim-y-PyPy-(3-ImImPy 1692(3) 5'-WG C C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImImPy 1693(3) 5'-WG C C G A TW-3' ImPy-~3-ImPyHp-y-PyHp-(3-ImImPy 1694(3) 5'-WG C C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-(3-ImImPy 16953) 5'-WG C C G A GW-3' ImPy-(3-ImPyIm-y-PyHp-~3-ImImPy 16963) 5'-WG C C G A CW-3' ImPy-~-ImPyPy-y-ImHp-(3-ImImPy 16973) 5'-WG C C G G TW-3' ImPy-(3-ImImHp-y-PyPy-(3-ImImPy 16983) 5'-WG C C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImImPy 1699(3) 5'-WG C C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-~3-ImImPy 17003) 5'-WG C C G C AW-3' ImPy-~i-ImPyPy-y-Hplm-~3-ImImPy 170/(3) 5'-WG C C C T TW-3' ImPy-~3-PyHpHp-y-Py-/3-ImImImPy 1702(3) 5'-WG C C C T AW-3' ImPy-p-PyHpPy-y-Hp-J3-ImImImPy 1703(3) 5'-WG C C C T GW-3' ImPy-(~-PyHpIm-y-Py-(3-ImImImPy 1704(3) 5'-WG C C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImImPy 1705(3) 5'-WG C C C A TW-3' ImPy-(3-PyPyAp-y-Py-(3-ImImImPy 1706(3) 5'-WG C C C A AW-3' ImPy-(3-PyPyPy-y-Hp-(3-ImImImPy 1707(3) 5'-WG C C C A GW-3' ImPy-(3-PyPyIm-y-Py-~3-ImImImPy 1708(3) 5'-WG C C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImImPy 1709(3) 5'-WG C C C G TW-3' ImPy-(3-PyImHp-y-Py-(3-ImImImPy 17100 5'-WG C C C G AW-3' ImPy-(3-PyImPy-y-Hp-(3-ImImImPy G73~3) 5'-WG C C G G GW-3' 'ImPy-p-ImImIm-y-PyPy-~i-ImImPy G74(3) 5'-WG C C G G CW-3' ImPy-~3-ImImPy-y-ImPy-~i-ImImPy G75(3) 5'-WG C C G C GW-3' ImPy-(3-ImPyIm-y-PyIm-p-ImImPy G76(3) 5'-WG C C G C CW-3' ImPy-(3-ImPyPy-y-Imlm-~i-ImImPy G77~3) 5'-WG C C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImImPy G78(3) 5'-WG C C C G CW-3' ImPy-(3-PyImPy-y-Im-~3-ImImImPy ...~. , . , TABLE 164: 12-ring Hairpin (3- Polyamides for recognition of 8-by 5'-WGAGWNNW-3' .
DNA aromatic amino acid sequence sequence 1713(3) 5' G AG T T T W-3' Im-(3-ImHpHpHp-y-pypypypY-(3-PY
-W
1714(3) 5' G AG T T A W-3' Im-(3-ImHpHppy-y-HppypypY_~_pY
-W
1715(3) .5' G AG T T G W-3' Im-(3-ImHpHpIm-y-pypypypy_~_py -W
1716(3) 5'-W G AG T T C W-3' Im-(3-ImHpIipPy-y-ImPYPYPy-~-py 1717(3) 5' G AG T A T W-3' Im-(3-ImHpPyHp-y-PYHpPYPy-(3-pY
-W
1718(3) 5' G AG T A A W-3' Im-~3-ImHpPyPY-y-HpHpPyPy-(3-Py -W
1719(3) 5' G AG T A G W-3' Im-(3-ImHpPyIm-y-PyHpPyPy-(3-Py -W
1720(3) 5' G AG T A C W-3' Im-~3-ImHppypY_y_Iml.lppypY-(3-pY
-W
1721(3) 5' G AG T G T W-3' Im-~3-ImHpImHp-y-pypypypY-p-pY
-W
1722(3) 5' G AG T G A W-3' Im-(3-ImHpImPY-y-HpPypyPY-(3-py -W
1723(3) 5' G AG T G G W-3' Im-p-ImHpImIm-y-Pypypypy-~3-pY
-W
1724(3) 5' G AG T G C W-3' Im-~3-ImHpImPy-y-ImPyPYPy-(3-Py -W
1725~i) 5' G AG T C T W-3' Im-/3-ImHpPyHp-y-PyImPYPy-~3-Py -W
17263) 5' G AG T C A W-3' Im-~3-ImHpPyPy-y-HpImPYPy-(3-Py -W
1727(3) 5' G AG T C G W-3' Im-(3-ImHpPyIm-y-PYImPYPy-(3-Py -W
1728(3) 5' G AG T C C W-3' Im-(3-ImHpPypY-y-ImImPyPy-J3-py -W
1729) 5' G AG A T T W-3' Im-/3-ImPyHpHp-y-pypYHppy-(3-pY
-W
17300 5' G AG A T A W-3' Im-p-ImPyHpPy-y-HpPyHpPy-(3-py -W
1731(3) 5' G AG A T G W-3' Im-(3-ImPYHpIm-y-pypygppy-(3-Py -W
1732~i) 5' G AG A T C W-3' Im-(3-ImpyHppy-y-ImpyHpPy-(3-Py -W
1733(3) 5' G AG A A T W-3' Im-p-ImPyPyHp-y-PyHpHpPy-(3-Py -W
1734(3) 5' G AG A A A W-3' Im-~-ImPyPYPy-y-HpHpHpPy-(3-Py -W
1735~i) 5' G AG A A G W-3' Im-~i-ImPyPYIm-y-pyHpHpPy-~3-Py -W
1736(3) 5' G AG A A C W-3' 'Im-~3-ImPyPyPy-y-ImHpHpPy-~3-Py -W
1737(3) 5' G AG A G T W-3' Im-(3-ImPYImHp-y-pypygpPy-(3-Py -W
1738(3) 5' G AG A G A W-3' Im-~i-ImPYImPy-y-HpPyHpPy-(3-Py -W
17393) 5' G AG A G G W-3' Im-(3-ImPYImIm-y-PYPyHpPy-(3-py -W
17403) 5' G AG A G C W-3' Im-(3-ImPyImPy-y-ImPyHpPy-(3-Py -W
1741~i) 5' G AG A C T W-3' Im-~3-ImPyPyHp-y-PyImHpPy-(3-Py -W
1742(3) 5' G AG A C A W-3' Im-(3-ImPyPyPy-y-HpImHpPy-(3_pY
-W
1743(3) 5' G AG A C G W-3' Im-(3-ImPyPyIm-y-PyImHpPy-(3-Py -W
1744(3) 5' G AG A C C W-3' Im-(3-ImPyPyPy-y-ImImHpPy-(3-Py -W
TABLE 165: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGAGSNNW-3' DNA sequence aromatic amino acid sequence 1745(3) 5' -W G A G G T T W-3' Im-(3-ImImHpHp-y-PyPyPyPy-~3-Py 1746(3) 5' -W G A G G T A W-3' Im-(3-ImImHpPy-y-HpPyPyPy-(3-Py 1747(3) 5' -W G A G G T G W-3' Im-(3-ImImHpIm-y-PyPyPyPy-(3-Py 1748(3) 5' -W G A G G T C W-3' Im-(3-ImImHpPy-y-ImPyPyPy-(3-Py 1749(3) 5' -W G A G G A T W-3' Im-(3-ImImPyHp-y-PyHpPyPy-~3-Py 17503) 5' -W G A G G A A W-3' Im-(3-ImImPyPy-y-HpHpPyPy-/3-Py 17513) 5' -W G A G G A G W-3' Im-~3-ImImPyIm-y-PyHpPyPy-(3-Py 1752(3) 5' -W G A G G A C W-3' Im-(3-ImImPyPy-y-ImHpPyPy-~3-Py 1753(3) 5' -W G A G G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-(3-Py 1754(3) 5' -W G A G G G A W-3' Im-(3-ImImImPy-y-HpPyPyPy-~3-Py 1755(3) 5'-W G A G G C T W-3' Im-(3-ImImPyHp-y-PyImPyPy-(3-Py 1756(3) 5' -W G A G G C A W-3' Im-(3-ImImPyPy-y-HpImPyPy-~3-Py 17573) 5' -W G A G C T T W-3' Im-(3-ImPyHpHp-y-PyPyImPy-(3-Py 1758j3) 5' -W G A G C T A W-3' Im-~3-ImPyHpPy-y-HpPyImPy-~3-Py 1759(3) 5' -W G A G C T G W-3' Im-~-ImPyHpIm-y-PyPyImPy-J3-Py 17603) 5' -W G A G C T C W-3' Im-~3-ImPyHpPy-y-ImPyImPy-(3-Py 1761~i) 5' -W G A G C A T W-3' Im-/3-ImPyPyHp-y-PyHpImPy-(3-Py 1762(3) 5' -W G A G C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~3-Py 1763(3) 5' -W G A G C A G W-3' Im-(3-ImPyPyIm-y-PyHpImPy-(3-Py 1764(3) 5' -W G A G C A C W-3' Im-(3-ImPyPyPy-y-ImHpImPy-(3-Py 17653) 5' -W G A G C G T W-3' Im-~3-ImPyImHp-y-PyPyImPy-~3-Py 1766~i) 5'-WG A G C GA W-3' Im-(3-IrnPyImPy-y-HpPyImPy-(3-Py 1767(3) 5'-WG A G C CT W-3' 'Im-~3-ImPyPyHp-y-PyImImPy-/3-Py 1768(3) 5'-WG A G C CA W-3' Im-j3-ImPyPyPy-y-HpImImPy-(3-Py 1769(3) 5'-WG A G G GG W-3' Im-(3-ImImImIm-y-PyPyPyPy-[3-Py 1770(3) 5'-WG A G G GC W-3' Im-(3-ImImImPy-y-ImPyPyPy-~-Py 1771(3) 5'-WG A G G CG W-3' Im-(3-ImImPyIm-y-PyImPyPy-(3-Py 1772(3) 5'-WG A G G CC W-3' Im-p-ImImPyPy-y-ImImPyPy-~3-Py 17733) 5'-WG A G C GG W-3' Im-~i-ImPyImIm-y-PyPyImPy-(3-Py 1774(3) 5'-WG A G C GC W-3' Im-(3-ImPyImPy-y-ImPyImPy-~i-Py 1775(3) 5'-WG A G C CG W-3' Im-(3-ImPyPyIm-y-PyImimPy-p-Py 1776(3) 5'-WG A G C CC W-3' Im-~i-ImPyPyPy-y-ImImImPy-(i-Py W.. . ~.. , 166: 12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGATWNNW-3' DNA aromatic amino acid sequence sequence 1777(3) 5' GA T T T T W-3' ImPy-(3-HpHpHp-y-PYPyPy-(3-HpPy -W
1778(3) 5' GA T T T A W-3' ImPy-~3-HpHpPy-y-HpPYPy-~3-HpPy . -W
17793) 5' GA T T T G W-3' ImPy-(3-HpHpIm-y-PyPyPy-(3-HpPy -W
1780(3) 5' GA T T T C W-3' ImPy-(3-HpHpPy-y-ImPYPy-~3-HpPy -W
17810 5' GA T T A T W-3' ImPy-(3-HppyHp-y-PYHpPy-(3-HpPy -W
17823) 5' GA T T A A W-3' ImPy-/3-HpPyPy-y-HpHpPy-(3-HpPy -W
1783(3) 5' GA T T A G W-3' ImPy-(3-HpPYIm-y-PyHpPy-~3-HpPy -W
1784(3) 5' GA T T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-~-HpPy -W
17853) 5' GA T T G T W-3' -W ImPy-/3-HpImHp-y-PyPypY-(3 _HppY
1786(3) 5' GA T T G A W-3' -W ImPy-~3-HpImPy-y-HpPYpy-~3-Hppy 1787~i) 5' GA T T G G W-3' ImPy-(3-HpImIm-y-Pypypy-(3-Hppy -W
1788(3) 5' GA T T G C W-3' ImPy-(3-HpImPy-y-ImPyPy-(3-Hppy -W
17893) 5' GA T T C T W-3' ImPy-(3-HpPyHp-y-PyImPy-(3-HpPy -W
17903) 5' GA T T C A W-3' ImPy-~3-HppyPy-y-HpImPy-~i-HpPy -W
1791(3) 5' GA T T C G W-3' ImPy-(3-HpPyIm-y-pylmPy-~i-HpPy -W
17923) 5' GA T T C C W-3' ImPy-(3-HpPYPy-y-ImImPy-R-HpPy -W
17933) 5' GA T A T T W-3' ImPy-~-PyHpHp-y-PYPyHp-(3-HpPy -W
1794(3) 5' GA T A T A W-3' ImPy-(3-PyHpPy-y-HpPyHp-(3-HpPy -W
17953) 5' GA T A T G W-3' ImPy-(3-PYHpIm-y-pypyHp-(3-HpPy -W
1796~i) 5' GA T A T C W-3' ImPy-(3-PYHpPy-y-ImPYHp-~3-HpPy -W
1797(3) 5' GA T A A T W-3' ImPy-(3-PyPyHp-y-pyHpHp-(3-HpPy -W
1798(3) 5' GA T A A A W-3' Impy-(3-PyPyPY-y-HpHpHp-(3-HpPy -W
1799(3) 5' GA T A A G W-3' ImPy-(3-PyPyIm-y-pyHpHp-/3-HpPy -W
1800(3) 5' GA T A A C W-3' ImPy-~3-PyPyPy-y-ImHpHp-(3-HpPy -W
1801(3) 5' GA T A G T W-3' -W ImPy-(3-PyImHp-y-pypyHp-p-Hppy 18023) 5' GA T A G A W-3' ImPy-~i-pyImPy-y-HpPYHp-(3-HpPy -W
18033) 5' GA T A G G W-3' Impy-~3-pylmIm-y-pypygp-~3-HppY
-W
1804(3) 5' GA T A G C W-3' ImPy-(3-PyImPy-y-ImPyHp-(3-HpPy -W
1805(3) 5' GA T A C T W-3' ImPy-(3-pypyHp-y-PyImHp-~i-Hppy -W
1806(3) 5' GA T A C A W-3' ImPy-(3-PYPyPy-y-HpImHp-~3-HpPy -W
1807(3) 5' GA T A C G W-3' ImPy-~i-PyPyIm-y-PyImHp-(3-HpPy -W
1808(3) 5' GA T A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPY
-W
TABLE 167: 12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGATSNNW-3' -DNA sequence aromatic amino acid sequence 1809(3) 5' -W G A T G T T W-3' ImPy-~-ImHpHp-y-PyPyPy-p-HpPy 1810(3) 5' -W G A T G T A W-3' ImPy-(3-ImHpPy-y-HpPyPy-~3-HpPy 1811(3) 5' -W G A T G T G W-3' ImPy-~i-ImHpIm-y-PyPyPy-~3-HpPy 1812(3) 5' -W G A T G T C W-3' ImPy-(3-ImHpPy-y-ImPyPy-J3-HpPy 1813(3) 5' -W G A T G A T W-3' ImPy-~3-ImPyHp-y-PyHpPy-(3-HpPy 1814(3) 5' -W G A T G A A W-3' ImPy-(3-ImPyPy-y-HpHpPy-(3-HpPy 1815(3) 5' -W G A T G A G W-3' ImPy-~-ImPyIm-y-PyHpPy-(3-HpPy 1816(3) 5' -W G A T G A C W-3' ImPy-(3-ImPyPy-y-ImHpPy-~i-HpPy 18173) 5' -W G A T G G T W-3' ImPy-p-ImImHp-y-PyPyPy-(3-HpPy 1818(3) 5' -W G A T G G A W-3' ImPy-~3-ImImPy-y-HpPyPy-p-HpPy 1819(3) 5' -W G A T G C T W-3' ImPy-~i-ImPyHp-y-PyImPy-(3-HpPy 1820(3) 5' -W G A T G C A W-3' ImPy-(3-ImPyPy-y-HpImPy-~3-HpPy 1821(3) 5' -W G A T G G G W-3' ImPy-~3-ImImIm-y-PyPyPy-(3-HpPy 1822(3) 5' -W G A T G G C W-3' ImPy-(3-ImImPy-y-ImPyPy-(3-HpPy 1823~i) 5' -W G A T G C G W-3' ImPy-(3-ImPyIm-y-PyImPy-p-HpPy 18243) 5' -W G A T G C C W-3' ImPy-[3-ImPyPy-y-ImImPy-(3-HpPy 1825(3) 5' -W G A T C T T W-3' ImPy-(3-PyHpHp-y-PyPyIm-(3-HpPy 1826(3) 5' -W G A T C T A W-3' ImPy-~3-PyHpPy-y-HpPyIm-(3-HpPy 1827) 5' -W G A T C T G W-3' ImPy-(3-PyHpIm-y-PyPyIm-~-HpPy 1828(3) 5'-WG A T C T CW-3' ImPy-(3-PyHpPy-y-ImPyIm-/3-HpPy 1829(3) 5'-WG A T C A TW-3' ImPy-~3-PyPyHp-y-PyHpIm-p-HpPy 18303) 5'-WG A T C A AW-3' ImPy-(3-PyPyPy-y-HpHpIm-(3-HpPy 18313) 5'-WG A T C A GW-3' 'ImPy-(3-PyPyIm-y-PyHpIm-~i-HpPy 1832(3) 5'-WG A T C A CW-3' ImPy-(3-PyPyPy-y-ImHpIm-~3-HpPy 1833(3) 5'-WG A T C G TW-3' ImPy-(3-PyImHp-y-PyPyIm-(3-HpPy 18343) 5'-WG A T C G AW-3' ImPy-(3-PyImPy-y-HpPyIm-(3-HpPy 18353) 5'-WG A T C C TW-3' ImPy-p-PyPyHp-y-PyImIm-(3-HpPy 1836~i) 5'-WG A T C C AW-3' ImPy-(3-PyPyPy-y-HpImIm-~-HpPy 1837(3) 5'-WG A T C G GW-3' ImPy-~3-PyImIm-y-PyPyIm-~3-HpPy 1838(3) 5'-WG A T C G CW-3' ImPy-~3-PyImPy-y-ImPyIm-(3-HpPy 18393) 5'-WG A T C C GW-3' ImPy-(3-PyPyIm-y-PyImIm-(3-HpPy 18403) 5'-WG A T C C CW-3' ImPy-(3-PyPyPy-y-ImImIm-(3-HpPy f , , WO 98'37067 PCT/US98/01714 ~1'ABLE 168;
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGAAWNNW-3' -DNA aromatic amino acid sequence sequence 1841(3) 5' G A A TT T W-3' ImPy-(3-HpHpHp-y-pyPypy-(3-HpPy -W
1842(3) 5' G A A TT A W-3' ImPy-[3-HpHpPy-y-HpPyPy-~3-HpPy -W
18433) 5' G A A TT G W-3' ImPy-(3-HpHpIm-y-Pypypy-~3-HppY
-W
1844(3) 5' G A A TT C W-3' ImPy-~i-HpHpPy-y-ImPYPy-~3-HpPy -W
1845(3) 5' G A A TA T W-3' ImPy-(3-HpPyHp-y-PyHpPy-(3-HpPy -W
18463) 5' G A A TA A W-3' ImPy-(3-HppyPy-y-HpHppy-[3-HpPy -W
1847(3) 5' G A A TA G W-3' ImPy-~3-HpPYIm-y-PYHpPy-(3-HpPy -W
1848(3) 5' -W G A A T A C W-3' ImPy-(3-HpPYPy-y-ImHpPy-(3-HpPy 1849(3) 5' -W G A A T G T W-3' ImPy-~3-HpImHp-y-Pypypy-(3-HpPy 1850(3) 5' -W G A A T G A W-3' ImPy-~-HpImPy-y-HpPyPy-(3-HpPy 1851(3) 5' -W G A A T G G W-3' ImPy-(3-HpImIm-y-PyPyPy-(3-HpPy 1852(3) 5' -WG A A TG C W-3' ImPy-~3-HpImPy-y-ImPyPy-(3-HpPy 1853(3) 5' -WG A A TC T W-3' ImPy-(3-HpPyHp-y-PYImPy-(3-HpPy 1854(3) 5' -WG A A TC A W-3' ImPy-(3-HpPyPy-y-HpImPy-(3-HpPy 1855(3) 5' -WG A A TC G W-3' ImPy-(3-HpPyim-y-PyImPy-~-HpPy 1856(3) 5' -WG A A TC C W-3' ImPy-(3-HpPyPy-y-ImImPy-(3-HpPy 18573) 5' -WG A A AT T W-3' ImPy-~3-PyHpHp-y-PyPyHp-~3-HpPy 18583) 5' -WG A A AT A W-3' ImPy-~3-PYHpPy-y-HpPyHp-~3-HpPy 1869(3) 5' -W G A A A T G W-3' ImPy-(3-PyHpIm-y-PypyHp-~3-HpPy 1860(3) 5' -W G A A A T C W-3' ImPy-(3-PYHpPy-y-ImPyHp-(3-HpPy 18613) 5' -W G A A A A T W-3' ImPy-~-PYPyHp-y-PyHpHp-(3-HpPy 1862(3) 5'-WG A A A A A W-3' ImPy-(3-Pypypy-y-HpHpHp-(3-HpPy 1863(3) 5'-WG A A A A G W-3' ImPy-~i-PyPYIm-y-PyHpHp-(3-HpPy 1864~i} 5'-WG A A A A C W-3' ImPy-(3-PYPyPy-y-ImHpHp-~3-HpPy 1865(3) 5'-WG A A A G T W-3' ImPy-(3-PyImHp-y-PYPYHp-~3-HpPy 1866(3) 5'-WG A A A G A W-3' ImPy-(3-PyImPy-y-HppyHp-p-HpPy 1867(3) 5'-WG A A A G G W-3' ImPy-~3-PyImIm-y-PYPyHp-p-HpPy 1868(3) 5'-WG A A A G C W-3' ImPy-J3-PyImPy-y-ImPyHp-(3-Hppy 1869(3) 5'-WG A A A C T W-3' ImPy-/3-PyPyHp-y-PYImHp-~3-HpPy 1870(3) 5'-WG A A A C A W-3' ImPy-(3-PyPyPy-y-HpImHp-(3-HpPy 1871(3) 5'-WG A A A C G W-3' ImPy-~3-PyPYIm-y-PyImHp-p-HpPy 1872(3) 5'-WG A A A C C W-3' ImPy-(3-PyPyPy-y-ImImHp-(3-HpPy TABLE 169:
12-ring -Hairpin Polyamides for recognition of 8-by 5'-WGAASN1VW-3' DNA aromatic amino acid sequence sequence 1873(3) 5' -WG A A G TT W-3' ImPy--ImHpHp-y-PyPyPy--HpPy 1874(3) . -WG A A G TA W-3' ImPy--ImHpPy-y-HpPyPy--HpPy 5' 1875(3) 5' -WG A A G TG W-3' ImPy--ImHpIm-y-PyPyPy--HpPy 1876(3) 5' -WG A A G TC W-3' ImPy--ImHpPy-y-ImPyPy--HpPy 1877 ) 5' -WG A A G AT W-3' ImPy--ImPyHp-y-PyHpPy--HpPy 18783) 5' -WG A A G AA W-3' ImPy--ImPyPy-y-HpHpPy--HpPy 1879) 5' -WG A A G AG W-3' ImPy--ImPyIm-y-PyHpPy--HpPy 1880) 5' -WG A A G AC W-3' ImPy--ImPyPy-y-ImHpPy--HpPy 18813) 5' -WG A A G GT W-3' ImPy--ImImHp-y-PyPyPy--HpPy 18823) 5' -WG A A G GA W-3' ImPy--ImImPy-y-HpPyPy--HpPy 1883(3) 5' -WG A A G CT W-3' ImPy--ImPyHp-y-PyImPy--HpPy 1884(3) 5' -WG A A G CA W-3' ImPy--ImPyPy-y-HpImPy--HpPy 1885) 5' -WG A A G GG W-3' ImPy--ImImIm-y-PyPyPy--HpPy 1886) 5' -WG A A G GC W-3' ImPy--ImImPy-y-ImPyPy--HpPy 1887) 5' -WG A A G CG W-3' ImPy--ImPyIm-y-PyImPy--HpPy 1888) 5' -WG A A G CC W-3' ImPy--ImPyPy-y-ImImPy--HpPy 1889~i) 5' -WG A A C TT W-3' ImPy--PyHpHp-y-PyPyIm-(3-HpPy 18903) 5' -WG A A C TA W-3' ImPy--PyHpPy-y-HpPyIm--HpPy 1891(3) 5' -WG A A C TG W-3' ImPy--PyHpIm-y-PyPyIm--HpPy 1892) 5' -WG A A C TC W-3' ImPy--PyHpPy-'y-ImPyIm--HpPy 1893(3) 5' -WG A A C AT W-3' ImPy--PyPyHp-y-PyHpIm--HpPy 1894(3) 5' -WG A A C AA W-3' ImPy--PyPyPy-y-HpHpIm--HpPy 18953) 5' -WG A A C AG W-3' ImPy--PyPyIm-y-PyHpIm--HpPy 1896(3) 5' -WG A A C AC W-3' ImPy--PyPyPy-y-ImHpIm--HpPy 1897p) 5' -WG A A C GT W-3' ImPy--PyImHp-y-PyPyIm--HpPy 1898(3) 5' -WG A A C GA W-3' ImPy--PyImPy-y-HpPyIm--HpPy 1899(3) 5' -WG A A C CT W-3' ImPy--PyPyHp-y-PyImIm--HpPy 1900) 5' -WG A A C CA W-3' ImPy--PyPyPy-y-HpImIm--HpPy 1901(3) 5' -WG A A C GG W-3' ImPy--PyImIm-y-PyPyIm--HpPy 1902) 5' -WG A A C GC W-3' ImPy--PyImPy-y-ImPyIm--HpPy 1903) 5' -WG A A C CG W-3' ImPy--PyPyIm-y-PyImIm--HpPy 1904~i) 5' -WG A A C CC W-3' ImPy--PyPyPy-y-ImImIm--HpPy r , , WO 9t1~370b7 PCT/US98/01714 'TABLE 170: 12-ring (3-Hairpin Polyamides for recognition of 8-by S'-WGACWNNW-3' -DNA sequence aromatic amino acid sequence - 1905~i) 5' -W G A C T T T W-3' ImPyPy-~3-HpHp-y-PyPy-(3-ImHpPy _ 1906(3) ~5' -W G A C T T A W-3' ImPyPy-(3-Hppy-y-Hppy_R-ImHpPy 1907~i) 5' -W G A C T T G W-3' ImPyPy-(3-Hplm-y-PyPy-(3-ImHpPy 1908(3) 5'-W G A CT T C W-3' ImPyPy-~-HpPy-y-ImPy-(3-ImHpPy 1909(3) 5'-W G A CT A T W-3' ImPyPy-~3-pyHp-y-PyHp-(3-ImHpPy 19103) 5'-W G A CT A A W-3' ImPyPy-~3-Pypy-y-HpFip-(3-ImHpPy 1911(3) 5'-W G A CT A G W-3' ImPyPy-(3-Pylm-y-PyHp-~i-ImHpPy 1912 5'-W G A CT A C W-3' ) ImPyPy-~i-PyPy-y-ImHp-p-ImHpPy 19133) 5'-W G A CT G T W-3' ImPyPy-p-ImHp-y-pypy-(3-I~ppy 19143) 5'-W G A CT G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy 1915(3) 5'-W G A CT G G W-3' ImPyPy-j3-ImIm-y-Pypy-p-ImHpPy 1916(3) 5'-W G A CT G C W-3' ImPyPy-(3-ImPy-y-ImPy-(3-ImHpPy 19173) 5'-W G A CT C T W-3' ImPyPy-(3-pygp-y-pyIm-~i-ImHpPy 19183) 5'-W G A CT C A W-3' ImPyPy-~-PyPy-y-HpIm-p-ImHpPy 1919(3) 5'-W G A CT C G W-3' ImPyPy-~3-PyIm-y-PyIm-(3-ImHpPy 1920~i) 5'-W G A CT C C W-3' ImPyPy-(3-PyPy-y-ImIm-(3-ImHpPy 1921(3) 5'-W G A CA T T W-3' ImPyPy-~i-HpHp-y-Pypy-(3-ImHpPy 1922(3) 5'-W G A CA T A W-3' ImPyPy-(3-HpPy-y-HpPy-(3-ImHpPy 1923(3) 5'-W G A CA T G W-3' ImPyPy-(3-HpIm-y-PyPy-p-ImHpPy 19243) 5'-W G A CA T C W-3' ImPyPy-(3-HpPy-y-ImPy-~-ImHpPy 1925(3) 5'-W G A CA A T W-3' ImPyPy-(3-PyHp-y-PyHp-(3-ImHpPy 1926(3) 5'-W G A CA A A W-3' ImPyPy-(3-pypy-y-HpHp-(3-ImHpPy 1927(3) 5'-W G A CA A G W-3' ImPypy-(3-pylm-y-pyHp-~i-ImHpPy 1928) 5'-W G A CA A C W-3' ImPyPy-p-PyPy-y-ImHp-p-ImHpPy 1929(3) 5'-W G A CA G T W-3' ImPyPy-(3-ImHp-y-PyPy-~3-ImHpPy 19303) 5'-W G A CA G A W-3' ImPyPy-(3-ImPy-y-HpPy-(3-ImHpPy 1931(3) 5'-W G A CA G G W-3' ImPyPy-(3-Imlm-y-PyPy-(3-ImHpPy 19323) 5' -W G A C A G C W-3' ImPyPy-(3-Impy-y-ImPy-(3-ImHpPy 19333) 5' -W G A C A C T W-3' ImPyPy-~3-PyHp-y-PyIm-(3-ImHpPy 19343) 5' -W G A C A C A W-3' ImPyPy-(3-PyPy-y-Hplm-(3-ImHpPy 19350 5' -W G A C A C G W-3' ImPyPy-R-pylm-y_pylm_(3-ImHpPy 1936(3) 5' -W G A C A C C W-3' ImPyPy-p-Pypy-y-ImIm-(3-ImHpPy TABLE
171:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGACSNNW-3' -DNA aromatic amino acid sequence sequence 1937(3) 5'-W GA C G T TW-3 T ImPy-(3-ImHpHp-y-PyPy-(3-ImHpPy 1938(3) 5'-W GA C G T AW-3' ImPy-(3-ImHpPy-y-HpPy-(3-ImHpPy 1939(3) 5'-W GA C G T GW-3' ImPy-[3-ImHpIm-y-PyPy-(3-ImHpPy 1940(3) 5'-W GA C G T CW-3' ImPy-(3-ImHpPy-y-ImPy-(3-ImHpPy 1941(3) 5'-W GA C G A TW-3' ImPy-(3-ImPyHp-y-PyHp-(3-ImHpPy 1942~i) 5'-W GA C G A AW-3' ImPy-(3-ImPyPy-y-HpHp-~3-ImHpPy 1943(3) 5'-W GA C G A GW-3' ImPy-~3-ImPyIm-y-PyHp-(3-ImHpPy 19443) 5'-W GA C G A CW-3' ImPy-(3-ImPyPy-y-ImHp-(3-ImHpPy 19453) 5'-W GA C G G TW-3' ImPy-(3-ImImHp-y-PyPy-p-ImHpPy 19463) 5'-W GA C G G AW-3' ImPy-(3-ImImPy-y-HpPy-(3-ImHpPy 1947(3) 5'-W GA C G C TW-3' ImPy-(3-ImPyHp-y-PyIm-(3-ImHpPy 1948(3) 5'-W GA C G C AW-3' ImPy-(3-ImPyPy-y-HpIm-J3-ImHpPy 19493) 5'-W GA C C T TW-3' ImPy-~3-PyHpHp-y-Py-~3-ImImHpPy 1950(3) 5'-W GA C C T AW-3' ImPy-(3-PyHpPy-y-Hp-(3-ImImHpPy 1951(3) 5'-W GA C C T GW-3' ImPy-(3-PyHpim-y-Py-(3-ImImHpPy 19523) 5'-W GA C C T CW-3' ImPy-(3-PyHpPy-y-Im-(3-ImImHpPy 1953(3) 5'-W GA C C A TW-3' ImPy-(3-PyPyHp-y-Py-p-ImImHpPy 1954(3) 5'-W GA C C A AW-3' ImPy-(3-PyPyPy-y-Hp-p-ImImHpPy 1955(3) 5'-W GA C C A GW-3' ImPy-(3-PyPyIm-y-Py-(3-ImImHpPy 1956(3) 5'-W GA C C A CW-3' ImPy-(3-PyPyPy-y-Im-(3-ImImHpPy 1957(3) 5'-W GA C C G TW-3' ImPy-/3-PyImHp-y-Py-p-ImImHpPy 1958(3) 5'-W GA C C G AW-3' ImPy-(3-PyImPy-y-Hp-~3-ImImHpPy 1959(3) 5'-W GA C C C TW-3' ImPy-p-PyPyHp-y-PyImImIm-(3-Py 1960(3) 5'-W GA C C C AW-3 T ImPy-(3-PyPyPy-y-HpImImIm-(3-Py 1961(3) 5'-W GA C G G GW-3' ImPy-(3-ImImIm-y-PyPy-~-ImHpPy 19623) 5'-W GA C G G CW-3' ImPy-(3-ImImPy-y-ImPy-p-ImHpPy 1963(3) 5'-W GA C G C GW-3' ImPy-~i-ImPyIm-y-Pylm-(3-ImHpPy 1964(3) 5'-W GA C G C CW-3' ImPy-(3-ImPyPy-y-ImIm-(3-ImHpPy 1965~i) 5'-W GA C C G GW-3' ImPy-(3-PyImIm-y-Py-(3-ImImHpPy 1966~i) 5'-W GA C C G CW-3' ImPy-~3-PyImPy-y-Im-~3-ImImHpPy 1967(3) 5'-W GA C C C GW-3' ImPy-(3-PyPyIm-y-PyImImIm-(3-Py 1968(3) 5'-W GA C C C CW-3' ImPy-(3-PyPyPy-y-ImImImIm--Py .~. , , , WO 98/?7067 PCT/US98101714 ~hABLE 2:
17 12-ring [3-Hairpin Polyamides for recognition of 8-by 5'-WGTGVVNIVW-3' -DNA aromatic amino acid sequence sequence 1969(3) 5' G TG T T T W-3' Im-(3-ImHpHpHp-y-pypypypy-(3-py -W
1970(3) 5' G TG T T A W-3' Im-(3-ImHpHpPy-y-HpPyPYPy-(3-py -W
19713) 5' G TG T T G W-3' Im-(3-ImHpHpIm-y-PypypypY-~j-py -W
1972(3) 5' G TG T T C W-3' Im-~3-ImHpHpPy-y-ImPyPYPy-(3-Py -W
19733) 5' G TG T A T W-3' Im-(3-ImHpPYHp-y-PYHpPyPy-(3-Py -W
1974(3) 5' G TG T A A W-3' Im-~-ImHpPyPy-y-HpHpPyPy-(3-Py -W
1975(3) 5' G TG T A G W-3' Im-(3-ImHpPyIm-y-pYHpPYPy-p-py -W
1976(3) 5' G TG T A C W-3' Im-(3-ImHpPyPy-y-ImHpPyPy-(3-Py -W
19773) 5' G TG T G T W-3' Im-p-ImHpImHp-y-PypypypY-~-py -W
1978(3) 5' G TG T G A W-3' Im-(3-ImHpImPy-y-HpPyPyPy-~3-Py -W
1979(3) 5' G TG T G G W-3' Im-~-ImHpImIm-y-PYPyPyPy-(3-Py -W
19803) 5' G TG T G C W-3' Im-(3-ImHpImPy-y-ImPyPYPy-~3-py -W
1981(3) 5' G TG T C T W-3' Im-(3-ImHppyHp-y-pyImPyPy-(3-Py -W
1982(3) 5' G TG T C A W-3' Im-~i-ImHpPYPy-y-HpImPyPy-(3-Py -W
19833) 5' G TG T C G W-3' Im-(3-ImHpPyIm-y-PyImPyPy-(3-Py -W
1984(3) 5' G TG T C C W-3' Im-p-ImHpPYPy-y-ImImPyPy-~3-Py -W
19853) 5' G TG A T T W-3' Im-(3-ImPyHpHp-y-PypyHpPy-(3-Py -W
1986(3) 5' G TG A T A W-3' Im-~3-ImPYHpPy-y-HpPYHpPy-~i-py -W
1987(3) 5' G TG A T G W-3' Im-(3-ImPYHpIm-y-PYPYHpPy-(3-Py -W
1988(3) 5' G TG A T C W-3' Im-p-ImPyHpPy-y-ImPYHpPy-p-Py -W
1989(3) 5' G TG A A T W-3' Im-~-ImPYPYHp-y-pyI-IpHppy-~i-py -W
1990(3) 5' G TG A A A W-3' Im-(3-ImPYPyPy-y-HpHpHpPy-(3-Py -W
1991(3) 5' G TG A A G W-3' Im-(3-ImPyPyIm-y-PYHpHpPy-(3-Py -W
1992(3) 5' G TG A A C W-3' Im-p-ImPyPYPy-y-ImHpI-IpPy-p-Py -W
19933) 5' G TG A G T W-3' Im-(3-ImPyImHp-y-PyPyHpPy-(3-Py -W
19943) 5' G TG A G A W-3' Im-~3-ImPyImPy-y-HpPyHpPy-~3-py -W
19950 5' G TG A G G W-3' Im-(3-ImPyImIm-y-PyPyHpPy-(3-Py -W
19963) 5' G TG A G C W-3' Im-p-ImPyImPy-y-ImPYHpPy-~3-py -W
1997(3) 5' G TG A C T W-3' Im-(3-ImPyPyHp-y-PyImHpPy-p-Py -W
1998(3) 5' G TG A C A W-3' Im-p-ImPyPyPy-y-HpImHpPy-p-Py -W
1999~i) 5' G TG A C G W-3' Im-(3-ImPyPyIm-y-PYImHpPy-(3-Py -W
20003) 5' G TG A C C W-3' Im-/3-ImpyPypy-y-ImImHpPy-(3-Py -W
TABLE
173:
I2-ring (3-Hairpin Poiyamides for recognition of 8-by 5'-WGTGSNNW-3' DNA aromatic amino acid sequence sequence 2001(3) 5'-W G TG G T T W-3' Im-~3-ImImHpHp-y-PyPyPyPy-(3-Py 2002(3) '5'-W G TG G T A W-3' Im-~3-ImImHpPy-y-HpPyPyPy-~-Py 20033) 5'-W G TG G T G W-3' Im-/3-ImImHpIm-y-PyPyPyPy-(3-Py 20043) 5'-W G TG G T C W-3' Im-p-ImImHpPy-y-ImPyPyPy-(3-Py 2005~i) 5'-W G TG G A T W-3' Im-p-ImImPyHp-y-PyHpPyPy-~3-Py 2006~i) 5'-W G TG G A A W-3' Im-p-ImImPyPy-y-HpHpPyPy-p-Py 20070 5'-W G TG G A G W-3' Im-p-ImImPyIm-y-PyHpPyPy-p-Py 20083) 5'-W G TG G A C W-3' Im-~3-ImImPyPy-y-ImHpPyPy-p-Py 2009(3) 5'-W G TG G G T W-3' Im-(3-ImImImHp-y-PyPyPyPy-p-Py 20103) 5'-W G TG G G A W-3' Im-~3-ImImImPy-y-HpPyPyPy-(3-Py 2011(3) 5'-W G TG G C T W-3' Im-~3-ImIrnPyHp-y-PyImPyPy-(3-Py 2012(3) 5'-W G TG G C A W-3' Im-~i-ImImPyPy-y-HpImPyPy-(3-Py 2013(3) 5'-W G TG C T T W-3' Im-p-ImPyHpHp-y-PyPyImPy-p-Py 20143) 5'-W G TG C T A W-3' Im-(3-ImPyHpPy-y-HpPyImPy-(3-Py 20153) 5'-W G TG C T G W-3' Im-(3-ImPyHpIm-y-PyPyImPy-~3-Py 20160 5'-W G TG C T C W-3' Im-(3-ImPyHpPy-y-ImPyImPy-(3-Py 2017(3) 5'-W G TG C A T W-3' Im-(3-ImPyPyHp-y-PyHpImPy-(3-Py 2018(3) 5'-W G TG C A A W-3' Im-(3-ImPyPyPy-y-HpHpImPy-~i-Py 2019) 5'-W G TG C A G W-3' Im-~-ImPyPyIm-y-PyHpImPy-(3-Py 2020(3) 5'-W G TG C A C W-3' Im-~i-ImPyPyPy-y-ImHpImPy-~3-Py 2021(3) 5'-W G TG C G T W-3' Im-(3-ImPyImHp-y-PyPyImPy-(3-Py 2022~i) 5'-W G TG C G A W-3' Im-(1-ImPyImPy-y-HpPyImPy-(3-Py 2023(3) 5'-W G TG C C T W-3' ~Im-(3-ImPyPyHp-y-PyImImPy-p-Py 2024) 5'-W G TG C C A W-3' Im-~i-ImPyPyPy-y-HpImImPy-(3-Py 2025R) 5'-W G TG G G G W-3' Im-(3-ImImImIm-y-PyPyPyPy-(3-Py 2026(3) 5'-W G TG G G C W-3' Im-R-ImImImPy-y-ImPyPyPy-(3-Py 2027(3) 5'-W G TG G C G W-3' Im-~3-ImImPyIm-y-PyImPyPy-(3-Py 20283) 5'-W G TG G C C W-3' Im-~i-ImImPyPy-y-ImImPyPy-p-Py 20293) 5'-W G TG C G G W-3' Im-(3-mPyImIm-y-PyPyImPy-~3-Py 2030(3) 5'-W G TG C G C W-3' Im-(3-ImPyImPy-y-ImPyImPy-(3-Py 2031(3) 5'-W G TG C C G W-3' Im-~3-ImPyPyIm-y-PyImImPy-~i-Py 2032(3) 5'-W G TG C C C W-3' Im-(3-ImPyPyPy-y-ImImImPy-(3-Py i_ PCT/US98l01714 TABLE 174:
12-ring (3-Hairpin Polyamides for recogmUon of 8-by S'-WGTTWNNW-3' DNA sequence aromatic amino acid sequence 2033(3) 5' -W G T ImHp-/3-HpApHp-y-pypypy_a_pypY
T T T T
W-3' 2034(3) ~ 5' -W G ImHp-(3-HpHpPy-y-HpPyPy-~3-pypy T T T T
A W-3' 20353) 5' -W G T ImHp-(3-HpHpIm-y-pypypy-R_pypy T T T G
W-3' 20363) 5' -W G T ImHp-(3-HpHpPy-y-ImPyPy-(3-PyPy T T T C
W-3' 2037(3) 5' -W G T ImHp-(3-HpPYHp-y-pyHpPy-(3-PYPy T T A T
W-3' 2038(3) 5' -W G T A A W-3' ImHp-J3-HpPYPy-y-HpHpPy-(3-Pypy T T
2039(3) 5' -W G T A G W-3' ImHp-~3-HpPYIm-y-PyHpPy-(3-PYPy T T
2040(3} 5' -W G T A C W-3' ImHp_~3_Hppypy_y_ImHppy-(3_pypy T T
20413) 5' -W G T G T W-3' ImHp-(3-HpImHp-y_PyPypy-(3-pypY
T T
2042(3) 5' -W G T G A W-3' ImHp-(3-Hplmpy_y_HpPyPy-(3-PyPy T T
20433) 5' -W G T G G W-3' ImHp-~i-HpImIm-y-PypypY-~3_pypy T T
2044(3} 5' -W G T G C W-3' _ _ T T Imp R HpImPy y ImPyPy-(3-PyPy 2045(3) 5' -W G T C T W-3 ImHp-(3-HpPyHp-y-PYImPy-~-PyPy T T T
20463) 5' -W G T C A W-3' ImHp-(3-Hppypy_y_HpImPy-~3-pypy T T
20473) 5' -W G T C G W-3' ImHp-(3-HpPyIm-y-PYImPy-J3-pypY
T T
2048(3) 5'-W G T C C W-3' ImHp-~3-Hppypy_y_ImImpy-(3-PYPy T T
20493) 5' -W G T T T W-3' T A ImHp-~-PyHpHp-y-PyPyHp-p-PyPy 20503) 5'-W G T T A W-3' ImHp-~3-PyHpPy-y-HpPYHp-(3-PyPy T A
2051(3) 5' -W G T T G W-3' ImHp-(3-PYHpIm-y-PypyHp-(3_pypy T A
20523) 5' -W G T T C W-3' ImHp-~i-PyHppy-y-ImPYHp-(3-Pypy T A
2053J3) 5' -W G T A T W-3' ImHp-~3-pypyHp_y_pyHpHp-~3-pypy T A
2054(3) 5' -W G T A A W-3' ImHp-(3-PYPYpy-y_HpHpHp-~i-pypY
T A
2055(3) 5' -W G T A G W-3' ImHp-~3-PyPYIm-y-PyHpHp-(3-PYPy T A
2056(3) 5' -W G T A C W-3' ImHp-(3-PyPYPy-y-ImHpHp-~3-pypY
T A
2057~i) 5' -W G T G T W-3' ImHp-(3-pylmHp_y_pypYHp_~3_PyPy T A
2058(3) 5' -W G T G A W-3' ImHp-(3-PyImPY-y-Hppygp-(3-PyPy T A
2059~i) 5' -W G T G G W-3' ImHp-~-PyImIm-y-pyPyHp-(3-pypy T A
20603) 5' -W G T G C W-3' ImHp-~3-PyImPy-y_ImPYHp-~3-Pypy T A
2061~i) 5' -W G T C T W-3' Imp-(3_pypyHp_y_pyl~p_a-pYpy T A
2062(3) 5' -W G T C A W-3' ImHp-(3-pypypy-y_HpImHp-/3-PyPy T A
20633) 5' -W G T C G W-3' ImHp-(3-PYPyIm-y-pylmHp-p_pypy T A
2064(3) 5' -W G T C C W-3' ImHp-/3-PyPYPY-y-ImImHp-(3-Pypy T A
TABLE
175:
12-ring (3-Hairpin Polyamides for recognition of 8-by 5'-WGTTSNNW-3' -DNA aromatic amino acid sequence sequence 2065(3) 5'-W G TT G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~-PyPy 20663) ~5'-W G TT G T A W-3' ImHp-(3-ImHpPy-y-HpPYPy-(3-PYPy 20673) 5'-W G TT G T G W-3' ImHp-(3-ImHpIm-y-PYPYPy-~3-PYPy 2068(3) 5'-W G TT G T C W-3' ImHp-(3-ImHpPy-y-ImPYPy-(3-PyPy 2069(3) 5'-W G TT G A T W-3' ImHp-p-ImPYHp-y-PyHpPy-p-PyPy 2070(3) 5'-W G TT G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-(3-PyPy 2071(3) 5'-W G TT G A G W-3' ImHp-p-ImPyIm-y-PyHpPy-(3-PYPy 20723) 5'-W G TT G A C W-3' ImHp-(3-ImPYPy-y-ImHpPy-(3-PYPy 2073(3) 5'-W G TT G G T W-3' ImHp-a-ImImHp-y-PyPYPy-(3-PYPy 20743) 5'-W G TT G G A W-3' ImHp-p-ImImPy-y-HpPyPy-(3-PYPy 2075(3) 5'-W G TT G C T W-3' ImHp-p-ImPyHp-y-PyImPy-(3-PYPy 2076(3) 5'-W G TT G C A W-3' ImHp-p-ImPyPy-y-HpImPy-(3-PYPy 2077(3) 5'-W G TT G G G W-3' ImHp-~3-ImImIm-y-PyPYPy-(3-PyPy 2078(3) 5'-W G TT G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-(3-PYPy 2079R) 5'-W G TT G C G W-3' ImHp-(3-ImPYIm-y-PyImPy-~-PYPy 2080(3) 5'-W G TT G C C W-3' ImHp-(3-ImPyPy-y-ImImPy-(3-PYPy 2081(3) 5'-W G TT C T T W-3' ImHp-(3-PYHpHp-y-PYPYIm-(3-PYPy 2082(3) 5'-W G TT C T A W-3' ImHp-(3-PYHpPy-y-HpPyIm-(3-PYPy 2083(3) 5'-W G TT C T G W-3' ImHp-(3-PYHpIm-y-PyPYIm-~3-PyPy 2084(3) 5'-W G TT C T C W-3' ImHp-(3-PYHpPy-y-ImPyIm-p-PyPy 20853) 5'-W G TT C.A T W-3' ImHp-(3-PYPyHp-y-PYHpIm-(3-PyPy 2086(3) 5'-W G TT C A A W-3' ImHp-p-PYPYPy-y-HpHpIm-(3-PyPy 2087(3) 5'-W G TT C A G W-3' ' ImHp-p-PyPYIm-y-PyHpIm-(3-PyPy 20883) 5'-W G TT C A C W-3' ImHp-J3-PYPyPy-y-ImHpIm-(3-PYPy 2089(3) 5'-W G TT C G T W-3' ImHp-(3-PyImHp-y-PyPYIm-~3-PyPy 2090(3) 5'-W G TT C G A W-3' ImHp-~i-PYImPy-y-HpPYIm-~3-PYPy 2091(3) 5'-W G TT C C T W-3' ImHp-(3-PYPyHp-y-PyImIm-(3-PyPy 2092(3) 5'-W G TT C C A W-3' ImHp-p-PYPyPy-y-HpImIm-p-PyPy 2093~i) 5'-W G TT C G G W-3' ImHp-p-PYImIm-y-PYPyIm-(3-PyPy 2094(3) 5'-W G TT C G C W-3' ImHp-[3-PYImPy-y-ImPYIm-(3-PYPy 2095(3) 5'-W G TT C C G W-3' ImHp-(3-PYPyIm-y-PyImIm-p-PYPy 2096(3) 5'-W G TT C C C W-3' ImHp-(3-PYPyPy-y-ImImIm-~3-PyPy ......~_.......-.. n TABLE 176: r recognition of 8-by 5'-WGTAWNNW-3' 12-ring -~3-Hairpin Polyamides fo DNA aromatic amino acid sequence sequence 2097(3) 5' G A T T W-3' ImHp-/3-HpHpHp-y-pypypy_p_pypy -W T T
20983) 5' G A TT A W-3' ImHp-(3-HpHpPy-y-HpPYPy-(3-PYPy -W T
2099(3) 5' G A TT G W-3' ImHp-(3-HpHpIm-y-Pypypy-(3-pypY
-W T
' 2100(3) 5' G A TT C W-3' -W T ImHp-p-HpHpPy-y-ImPyPy-~3-PYPy 2101) 5' G A TA T W-3' ImHp-(3-HpPYHp-y-PYHpPy-~i-Pypy -W T
2102(3) 5' G A TA A W-3' ImHp-~3-HpPYPy-y-HpHpPy-~3-PYpY
-W T
2103(3) 5' G A TA G W-3' ImHp-(3-HpPyIm-Y-PYHpPy-~3-PYPy -W T
2104(3) 5' G A TA C W-3' I~p_~_HppypY-Y_I~ppy-~_PypY
-W T
2105(3) 5' G A TG T W-3' I~p_~_Hpl~p_Y_pypypy-a-pYpY
-W T
21063) 5' G A TG A W-3' Imi-Ip-~_Hplmpy_y_HpPYpy-(3-pypy -W T
21073) 5' G A TG G W-3' ImHp-(3-HpImIm-y-PypypY-(3-pypY
-W T
2108~i) 5' G A TG C W-3' ImHp-~-HpImPy-y-ImPyPy-(3-pypy -W T
2109(3) 5' G A TC T W-3' ImHp-(3-HpPyHp-y-PyImPy-(3-PYPy -W T
21103) 5' G A TC A W-3' ImHp-(3-HpPyPy-y-HpImPy-~3-Pypy -W T
2111(3) 5' G A TC G W-3' ImHp-(3-HpPyIm-y-PyImPy-(3-Pypy -W T
21123) 5' G A TC C W-3' ImHp-~3-HpPyPy-y-ImImPy-(3-PyPy -W T
2113(3) 5' G A AT T W-3' ImHp-(3-PyHpHp-y-pypygp-(~-pypy -W T
2114) 5' G A AT A W-3' ImHp-(3-PYHpPy-y-HpPyHp-(3-PyPy -W T
2115(3) 5' G A AT G W-3' ImHp-~3-pyHplm-y-PypyHp-(3-Pypy -W T
2116(3) 5' G A AT C W-3' ImHp-p-pygppY_y_ImPYHp-(3-PYPy -W T
2117(3) 5' G A AA T W-3' ImHp-(3-PyPyHp-y-pYHpHp-(3-PYPy -W T
2118(3} 5' G A AA A W-3' ImHp-(3-PyPyPy-Y-HpHpHp-/3-Pypy -W T
2119(3) 5' G A AA G W-3' 'ImHp-p-pypylm-y-PYHpHp-(3-PyPy -W T
21203) 5' G A AA C W-3' I~p_R_p~,p~,py_y_I~pHp-p-PyPY
-W T
21213) 5' G A AG T W-3' I~p_~_p~,I~p_y-pYpYHp-~-pYpY
-W T
2122(3) 5' G A AG A W-3' ImHp-~i-pylmpy_y_HppYHp-~-pypY
-W T
2123(3) 5' G A AG G W-3' ImHp-p-PYImIm-y-Pypygp-(3-pYPy -W T
2124(3) 5' G A AG C W-3' ImHp-R-PYImPY-y-ImPYHp-~3-Pypy -W T
2125(3) 5' G A AC T W-3' ImHpPyPYPyHp-Y-PyImHp-(3-PyPy -W T
2126(3) 5' G A AC A W-3' ImHpPyPYPYPy-y-Hpl~p_~3-pypy -W T
2127(3) 5' G A AC G W-3' ImHpPyPYPYIm-y-PYImHp-(3-PYpY
-W T
2128(3) 5' G A AC C W-3' ImHpPYPYPYPY-Y-ImImHp-(3-PyPY
-W T
TABLE 177: 1-Iairpin 12-ring Polyamides p- for recognition of 8-by 5'-WGTASNNW-3' -DNA aromatic amino acid sequence sequence 2129(3) 5' -WG T A G T T W-3' ImHp-(3-ImHpHp-y-PyPyPy-~3-PyPy 21303) ~ -WG T A G T A W-3' ImHp-(3-ImHpPy-y-HpPyPy-~3-PyPy 5' 21313) 5' -WG T A G T G W-3' ImHp-(3-ImHpIm-y-PyPypy-p-PyPy 2132(3) 5' -WG T A G T C W-3' ImHp-(3-ImHpPy-y-ImPyPy-[3-PyPy 21333) 5' -WG T A G A T W-3' ImHp-(3-ImPyHp-y-PyHpPy-(3-Pypy 2134(3) 5' -WG T A G A A W-3' ImHp-(3-ImPyPy-y-HpHpPy-~3-PyPy 2135(3) 5' -WG T A G A G W-3' ImHp-(3-ImPyIm-y-PyHpPy-~3-PyPy 2136(3) 5' -WG T A G A C W-3' ImHp-(3-ImPyPy-y-ImHpPy-~3-PyPy 21373) 5' -WG T A G G T W-3' ImHp-(3-ImImHp-y-PypyPy-~3-PyPy 21383) 5' -WG T A G G A W-3' ImHp-(3-ImImPy-y-HpPyPy-~-PyPy 2139(3) 5' -WG T A G C T W-3' ImHp-/3-ImPyHp-y-PyImPy-(3-PyPy 2140(3) 5' -WG T A G C A W-3' ImHp-(3-ImpyPy-y-HpImPy-(3-PyPy 2141(3) 5' -WG T A G G G W-3' ImHp-(3-ImImIm-y-PyPyPy-p-PyPy 2142(3) 5' -WG T A G G C W-3' ImHp-(3-ImImPy-y-ImPyPy-~i-PyPy 2143(3) 5' -WG T A G C G W-3' ImHp-(3-ImPyIm-y-PyImPy-(3-PyPy 2144(3) 5' -WG T A G C C W-3' ImHp-~3-ImPyPy-y-ImImPy-~i-PyPy 2145(3) 5' -WG T A C T T W-3' ImHp-(3-PyHpHp-y-PyPyIm-R-PyPy 2146(3) 5' -WG T A C T A W-3' ImHp-(3-PyHpPy-y-HpPyIm-(3-PyPy 2147(3) 5' -WG T A C T G W-3' ImHp-j3-PyHpIm-y-PyPyIm-(3-PyPy 2148(3) 5' -WG T A C T C W-3' ImHp-(3-PyHpPy-y-ImPyIm-p-PyPy 2149(3) 5' -WG T A C A T W-3' ImHp-R-PyPyHp-y-PyHpIm-(3-PyPy 2150(3) 5' -WG T A C A A W-3' ImHp-(3-PyPyPy-y-HpHpIm-(3-PyPy 2151(3) 5' -WG T A C A G W-3' ImHp-~3-PyPyIm-y-PyHpIm-(3-PyPy 2152(3) 5' -WG T A C A C W-3' ImHp-(3-PyPyPy-y-ImHpim-~3-PyPy 2153(3) 5' -WG T A C G T W-3' ImHp-(3-PyImHp-y-PyPyIm-(3-PyPy 2154) 5' -WG T A C G A W-3' ImHp-(3-PyImPy-y-HpPyIm-(3-PyPy 2155(3) 5' -WG T A C C T W-3' ImHp-~i-PyPyHp-y-PyImIm-p-PyPy 2156(3) 5' -WG T A C C A W-3' ImHp-(3-PyPyPy-y-HpImIm--PyPy 2157(3) 5' -WG T A C G G W-3' ImHp-(3-PyImIm-y-PyPyIm-(3-PyPy 2158(3) 5' -WG T A C G C W-3' ImHp--PyImPy-y-ImPyIm-(3-PyPy 21593) 5' -WG T A C C G W-3' ImHp-~3-PyPyIm-y-PyImIm-(3-PyPy 21603) 5' -WG T A C C C W-3' ImHp-(3-PyPyPy-y-ImImIm-p-PyPy ,. , .
1A13LE 178: 12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGTCWNNW-3' DNA aromatic amino acid sequence sequence 2161(3) 5'-W G TC T T T W-3' ImHppy_~3_HpHp_y_pypy_~3-ImPyPy 21623) ~5'-W G TC T T A W-3' ImHpPy-J3-Hppy_y_Hppy-(3-ImPyPy 2163~i) 5'-W G TC T T G W-3' ImHpPy-~3-HpIm-y-PyPy-~3-ImPyPy ' 2164(3) 5'-W G TC T T C W-3' ImHpPy-(3-HpPy-y-ImPy-~3-ImPyPy 2165~i) 5'-W G TC T A T W-3' ImHpPy-~3-PyHp-y_pyHp-(3-ImPyPy 21663) 5'-W G TC T A A W-3' ImHpPy-(3-Pypy-y-HpHp-(3-ImPyPy 2167(3) 5'-W G TC T A G W-3' ImHpPy-(3-Pylm-y-PyHp-a-ImPyPy 2168(3) 5'-W G TC T A C W-3' ImHpPy-~i-PyPy-y-ImHp-p-ImPyPy 2169(3) 5'-W G TC T G T W-3' ImHpPy-(3-ImHp-y-pypy_R-ImPyPy 2170(3) 5'-W G TC T G A W-3' ImHpPy-(3-ImPy-y-HpPy-~3-ImPyPy 2171(3) 5'-W G TC T G G W-3' ImHpPy-(3-Imlm_y_pypy_~3-ImpyPy 2172(3) 5'-W G TC T G C W-3' ImHppy_~_Impy_y_Imp~,_(3-ImPyPy 2173(3) 5'-W G TC T C T W-3' ImHpPy-~3-PyHp-y-Pylm-(3-ImPyPy 21743) 5'-W G TC T C A W-3' ImHpPy-~3-Pypy-y-HpIm-(3-ImPyPy 2175(3) 5'-W G TC T C G W-3' ImHpPy-p-pyIm-y-PyIm-(3-ImPyPy 2176~i) 5'-W G TC T C C W-3' ImHpPy-(3-PyPy-y-Imlm-~3-ImPyPy 2177(3) 5'-W G TC A T T W-3' ImHpPy-~3-HpHp-y-Pypy-(3-ImPyPy 2178(3) 5'-W G TC A T A W-3' ImHpPy-(3-HpPy-y-HpPy-(3-ImPyPy 2179(3) 5'-W G TC A T G W-3' ImHpPy-(3-HpIm-y-PyPy-~i-ImPyPy 2180J3) 5'-W G TC A T C W-3' ImHpPy-~3-HpPy-y-ImPy-p-ImPyPy 21813) 5'-W G TC A A T W-3' ImHppy_(~_pyHp_y_pyHp_R-ImPyPy 2182~i) 5'-W G TC A A A W-3' ImApPy-(1-Pypy-y-HpHp-(3-ImPyPy 2183(3) 5' -W G T C A A G W-3' ImHpPy-(3-PyIm-y-PyHp-(3-ImPyPy 2184(3) 5' -W G T C A A C W-3' ImHpPy-(3-PyPy-y-ImHp-(3-ImPyPy 2185(3) 5' -W G T C A G T W-3' ImFipPy-~3-ImHp-y_pyp~,_~_ImPyPy 2186(3) 5' -W G T C A G A W-3' ImHpPy-(3-ImPy-y-HpPy-p-ImPyPy 2187(3) 5'-W G TC A G G W-3' ImHpPy-(3-ImIm-y-PyPy-(3-ImPyPy 2188(3) 5'-W G TC A G C W-3' ImHpPy-(3-ImPy-y-ImPy-~3-ImPyPy 2189(3) 5'-W G TC A C T W-3' ImHpPy-~i-PyHp-y-PyIm-(3-ImPyPy 2190~i) 5'-W G TC A C A W-3' ImHpPy-(3-PyPy-y-HpIm-/3-ImPyPy 2191(3) 5'-W G TC A C G W-3' ImHpPy-(3-PyIm-y-PyIm-(3-ImPyPy 2192(3) 5'-W G TC A C C W-3' ImHpPy-(3-PyPy-y-Imlm-(3-ImPyPy WO 981370b7 PCT/US98/01714 TABLE 179:
12-ring ~3-Hairpin Polyamides for recognition of 8-by 5'-WGTCSNNW-3' DNA aromatic amino acid sequence sequence 2193(3) 5'-WG T C G T TW-3' ImHp-(3-ImHpHp-y-PyPy-J3-ImPyPy 2194~i) 5'-WG T C G T AW-3' ImHp-(3-ImHpPy-y-HpPy-(3-ImPyPy 21953) 5'-WG T C G T GW-3' ImHp-j3-ImHpIm-y-PyPy-(3-ImPyPy 2196(3) 5'-WG T C G T CW-3' ImHp-~-ImHpPy-y-ImPy-(3-ImpyPy 21973) 5'-WG T C G A TW-3' ImHp-~3-ImPyHp-y-PyFip-(3-ImPyPy 2198(3) 5'-WG T C G A AW-3' ImHp-(3-ImPyPy-y-HpHp-(3-ImPyPy 2199(3) 5'-WG T C G A GW-3' ImHp-J3-ImPyIm-y-PyHp-(3-ImPyPy 22003) 5'-WG T C G A CW-3' ImHp-~i-ImPyPy-y-ImHp-(3-ImpyPy 2201(3) 5'-WG T C G G TW-3' ImHp-(3-ImImHp-y-PyPy-~3-ImPyPy 2202(3) 5'-WG T C G G AW-3' ImHp-(3-ImImPy-y-HpPy-p-ImPyPy 2203) 5'-WG T C G C TW-3' ImHp-(3-ImPyHp-y-PyIm-p-ImPyPy 2204~i) 5'-WG T C G C AW-3' ImHp-p-ImPyPy-y-HpIm-[3-ImpyPy 22053) 5'-WG T C C T TW-3' ImHp-(3-PyHpHp-y-Py-p-ImImPyPy 2206(3) 5'-WG T C C T AW-3' ImHp-(3-PyHpPy-y-Hp-(3-ImImPyPy 2207(3) 5'-WG T C C T GW-3' ImHp-(3-PyHpim-y-Py-(3-ImImPyPy 2208(3) 5'-WG T C C T CW-3' ImHp-~i-PyHpPy-y-Im-(3-ImImPyPy 2209(3) 5'-WG T C C A TW-3' ImHp-(3-PyPyHp-y-Py-(3-ImImPyPy 2210(3) 5'-WG T C C A AW-3' ImHp-(3-PyPypy-y-Hp-~3-ImImPyPy 22113) 5'-WG T C C A GW-3' ImHp-~3-PyPyIm-y-Py-~i-ImImpyPy 2212(3) 5'-WG T C C A CW-3' ImHp-(3-PypyPy-y-Im-~3-ImImPyPy 2213(3) 5'-WG T C C G TW-3' ImHp-(3-PyImHp-y-py-(3-ImImpyPy 2214(3) 5'-WG T C C G AW-3' ImHp-(3-PyImPy-y-Hp-~i-ImImPyPy 2215(3) 5'-WG T C C C TW-3' 'ImHp-~i-PyPyHp-y-PyImImIm-(3-Py 2216(3) 5'-WG T C C C AW-3' ImHp-(i-PyPyPy-y-HpImImIm-(3-Py 2217(3) 5'-WG T C G G GW-3' ImHp-~i-ImImIm-y-PyPy-(3-ImPyPy 2218(3) 5'-WG T C G G CW-3' ImHp-p-ImImPy-y-ImPy-~3-ImPyPy 22193) 5'-WG T C G C GW-3' ImHp-~3-ImPyIm-y-PyIm-p-ImPyPy 2220(3) 5'-WG T C G C CW-3' ImHp-(3-ImPyPy-y-ImIm-~-ImPyPy 22210 5'-WG T C C G GW-3' ImHp-(3-PyImIm-y-Py-(3-ImImPyPy 2222(3) 5'-WG T C C G CW-3' ImHp-(3-PyImPy-y-Im-~i-ImImPyPy 2223(3) 5'-WG T C C C GW-3' ImHp-(3-PyPyIm-y-PyImImIm-p-Py 2224~i) 5'-WG T C C C CW-3' ImHp-(3-PyPyPy-y-ImImImIm-~i-Py
Claims (48)
1. A method for designing a specific polyamide X1X2...X m-.gamma.-X(m + 1)...X(2m-1)X2m wherein X1, X2, Xm, X(m + 1), X(2m - 1), and X2m are carboxamide residues forming carboxamide binding pairs X1/X2m, X2/X(2m-1), Xm/X(m + 1), and .gamma. is .gamma.-aminobuytic acid or 2,4 diaminobutyric acid and Dp is dimethylaminopropylamide, suitable for use as a DNA-binding ligand that is selective for identified target DNA sequences 5'-WN1N2, ... N m W-3' where m is an integer having a value from 3 to 6, comprising the steps of:
a. identifying a target sequence of double stranded DNA having the form S'-WN1N2 .
.. N m W-3', N1N2 ... N m being the sequence to be bound by carboxamide residues, wherein each N is independently chosen from the group A, G, C, and T, each W is independently chosen from the group A and T, and m is an integer having a value from 3 to 6;
b. representing the identified sequence as 5'-Wab ... x W-3', wherein a is a first nucleotide to be bound by the X1 carboxamide residue, b is a second nucleotide to be bound by the X2 carboxamide residue, and x is the corresponding nucleotide to be bound by the X m carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified sequence;
d, selecting Im as the X1 carboxamide residue and Py as the X2m carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X2m carboxamide residue if a=C;
f. selecting Hp as the X 1 carboxamide residue and Py as the X2m carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X2m carboxamide residue if a=A; and h. repeating steps c - g for b through x until all carboxamide residues are selected.
a. identifying a target sequence of double stranded DNA having the form S'-WN1N2 .
.. N m W-3', N1N2 ... N m being the sequence to be bound by carboxamide residues, wherein each N is independently chosen from the group A, G, C, and T, each W is independently chosen from the group A and T, and m is an integer having a value from 3 to 6;
b. representing the identified sequence as 5'-Wab ... x W-3', wherein a is a first nucleotide to be bound by the X1 carboxamide residue, b is a second nucleotide to be bound by the X2 carboxamide residue, and x is the corresponding nucleotide to be bound by the X m carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified sequence;
d, selecting Im as the X1 carboxamide residue and Py as the X2m carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X2m carboxamide residue if a=C;
f. selecting Hp as the X 1 carboxamide residue and Py as the X2m carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X2m carboxamide residue if a=A; and h. repeating steps c - g for b through x until all carboxamide residues are selected.
2. The method of claim 1 further comprising the step of synthesizing the polyamide X1X2... Xm-.gamma.-X(m + 1)...X(2m-1)X2m.
3. The method of claim 2 further comprising the step of determining if the binding affinity of the polyamide to the identified sequence is subnanomolar.
4. The method of claim 2 further comprising the step of determining if the sequence specificity of the polyamide is greater or equal to ten.
5. The method of claim 2 further comprising the step of replacing at least one pyrrole residue with a .beta.-alanine residue.
6. A method for designing a selective polyamide molecule X1X2X3X4-.gamma.-X5X6X7X8, wherein X1, X2, X3, X4, X5, X6, X7, and X8, are carboxamide residues forming binding pairs X1/X8 X2/X7, X3/X6 and X4/X5, and .gamma. is .gamma.-aminobuytic acid or 2,4 diaminobutyric acid suitable for binding to a six base pair sequence of the form 5'-WNNNNW-3' in the minor groove of double stranded DNA, comprising the steps of:
a. identifying a six base pair sequence of double stranded DNA having the form 5'-WNNNNW-3', wherein W is either A or T, NNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, and d is a fourth nucleotide to be bound by a carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X8 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X8 carboxamide residue if a=A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X7 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=T;
1. selecting Py as the X2 carboxamide residue and Hp as the X7 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X6 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=T;
d. selecting Py as the X3 carboxamide residue and Hp as the X6 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X5 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=T; and v. selecting Py as the X4 carboxamide residue and Hp as the X5 carboxamide residue if d=A.
a. identifying a six base pair sequence of double stranded DNA having the form 5'-WNNNNW-3', wherein W is either A or T, NNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, and d is a fourth nucleotide to be bound by a carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X8 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X8 carboxamide residue if a=A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X7 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=T;
1. selecting Py as the X2 carboxamide residue and Hp as the X7 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X6 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=T;
d. selecting Py as the X3 carboxamide residue and Hp as the X6 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X5 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=T; and v. selecting Py as the X4 carboxamide residue and Hp as the X5 carboxamide residue if d=A.
7. The method of claim 6 further comprising the step of synthesizing the polyamide X1X2X3X4-.gamma.-X5X6X7X8.
8. The method of claim 7 further comprising the step of determining if the binding affinity of the polyamide to the identified sequence is subnanomolar.
9. The method of claim 7 further comprising the step of determining if the sequence specificity of the polyamide is greater or equal to ten.
10. The method of claim 7 further comprising the step of replacing at least one pyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X6, and X7.
11. The method of claim 7 further comprising the step of replacing at least ore 3-hydroxypyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X6, and X7.
12. A polyamide composition produced by the process comprising the steps of:
a. identifying a six base pair sequence of double stranded DNA having the form 5'-WNNNNW-3', wherein W is either A or T, NNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, and d is a fourth nucleotide to be bound by a carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X8 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X8 carboxamide residue if a=A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X7 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=T;
l. selecting Py as the X2 carboxamide residue and Hp as the X7 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X6 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X6 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X5 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X5 carboxamide residue if d=A; and w. synthesizing the polyamide X1X2X3X4-.gamma.-X5X6X7X8.
a. identifying a six base pair sequence of double stranded DNA having the form 5'-WNNNNW-3', wherein W is either A or T, NNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, and d is a fourth nucleotide to be bound by a carboxamide residue;
c. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X8 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X8 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X8 carboxamide residue if a=A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X7 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X7 carboxamide residue if b=T;
l. selecting Py as the X2 carboxamide residue and Hp as the X7 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X6 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X6 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X6 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the identified six base pair sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X5 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X5 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X5 carboxamide residue if d=A; and w. synthesizing the polyamide X1X2X3X4-.gamma.-X5X6X7X8.
13. The polyamides described by the formulas listed in Tables 4-19.
14. The polyamides described by the formulas listed in Tables 20-83.
15. The polyamides described by the formulas listed in Tables 84-179.
16. A method for designing a selective polyamide molecule X1X2X3X4X5-.gamma.-X6X7X8X9X10, wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, and X10 are carboxamide residues forming binding pairs X1/X10, X2/X9, X3/X8, X4/X5, and X5/X6, and .gamma. is .gamma.-aminobuytic acid or 2,4 diaminobutyric acid suitable for binding to a six base pair sequence of the form 5'-WNNNNNW-3' in the minor groove of double stranded DNA, comprising the steps of:
a. identifying a seven base pair sequence of double stranded DNA having the form 5'-WNNNNW3', wherein W is either A or T, NNNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdeW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, d is a fourth nucleotide to be bound by a carboxamide residue, and a is a fifth nucleotide to be bound by a carboxamide residue;
c. defining .alpha. as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X10 carboxamide residue if .alpha.=G;
e. selecting Py as the X1 carboxamide residue and Im as the X10 carboxamide residue if .alpha. = C;
f. selecting Hp as the X1 carboxamide residue and Py as the X10 carboxamide residue if .alpha. = T;
g. selecting Py as the X1 carboxamide residue and Hp as the X10 carboxamide residue if .alpha. = A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X9 carboxamide residue if b = G;
j. selecting Py as the X2 carboxamide residue and Im as the X9 carboxamide residue if b = C;
k. selecting Hp as the X2 carboxamide residue and Py as the X9 carboxamide residue if b = T;
l. selecting Py as the X2 carboxamide residue and Hp as the X9 carboxamide residue if b = A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X8 carboxamide residue if c = G;
o. selecting Py as the X3 carboxamide residue and Im as the X8 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X8 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X8 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the seven base pair sequence identified sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X7 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X7 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X7 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X7 carboxamide residue if d=A;
w. defining a as A, G, C, or T to correspond to the fifth nucleotide to be bound by a carboxamide residue in the seven base pair sequence identified sequence;
x. selecting Im as the X5 carboxamide residue and Py as the X6 carboxamide residue if e=G;
y. selecting Py as the X5 carboxamide residue and Im as the X6 carboxamide residue if e=C;
z. selecting Hp as the X5 carboxamide residue and Py as the X6 carboxamide residue if e=T; and aa. selecting Py as the X5 carboxamide residue and Hp as the X6, carboxamide residue if e=A.
a. identifying a seven base pair sequence of double stranded DNA having the form 5'-WNNNNW3', wherein W is either A or T, NNNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdeW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, d is a fourth nucleotide to be bound by a carboxamide residue, and a is a fifth nucleotide to be bound by a carboxamide residue;
c. defining .alpha. as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X10 carboxamide residue if .alpha.=G;
e. selecting Py as the X1 carboxamide residue and Im as the X10 carboxamide residue if .alpha. = C;
f. selecting Hp as the X1 carboxamide residue and Py as the X10 carboxamide residue if .alpha. = T;
g. selecting Py as the X1 carboxamide residue and Hp as the X10 carboxamide residue if .alpha. = A;
h. defining b as A, G, C, or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X9 carboxamide residue if b = G;
j. selecting Py as the X2 carboxamide residue and Im as the X9 carboxamide residue if b = C;
k. selecting Hp as the X2 carboxamide residue and Py as the X9 carboxamide residue if b = T;
l. selecting Py as the X2 carboxamide residue and Hp as the X9 carboxamide residue if b = A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified seven base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X8 carboxamide residue if c = G;
o. selecting Py as the X3 carboxamide residue and Im as the X8 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X8 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X8 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the seven base pair sequence identified sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X7 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X7 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X7 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X7 carboxamide residue if d=A;
w. defining a as A, G, C, or T to correspond to the fifth nucleotide to be bound by a carboxamide residue in the seven base pair sequence identified sequence;
x. selecting Im as the X5 carboxamide residue and Py as the X6 carboxamide residue if e=G;
y. selecting Py as the X5 carboxamide residue and Im as the X6 carboxamide residue if e=C;
z. selecting Hp as the X5 carboxamide residue and Py as the X6 carboxamide residue if e=T; and aa. selecting Py as the X5 carboxamide residue and Hp as the X6, carboxamide residue if e=A.
17. The method of claim 16 further comprising the step of synthesizing the polyamide X1X2X3X4X5-.gamma.-X6X7X8X9X10,.
18. The method of claim 17 further comprising the step of determining if the binding affinity of the polyamide to the identified sequence is subnanomolar.
19. The method of claim 17 further comprising the step of determining if the sequence specificity of the polyamide is greater or equal to ten.
20. The method of claim 17 further comprising the step of replacing at least one pyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X4, X7, X8, and X9.
21. The method of claim 17 further comprising the step of replacing at least one 3-hydroxypyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X4, X7, X8, and X9.
22. A polyamide composition produced by the method of claim 17.
23. A polyamide composition produced by the method of claim 18.
24. A polyamide composition produced by the method of claim 19.
25. A polyamide composition produced by the method of claim 20.
26. A polyamide composition produced by the method of claim 21.
27. A method for designing a selective polyamide molecule X1X2X3X4X5X6-.gamma.-X7X8X9X10X11X12, wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, and X12, are carboxamide residues forming binding pairs X1/X12, X2/X11, X3/X10, X4/X9, X5/X8, and X6/X7, and .gamma. is .gamma.-aminobuytic acid or 2,4 diaminobutyric acid suitable for binding to a eight base pair sequence of the form 5'-WNNNNNNW-3' in the minor groove of double stranded DNA, comprising the steps of:
a. identifying a eight base pair sequence of double stranded DNA having the form 5'-WNNNNNNW-3', wherein W is either A or T, NNNNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdefW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, d is a fourth nucleotide to be bound by a carboxamide residue, a is a fifth nucleotide to be bound by a carboxamide residue and f is a sixth nucleotide to be bound by a carboxamide residue;
e. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X12 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X10 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X12 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X12 carboxamide residue if a=A;
h. defining b as A, G, C; or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X11 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X11 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X11 carboxamide residue if b=T;
l. selecting Py as the X2 carboxamide residue and Hp as the X11 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X10 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X10 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X10 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X10 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X9 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X9 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X9 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X9 carboxamide residue if d=A;
w. defining a as A, G, C, or T to correspond to the fifth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
x. selecting Im as the X5 carboxamide residue and Py as the X8 carboxamide residue if e=G;
y. selecting Py as the X5 carboxamide residue and Im as the X8 carboxamide residue if e=C;
z. selecting Hp as the X5 carboxamide residue and Py as the X8 carboxamide residue if e=T;
aa. selecting Py as the X5 carboxamide residue and Hp as the X8 carboxamide residue if e=A;
bb. defining f as A, G, C, or T to correspond to the sixth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
ec. selecting Im as the X6 carboxamide residue and Py as the X7 carboxamide residue if f=G;
dd. selecting Py as the X6 carboxamide residue and Im as the X7 carboxamide residue if f=C;
ee. selecting Hp as the X6 carboxamide residue and Py as the X7 carboxamide residue if f=T; and ff. selecting Py as the X6 carboxamide residue and Hp as the X7 carboxamide residue if f=A.
a. identifying a eight base pair sequence of double stranded DNA having the form 5'-WNNNNNNW-3', wherein W is either A or T, NNNNNN is the sequence to be bound by carboxamide residues, and each N is independently A, G, C, or T;
b. representing the identified sequence as 5'-WabcdefW-3', wherein a is a first nucleotide to be bound by a carboxamide residue, b is a second nucleotide to be bound by a carboxamide residue, c is a third nucleotide to be bound by a carboxamide residue, d is a fourth nucleotide to be bound by a carboxamide residue, a is a fifth nucleotide to be bound by a carboxamide residue and f is a sixth nucleotide to be bound by a carboxamide residue;
e. defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
d. selecting Im as the X1 carboxamide residue and Py as the X12 carboxamide residue if a=G;
e. selecting Py as the X1 carboxamide residue and Im as the X10 carboxamide residue if a=C;
f. selecting Hp as the X1 carboxamide residue and Py as the X12 carboxamide residue if a=T;
g. selecting Py as the X1 carboxamide residue and Hp as the X12 carboxamide residue if a=A;
h. defining b as A, G, C; or T to correspond to the second nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
i. selecting Im as the X2 carboxamide residue and Py as the X11 carboxamide residue if b=G;
j. selecting Py as the X2 carboxamide residue and Im as the X11 carboxamide residue if b=C;
k. selecting Hp as the X2 carboxamide residue and Py as the X11 carboxamide residue if b=T;
l. selecting Py as the X2 carboxamide residue and Hp as the X11 carboxamide residue if b=A;
m. defining c as A, G, C, or T to correspond to the third nucleotide to be bound by a carboxamide residue in the identified eight base pair sequence;
n. selecting Im as the X3 carboxamide residue and Py as the X10 carboxamide residue if c=G;
o. selecting Py as the X3 carboxamide residue and Im as the X10 carboxamide residue if c=C;
p. selecting Hp as the X3 carboxamide residue and Py as the X10 carboxamide residue if c=T;
q. selecting Py as the X3 carboxamide residue and Hp as the X10 carboxamide residue if c=A;
r. defining d as A, G, C, or T to correspond to the fourth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
s. selecting Im as the X4 carboxamide residue and Py as the X9 carboxamide residue if d=G;
t. selecting Py as the X4 carboxamide residue and Im as the X9 carboxamide residue if d=C;
u. selecting Hp as the X4 carboxamide residue and Py as the X9 carboxamide residue if d=T;
v. selecting Py as the X4 carboxamide residue and Hp as the X9 carboxamide residue if d=A;
w. defining a as A, G, C, or T to correspond to the fifth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
x. selecting Im as the X5 carboxamide residue and Py as the X8 carboxamide residue if e=G;
y. selecting Py as the X5 carboxamide residue and Im as the X8 carboxamide residue if e=C;
z. selecting Hp as the X5 carboxamide residue and Py as the X8 carboxamide residue if e=T;
aa. selecting Py as the X5 carboxamide residue and Hp as the X8 carboxamide residue if e=A;
bb. defining f as A, G, C, or T to correspond to the sixth nucleotide to be bound by a carboxamide residue in the eight base pair sequence identified sequence;
ec. selecting Im as the X6 carboxamide residue and Py as the X7 carboxamide residue if f=G;
dd. selecting Py as the X6 carboxamide residue and Im as the X7 carboxamide residue if f=C;
ee. selecting Hp as the X6 carboxamide residue and Py as the X7 carboxamide residue if f=T; and ff. selecting Py as the X6 carboxamide residue and Hp as the X7 carboxamide residue if f=A.
28. The method of claim 17 further comprising the step of synthesizing the polyamide X1X2X3X4X5X6-.gamma.-X7X8X9X10X11X12.
29. The method of claim 28 further comprising the step of determining if the binding affinity of the polyamide to the identified sequence is subnanomolar.
30. The method of claim 28 further comprising the step of determining if the sequence specificity of the polyamide is greater or equal to ten.
31. The method of claim 28 further comprising the step of replacing at least one pyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X4, X5, X8, X9, X10 and X11.
32. The method of claim 28 further comprising the step of replacing at least one 3-hydroxypyrrole residue with a .beta.-alanine residue at a position chosen from the group consisting of X2, X3, X4, X5, X8, X9, X10, and X11.
33. A polyamide composition produced by the method of claim 28.
34. A polyamide composition produced by the method of claim 29.
35. A polyamide composition produced by the method of claim 30.
36. A polyamide composition produced by the method of claim 31.
37. A polyamide composition produced by the method of claim 32.
38. A polyamide composition produced by the method of claim 2 wherein one carboxamide binding pair is .beta./.beta..
39. A polyamide composition produced by the method of claim 7 wherein one carboxamide binding pair is .beta./.beta..
40. A polyamide composition produced by the method of claim 17 wherein one carboxamide binding pair is .beta./.beta..
41. A selective polyamide according to claim 1 whereby the polyamide is of the formula:
or a pharmaceutically acceptable salt wherein:
R1 is chosen from H, NH2, SH, Cl, Br, F, N-acetyl, or N-formyl;
R2 is chosen from H, (CH2)m CH3, (CH2)m NH2, (CH2)m SH, (CH2)m OH, (CH2)m NR5 2, (CH2)m OR5, (CH2)m SR5, where R5 - (CH2)m CH3, (CH2)m NH2, (CH2)m SH, (CH2)m OH and m is an integer from 0 to 6;
R3 is chosen from H, NH2, OH, SH, Br, Cl, F, OMe, CH2OH, CH2SH, CH2NH2;
R4 is chosen from -NH(CH2)0-100NR6R7 or NH(CH2)p CO NH(CH2)0-100NR6R7 or NHR6 or NH(CH2)p CONHR6, where R6 and R7 are independently chosen from H, Cl, NO, N-acetyl, benzyl, C1-100 alkyl, C1-100 alkylamine, C1-100 alkyldiamine, C1-100 alkylcarboxylate, C1-100 alkenyl, a C1-100 alkynyl, or a C1-100L, where L
groups can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-.alpha.-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, an oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-.alpha.-tocopheral;
where X and Y are chosen from the group consisting of N, CH, COH, CCH3, CNH2, CCl, CF;
a is an integer having values of 0 or 1;
b is an integer ranging from 1 to 5 inclusive; and c is an integer value ranging from 2 to 10 inclusive.
or a pharmaceutically acceptable salt wherein:
R1 is chosen from H, NH2, SH, Cl, Br, F, N-acetyl, or N-formyl;
R2 is chosen from H, (CH2)m CH3, (CH2)m NH2, (CH2)m SH, (CH2)m OH, (CH2)m NR5 2, (CH2)m OR5, (CH2)m SR5, where R5 - (CH2)m CH3, (CH2)m NH2, (CH2)m SH, (CH2)m OH and m is an integer from 0 to 6;
R3 is chosen from H, NH2, OH, SH, Br, Cl, F, OMe, CH2OH, CH2SH, CH2NH2;
R4 is chosen from -NH(CH2)0-100NR6R7 or NH(CH2)p CO NH(CH2)0-100NR6R7 or NHR6 or NH(CH2)p CONHR6, where R6 and R7 are independently chosen from H, Cl, NO, N-acetyl, benzyl, C1-100 alkyl, C1-100 alkylamine, C1-100 alkyldiamine, C1-100 alkylcarboxylate, C1-100 alkenyl, a C1-100 alkynyl, or a C1-100L, where L
groups can be independently chosen from but is not limited to arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens to which an antibody binds, solid phase supports, oligodeoxynucleotide, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-.alpha.-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, an oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, (+)-.alpha.-tocopheral;
where X and Y are chosen from the group consisting of N, CH, COH, CCH3, CNH2, CCl, CF;
a is an integer having values of 0 or 1;
b is an integer ranging from 1 to 5 inclusive; and c is an integer value ranging from 2 to 10 inclusive.
42. The polyamide of claim 1 wherein the duplex DNA sequence is a regulatory sequence.
43. The polyamide of claim 1 wherein the duplex DNA sequence is a promoter sequence.
44. The polyamide of claim 1 wherein the duplex DNA sequence is a coding sequence.
45. The polyamide of claim 1 wherein the duplex DNA sequence is a non-coding sequence.
46. The polyamide of claim 1 wherein the binding of the carboxamide binding pairs to the identified target DNA sequence modulates the expression of a gene.
47. A composition conprising an effective amount of the polyamide of claim 1 and a pharmologically suitable excipient.
48. A diagnostic kit comprising the polyamide of claim 1.
Applications Claiming Priority (13)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| WOPCT/US97/03332 | 1997-02-20 | ||
| PCT/US1997/003332 WO1997030975A2 (en) | 1996-02-26 | 1997-02-20 | Method for the synthesis of poly-pyrrole and poly-imidazole carboxamides on a solid support |
| US4202297P | 1997-04-06 | 1997-04-06 | |
| US4344497P | 1997-04-08 | 1997-04-08 | |
| US60/043,444 | 1997-04-08 | ||
| US60/042,022 | 1997-04-16 | ||
| US08/837,524 | 1997-04-21 | ||
| US08/837,524 US6143901A (en) | 1996-07-31 | 1997-04-21 | Complex formation between dsDNA and pyrrole imidazole polyamides |
| US08/853,522 | 1997-05-08 | ||
| US08/853,522 US6635417B1 (en) | 1996-07-31 | 1997-05-08 | Complex formation between DSDNA and oligomer of cyclic heterocycles |
| PCT/US1997/012722 WO1998050582A1 (en) | 1997-05-08 | 1997-07-21 | COMPLEX FORMATION BETWEEN dsDNA AND OLIGOMER OF HETEROCYCLES |
| WOPCT/US97/12722 | 1997-07-21 | ||
| PCT/US1998/001714 WO1998037067A1 (en) | 1996-02-26 | 1998-01-29 | Design, synthesis and use of specific polyamide dna-binding ligands |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2281930A1 true CA2281930A1 (en) | 1998-08-27 |
Family
ID=27556423
Family Applications (3)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002281947A Abandoned CA2281947A1 (en) | 1997-02-20 | 1998-01-21 | Improved polyamides for binding in the minor groove of double stranded dna |
| CA002281930A Abandoned CA2281930A1 (en) | 1997-02-20 | 1998-01-29 | Design, synthesis and use of specific polyamide dna-binding ligands |
| CA002281948A Abandoned CA2281948A1 (en) | 1997-02-20 | 1998-02-13 | Inhibition of major groove dna binding proteins by modified polyamides |
Family Applications Before (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002281947A Abandoned CA2281947A1 (en) | 1997-02-20 | 1998-01-21 | Improved polyamides for binding in the minor groove of double stranded dna |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002281948A Abandoned CA2281948A1 (en) | 1997-02-20 | 1998-02-13 | Inhibition of major groove dna binding proteins by modified polyamides |
Country Status (1)
| Country | Link |
|---|---|
| CA (3) | CA2281947A1 (en) |
-
1998
- 1998-01-21 CA CA002281947A patent/CA2281947A1/en not_active Abandoned
- 1998-01-29 CA CA002281930A patent/CA2281930A1/en not_active Abandoned
- 1998-02-13 CA CA002281948A patent/CA2281948A1/en not_active Abandoned
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| Publication number | Publication date |
|---|---|
| CA2281947A1 (en) | 1998-08-27 |
| CA2281948A1 (en) | 1998-08-27 |
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