CA2398750A1 - Nucleozymes with endonuclease activity - Google Patents

Abstract

The present invention relates to enzymatic nucleic acid molecules, including ribozymes and nucleozymes (DNA catalysts, DNA enzymes), methods of synthesis , and uses thereof.

Description

DESCRIPTION
NUCLEOZYMES WITH ENDONUCLEASE ACTIVITY
Background of the Invention This patent application claims priority from Breaker et al., USSN
(60/193,646), filed March 31, 2000, entitled "NUCLEOZYMES WITH ENDONUCLEASE ACTIVITY" and from Breaker et al., USSN (60/181,360), filed February 8, 2000, entitled "NUCLEIC ACID
CATALYSTS WITH
ENDONUCLEASE ACTIVITY". These patent applications are hereby incorporated by reference herein in their entirety including the drawings.
This invention relates to nucleic acid molecules (nucleozymes), including deoxyribonucleic acid molecules, with catalytic activity and derivatives thereof.
The following is a brief description of enzymatic nucleic acid molecules. This summary is not meant to be complete but is provided only for understanding of the invention that follows. This summary is not an admission that all of the work described below is prior art to the claimed invention.
Enzymatic nucleic acid molecules are nucleic acid molecules capable of catalyzing one or more of a variety of reactions, including the ability to repeatedly cleave (multiple turnover) other separate nucleic acid molecules in a nucleotide base sequence-specific manner.
Such enzymatic nucleic acid molecules can be used, for example, to target virtually any RNA
transcript (Zaug et al., 324, Nature 429 1986; Cech, 260 JAMA 3030, 1988).
Because of their sequence-specificity, tans-cleaving enzymatic nucleic acid molecules show promise as therapeutic agents for human disease (Usman & McSwiggen, 1995 Ann.
Rep. Med.
Chem. 30, 285-294; Christoffersen and Marr, 1995 J. Med. Chem. 38, 2023-2037).
Enzymatic nucleic acid molecules can be designed to cleave specific RNA targets within the background of cellular RNA. Such a cleavage event renders the mRNA non-functional and abrogates protein expression from that RNA. In this manner, synthesis of a protein associated with a disease state can be selectively inhibited.

In general, enzymatic nucleic acids with RNA cleaving activity act by first binding to a target RNA. Such binding occurs through the target-binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA.
Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA
through complementary base pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA
target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.
Several approaches have been used to evolve new nucleic acid catalysts, for example, in vitro selection and/or in vitro evolution strategies (Orgel, 1979, Proc. R. Soc.
London, B 205, 435). These approaches have been used to evolve new nucleic acid catalysts capable of catalyzing a variety of reactions, such as cleavage and ligation of phosphodiester linkages and amide linkages, (Joyce, 1989, Gene, 82, 83-87; Beaudry et al., 1992, Science 257, 635-641; Joyce, 1992, Scientific American 267, 90-97; Breaker et al., 1994, TIBTECH 12, 268; Bartel et a1.,1993, Science 261:1411-1418;
Szostak, 1993, TIBS 17, 89-93; Kumar et al., 1995, FASEB .L, 9, 1183; Breaker, 1996, Curr. Op.
Biotech., 7, 442).
The development of ribozymes that are optimal for catalytic activity would contribute significantly to any strategy that employs RNA-cleaving ribozymes for the purpose of regulating gene expression. The hammerhead ribozyme, for example, functions with a catalytic rate (kcat) of ~l min-1 in the presence of saturating (10 mM) concentrations of Mg2+ cofactor.
However, the rate for this ribozyme in Mg2+ concentrations that are closer to those found inside cells (0.5 - 2 mM) can be 10- to 100-fold slower. In contrast, the RNase P holoenzyme can catalyze pre-tRNA cleavage with a kcat of ~30 min-1 under optimal assay conditions. An artificial 'RNA ligase' ribozyme has been shown to catalyze the corresponding self modification reaction with a rate of 100 min-1. In addition, it is known that certain modified hammerhead ribozymes that have substrate binding arms made of DNA catalyze RNA cleavage with multiple turn-over rates that approach 100 min-1.
Finally, replacement of a specific residue within the catalytic core of the hammerhead with certain nucleotide analogues gives modified ribozymes that show as much as a 10-fold improvement in catalytic rate. These findings demonstrate that ribozymes can promote chemical transformations with catalytic rates that are significantly greater than those displayed in vitro by most natural self cleaving ribozymes. It is then possible that the structures of certain self cleaving ribozymes may be optimized to give maximal catalytic activity, or that entirely new RNA motifs can be made that display significantly faster rates for RNA phosphodiester cleavage.
An extensive array of site-directed mutagenesis studies have been conducted with ribozymes such as the hammerhead ribozyme and the hairpin ribozyme to probe relationships between nucleotide sequence and catalytic activity. These systematic studies have made clear that most nucleotides in the conserved core of the ribozyme cannot be mutated without significant loss of catalytic activity. In contrast, a combinatorial strategy that simultaneously screens a large pool of mutagenized ribozymes for RNAs that retain catalytic activity could be used more efficiently to define immutable sequences and to identify new ribozyme variants.
Tang et al., 1997, RNA 3, 914, reported novel ribozyme sequences with endonuclease activity, where the authors used an in vitro selection approach to isolate these ribozymes.
Vaish et al., 1998 PNAS 95, 2158-2162, describes the in vitro selection of a hammerhead-like ribozyme with an extended range of cleavable triplets.
Breaker, International PCT publication No. WO 98/43993, describes the in vitro selection of hammerhead-like ribozymes with sequence variants encompassing the catalytic core.
Catalytic nucleic acid molecules until recently were all known to require the presence of 2'-hydroxyl (2'-OH) groups within the molecule for their enzymatic function.
Usman and co-workers recently reported that nucleic acid molecules lacking a 2'-hydroxyl group, such as DNA molecules, can catalyze a chemical reaction (Chartrand et al., 1995, Nucleic Acids Research, 23(20), 4092-4096; Usman et al., US Patent No. 5,861,288). There have also been several reports of non-2'-OH
containing nucleic acid molecules that are capable of catalyzing chemical reactions (Li and Breaker, 1999, Cur. Opin. Struct. Biol., 9, 315-323; Breaker, 1999, Nature Biotechnology, 17, 422-423). The use of in vitro selection and/or in vitro evolution techniques applied to random pools of single-stranded DNA has provided catalytic DNA, or deoxyribozymes, capable of catalyzing the cleavage of RNA (Usman et al., US Patent No. 5,861,288; Breaker and Joyce, 1994, Chem.
Biol., 1, 223-229;
Breaker and Joyce, 1995, Chem. Biol., 655-660), facilitation of the ligation of chemically activated DNA (Cuenoud and Szostak, 1995, Nature, 375, 611-614), and the metallation of porphyrin rings (Li and Sen, 1996, Nat. Struct. Biol., 3, 743-747).

The cleavage of RNA by transesterification via catalytic DNA structures is often dependant on metal ion cofactors, such as Mg2+, Mn2+, Zn2+, pb2+, Ca2+, and Cd2+, or an amino acid cofactor such as histidine (Roth and Breaker, 1998, PNAS USA., 95, 6027-6031). However, the native structure of DNA alone may be sufficient in providing the chemical groups that are responsible for catalysis (Geyer and Sen, 1997, Chem. Biol., 4, 579-593).
Joyce and Breaker, US Patent No. 5,807,718, describe specific magnesium dependent RNA
cleaving DNA enzymes with defined structural and target sequence constraints.
Summary of the Invention This invention relates to nucleic acid molecules with catalytic activity, which are particularly useful for cleavage of RNA or DNA. The nucleic acid catalysts of the instant invention are distinct from other nucleic acid catalysts known in the art. The nucleic acid catalysts of the instant invention do not share sequence homology with other known enzymatic nucleic acid molecules, such as other known DNA enzymes. Specifically, the nucleic acid catalysts of the instant invention are capable of catalyzing an intermolecular or intramolecular endonuclease reaction.
In a preferred embodiment, the invention features a nucleic acid molecule with catalytic activity having either the formulae I or II:
Formula I
3' X Z Y 5' Formula II
3' X W V R Y 5' In the above formulae I and II, X and Y are independently oligonucleotides of length sufficient to stably interact (e.g., by forming hydrogen bonds with complementary nucleotides in the target) with a target nucleic acid molecule (the target can be an RNA, DNA or RNA/DNA
mixed polymers, including polymers that may include base, sugar, and/or phosphate nucleotide modifications; such 5 modifications are preferably naturally occurring modifications), preferably, the length of X and Y
are independently between 3-20 nucleotides long, e.g., specifically, 3, 4, S, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, and 20); X and Y may have the same lengths or may have different lengths;
represents a chemical linkage (e.g. a phosphate ester linkage, amide linkage or others known in the art); Z is independently a nucleotide sequence comprising 5'-GATGCAGCTGGGGAGGCGTTT-3' (SEQ ID NO 103), R is independently a nucleotide sequence comprising 5'-GGGGA-3', V
represents a nucleotide or non-nucleotide linker, which may be present or absent, (i.e., the molecule is assembled from two separate molecules), but when present, is a nucleotide and/or non-nucleotide linker, which may comprise a single-stranded and/or double-stranded region; W
is independently a nucleotide sequence selected from the group comprising 5'-TGGGGAAGCACAGGGT-3' (SEQ ID
NO 104), 5'-TGGGGAAGCTCTGGGT-3' (SEQ ID NO 105), 5'-TGGGGAAGCACAGGGT-3' (SEQ ID NO 106), and 5'-TGGGGAAGCACATGGT-3' (SEQ ID NO 107); additions, deletions, and substitutions to these sequences may be made without significantly altering the activity of the molecules and are hence within the scope of the invention; and C, G, A, and T
represent cytidine, guanosine, adenosine and thymidine nucleotides, respectively. The nucleotides in each of the formulae I and II are unmodified or modified at the sugax, base, and/or phosphate as known in the art.
In a preferred embodiment, the nucleotide linker (V) is a nucleic acid sequence selected from the group consisting of 5'-ACCTGAGGG-3', 5'-GCGTTAG-3' and 5'-AGGAAGCATCTTATGCGACC-3' (SEQ ID NO 108).
The nucleotide linker V is preferably 5-40 nucleotides in length, more preferably 7-20 nucleotides in length and still more preferably 7-12 nucleotides in length.
In yet another embodiment, the nucleotide linker (V) is a nucleic acid aptamer, such as an ATP aptamer, HIV Rev aptamer (RRE), HIV Tat aptamer (TAR) and others (for a review, see Gold et al., 1995, Annu. Rev. Biochem., 64, 763; and Szostak & Ellington, 1993, in The RNA World, ed.
Gesteland and Atkins, pp. 511, CSH Laboratory Press). A "nucleic acid aptamer"
as used herein is meant to indicate a nucleic acid sequence capable of interacting with a ligand. The ligand can be any natural or synthetic molecule, including but not limited to a resin, metabolites, nucleosides, nucleotides, drugs, toxins, transition state analogs, peptides, lipids, proteins, amino acids, nucleic acid molecules, hormones, carbohydrates, receptors, cells, viruses, bacteria and others.
In another embodiment, the non-nucleotide linker (V) is as defined herein. The term "non-nucleotide" as used herein includes either abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, or polyhydrocarbon compounds. These compounds can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base, such as adenine, guanine, cytosine, uracil or thymine. The terms "abasic" or "abasic nucleotide" as used herein encompass sugar moieties lacking a base or having other chemical groups in place of a nucleotide base at the 1' position. Specific examples of non-nucleotides include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res.
1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991, 113:6324; Richardson and Schepartz, J.
Am. Chem. Soc.
1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751;
Durand et al., Nucleic Acids Res. 1990, 18:6353; McCurdy et al., Nucleosides &
Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914;
Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO 95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000, all hereby incorporated by reference herein. Thus, in a preferred embodiment, the invention features an enzymatic nucleic acid molecule having one or more non-nucleotide moieties, and having enzymatic activity to cleave an RNA
or DNA molecule.
By 'nucleozyme' or 'DNA enzyme' or 'DNAzyme' or "deoxyribozyme" as used herein is meant, an enzymatic nucleic acid molecule that does not require the presence of a ribonucleotide (2'-OH) group in the molecule for its activity. These molecules are also referred to as catalytic DNA, nucleic acid catalysts, restriction endonucleases, catalytic oligonucleotides, and enzymatic DNA
molecules. In particular embodiments, the enzymatic nucleic acid molecule may have an attached linkers) or other attached or associated groups, moieties, or chains containing one or more nucleotides with 2'-OH groups. DNAzymes can be synthesized chemically or expressed endogenously in vivo, by means of a single stranded DNA vector or equivalent thereof.

By "enzymatic nucleic acid molecule" it is meant a nucleic acid molecule which has complementarity in a substrate binding region to a specified gene target, and also has an enzymatic activity which is active to specifically cleave target RNA. That is, the enzymatic nucleic acid molecule is able to intermolecularly cleave RNA and thereby inactivate a target RNA molecule.
These complementary regions allow sufficient hybridization of the enzymatic nucleic acid molecule to the target RNA and thus permit cleavage. One hundred percent complementarity is preferred, but complementarity as low as 50-75% can also be useful in this invention (see for example Werner and Uhlenbeck, 1995, Nucleic Acids Research, 23, 2092-2096; Hammann et al., 1999, Antisense and Nucleic Acid Drug Dev., 9, 25-31). The nucleic acids can be modified at the base, sugar, and/or phosphate groups.
The enzymatic nucleic acid molecule (e.g., the molecules of formulae I and II) of the instant invention are capable of catalyzing (altering the velocity and/or rate of) a variety of reactions including the ability to repeatedly cleave (multiple turnover) other separate nucleic acid molecules (endonuclease activity) in a nucleotide base sequence-specific manner. Such a molecule with endonuclease activity may have complementarity in a substrate binding region (e.g. X and Y in formulae I and II) to a specified gene target, and has an enzymatic activity that specifically cleaves RNA or DNA in that target. That is, the nucleic acid molecule with endonuclease activity is able to intramolecularly or intermolecularly cleave RNA or DNA and thereby inactivate a target RNA or DNA molecule. The complementarity functions to allow sufficient hybridization of the enzymatic DNA molecule to the target RNA or DNA to allow the cleavage to occur. 100%
complementarity is preferred, but complementarity as low as 50-75% may also be useful in this invention. The nucleic acids can be modified at the base, sugar, and/or phosphate groups. All that is required, as will be readily recognized by persons skilled in the art, is that the enzymatic nucleic acid molecule not be dependent on the presence of a ribonucleotide in the molecule for its catalytic activity.
In preferred embodiments, the enzymatic nucleic acids of formulae I and II
includes one or more stretches of non-ribonucleotide containing oligonucleotide, which provide the enzymatic activity of the molecule. The necessary non-ribonucleotide components are known in the art.
Thus, in one preferred embodiment, the invention features DNA enzymes that inhibit gene expression and/or cell proliferation. These chemically or enzymatically synthesized nucleic acid molecules contain substrate binding domains that bind to accessible regions of specific target nucleic acid molecules. The nucleic acid molecules also contain domains that catalyze the cleavage of target. Upon binding, the enzymatic nucleic acid molecules cleave the target molecules, preventing, for example, translation and protein accumulation. In the absence of the expression of the target gene, cell proliferation, for example, is inhibited. In another aspect of the invention, enzymatic nucleic acid molecules that cleave target molecules are expressed from a single stranded DNA intracellular expression vector. Preferably, the vectors capable of expressing the DNA
enzymes are delivered as described below, and persist in target cells.
Suitable vectors can be used that provide for transient expression of DNA enzymes. Such vectors can be repeatedly administered as necessary. Once expressed, the DNA enzymes cleave the target mRNA. Delivery of DNA
enzyme expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that would allow for introduction into the desired target cell (for a review, see Couture and Stinchcomb, 1996, TIG., 12, 510).
In a preferred embodiment, the invention features a nucleic acid molecule with catalytic activity having either the formulae III and IV:
Formula III
~ (N)n U G D X 3' (N)m A G A - (N)D (N)p Y 5 \/
Formula IV
3' X Z Y 5' In the above formulae III and IV, each N represents independently a nucleotide or a non-nucleotide linker, which can be same or different; X and Y are independently oligonucleotides of length sufficient to stably interact (e.g., by forming hydrogen bonds with complementary nucleotides in the target) with a target nucleic acid molecule (the target can be an RNA, DNA or RNA/DNA
mixed polymers, including polymers that can include base, sugar, and/or phosphate nucleotide modifications; such modifications are preferably naturally occurnng modifications), preferably, the length of X and Y are independently between 3-20 nucleotides long, e.g., specifically, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, and 20); X and Y can have the same lengths or can have different lengths; m, n, o, and p are integers independently greater than or equal to 1 and preferably less than about 100, specifically 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 50;
wherein if (I~m and (N)n and/or (N)o and (N)p are nucleotides, (lam and (N)n and/or (loo and (I~p are optionally able to interact by hydrogen bond interaction; preferably, (N)m and (l~n and/or (loo and (N)p independently form 1, 2, 3, 4, 5, 6, 7, 8, 9 base-paired stem structures; D is U, G or A; L~ and L2 are independently linkers, which can be the same or different and which can be present or absent (i.e., the molecule is assembled from two separate molecules), but when present, are nucleotide and/or non-nucleotide linkers, which can comprise a single-stranded and/or double-stranded region;
represents a chemical linkage (e.g. a phosphate ester linkage, amide linkage or others known in the art); ~ represents a base-pair interaction; Z is independently a nucleotide sequence selected from the group comprising 5'-AGAUAACGUGAAGAU-3' (SEQ ID NO 109) and 5'-AAUGGCCUAUCGGUGCGA-3' (SEQ ID NO 110), additions, deletions, and substitutions to these sequences can be made without significantly altering the activity of the molecules and are hence within the scope of the invention; and C, G, A, and U represent cytidine, guanosine, adenosine and uridine nucleotides, respectively. The nucleotides in each of the formulae III
and IV are unmodified or modified at the sugar, base, and/or phosphate as known in the art.
In a preferred embodiment, the invention features nucleic acid molecules of Formula III, where the sequence of oligonucleotide (N)m is selected from the group consisting of 5'-AC-3', 5'-GC-3', and 5'-CG-3'.
In another preferred embodiment, the invention features nucleic acid molecules of Formula III, where the sequence of oligonucleotide (N)n is selected from the group consisting of 5'-GU-3', 5'-GC-3', and. 5'-CG-3'.

In yet another preferred embodiment, the invention features nucleic acid molecules of Formula III, where the sequence of oligonucleotide (N)o is selected from the group consisting of 5'-AUUG-3', 5'-UUG-3', 5'-UUC-3', and 5'-UAG-3'.
In an additional preferred embodiment, the 'nvention features nucleic acid molecules of 5 Formula III, where the sequence of oligonucleotide (N)p is selected from the group consisting of 5' CAAU-3', 5'-CAA-3', 5'-GAA-3', and 5'-CUA-3'.
In another embodiment, the nucleotide linker (L~) is a nucleic acid sequence selected from the group consisting of 5'-CUUAA-3' and 5'-CUAAA-3'.
In another embodiment, the nucleotide linker (L2) is a nucleic acid sequence selected from the 10 group consisting of 5'-UGUGAA-3' and 5'-GUGA-3'.
In yet another embodiment, the nucleotide linker (L~ and/or L2) is a nucleic acid aptamer, such as an ATP aptamer, HIV Rev aptamer (RRE), HIV Tat aptamer (TAR) and others (for a review see Gold et al., 1995, Annu. Rev. Biochem., 64, 763; and Szostak & Ellington, 1993, in The RNA
World, ed. Gesteland and Atkins, pp. 511, CSH Laboratory Press). A "nucleic acid aptamer" as used herein is meant to indicate a nucleic acid sequence capable of interacting with a ligand. The ligand can be any natural or synthetic molecule, including but not limited to a resin, metabolites, nucleosides, nucleotides, drugs, toxins, transition state analogs, peptides, lipids, proteins, amino acids, nucleic acid molecules, hormones, carbohydrates, receptors, cells, viruses, bacteria and others.
In another embodiment, the non-nucleotide linker (L~ and/or L2) is as defined herein. The term "non-nucleotide" as used herein include either abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, or polyhydrocarbon compounds. These compounds can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base, such as adenine, guanine, cytosine, uracil or thymine. The terms "abasic" or "abasic nucleotide" as used herein encompass sugar moieties lacking a base or having other chemical groups in place of a nucleotide base at the 1' position. Specific examples of non-nucleotides include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res. 1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991,113:6324; Richardson and Schepartz, J. Am.
Chem. Soc. 1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751; Durand et al., Nucleic Acicls Res. 1990, 18:6353; McCurdy et al., Nucleosides &
Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914; Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO
95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000, all hereby incorporated by reference herein. Thus, in a preferred embodiment, the invention features an enzymatic nucleic acid molecule having one or more non-nucleotide moieties, and having .enzymatic activity to cleave an RNA or DNA molecule.
In preferred embodiments, the enzymatic nucleic acids of formulae III and IV
includes one or more stretches of RNA, which provide the enzymatic activity of the molecule, linked to the non-nucleotide moiety. The necessary RNA components are known in the art (see for e.g., Usman et al., supra).
Thus, in one preferred embodiment, the invention features ribozymes that inhibit gene expression and/or cell proliferation. These chemically or enzymatically synthesized nucleic acid molecules contain substrate binding domains that bind to accessible regions of specific target . nucleic acid molecules. The nucleic acid molecules also contain domains that catalyze the cleavage of target. Upon binding, the enzymatic nucleic acid molecules cleave the target molecules, preventing, for example, translation and protein accumulation. In the absence of the expression of the target gene, cell proliferation, for example, is inhibited. In another aspect of the invention, enzymatic nucleic acid molecules that cleave target molecules are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors are preferably DNA
plasmids or viral vectors. Ribozyme expressing viral vectors could be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. Preferably, the recombinant vectors capable of expressing the ribozymes are delivered as described below, and persist in target cells.
Alternatively, viral vectors can be used that provide for transient expression of ribozymes. Such vectors can be repeatedly administered as necessary. Once expressed, the ribozymes cleave the target mRNA. Delivery of ribozyme expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that would allow for introduction into the desired target cell (for a review, see Couture and Stinchcomb, 1996, TIG., 12, 510).

"Complementarity" refers to the ability of a nucleic acid to form hydrogen bonds) with another RNA sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules of the present invention, the binding free energy for a nucleic acid molecule with its target or complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., cleavage via a DNAzyme. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant.
Biol. LII pp.123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785). A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). "Perfectly complementary" means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence.
By "sufficient length" is meant an oligonucleotide of greater than or equal to 3 nucleotides that is of a length great enough to provide the intended function under the expected condition. For example, for binding arms of enzymatic nucleic acid "sufficient length" means that the binding arm sequence is long enough to provide stable binding to a target site under the expected binding conditions. Preferably, the binding arms are not so long as to prevent useful turnover of the nucleic acid molecule.
By "stably interact" is meant interaction of the oligonucleotides with target nucleic acid (e.g., by forming hydrogen bonds with complementary nucleotides in the target under physiological conditions) that is sufficient to the intended purpose (e.g., cleavage of target RNA by an enzyme).
By "inhibit" it is meant that the activity of a given protein or level of RNAs or equivalent RNAs encoding one or more protein subunits of a given protein target is reduced below that observed in the absence of the nucleic acid molecules of the invention. In one embodiment, inhibition with enzymatic nucleic acid molecule preferably is below that level observed in the presence of an enzymatically inactive or attenuated molecule that is able to bind to the same site on the target RNA, but is unable to cleave that RNA. In another embodiment, inhibition of target genes with the nucleic acid molecule of the instant invention is greater than in the presence of the nucleic acid molecule than in its absence.

By "nucleic acid molecule" as used herein is meant a molecule having nucleotides. The nucleic acid can be single, double, or multiple stranded and may comprise modified or unmodified nucleotides or non-nucleotides or various mixtures and combinations thereof.
By "gene" it is meant a nucleic acid that encodes an RNA, for example, nucleic acid sequences including but not limited to structural genes encoding a polypeptide.
By "RNA" is meant a molecule comprising at least one ribonucleotide residue.
By "ribonucleotide" is meant a nucleotide with a hydroxyl group at the 2' position of a beta-D-ribo-furanose moiety.
As used in herein "cell" is used in its usual biological sense, and does not refer to an entire multicellular organism, e.g., specifically does not refer to a human. The cell may be present in an organism which may be a human but is preferably a non-human multicellular organism, e.g., birds, plants and mammals such as cows, sheep, apes, monkeys, swine, dogs, and cats.
The cell may be prokaryotic (e.g., bacterial cell) or eukaryotic (e.g., mammalian or plant cell).
By "patient" is meant an organism which is a donor or recipient of explanted cells or the cells themselves. "Patient" also refers to an organism to which enzymatic nucleic acid molecules can be administered. Preferably, a patient is a mammal or mammalian cells. More preferably, a patient is a human or human cells.
By "vectors" is meant any nucleic acid- and/or viral-based technique used to deliver a desired nucleic acid.
In another preferred embodiment, catalytic activity.of the molecules described in the instant invention can be optimized. Modifications which enhance their efficacy in cells, and removal of bases from stem loop structures to shorten enzymatic nucleic acid molecule synthesis times and reduce chemical requirements are desired. Catalytic activity of the molecules described in the instant invention can be optimized as described by Usman et al., US Patent No.
5,861,288. The details will not be repeated here, but include altering the length of the enzymatic nucleic acid molecule binding arms, or chemically synthesizing enzymatic nucleic acid molecules with modifications (base, sugar and/or phosphate) that prevent their degradation by serum nucleases and/or enhance their enzymatic activity (see e.g., Eckstein et al., International Publication No. WO
92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991 Science 253, 314; Usman and Cedergren, 1992 Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO
93/1 S 187; and Rossi et al., International Publication No. WO 91/03162;
Sproat, US Patent No.
5,334,711; and Burgin et al., supra; all of these describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of enzymatic nucleic acid molecules). All these publications are hereby incorporated by reference herein.
By "enhanced enzymatic activity" is meant to include activity measured in cells and/or in vivo where the activity is a reflection of both catalytic activity and enzymatic nucleic acid molecule stability.
In yet another preferred embodiment, nucleic acid catalysts having chemical modifications which maintain or enhance enzymatic activity are provided. Such nucleic acid is also generally more resistant to nucleases than unmodified nucleic acid. Thus, in a cell and/or in vivo the activity may not be significantly lowered. As exemplified herein such enzymes are useful in a cell and/or in vivo even if activity over all is reduced 10-fold (Burgin et al., 1996, Biochemistry, 35, 14090).
In a preferred embodiment, the invention provides a method for producing a class of enzymatic nucleic acid molecule-based gene inhibiting agents which exhibit a high degree of specificity for the RNA of a desired target. For example, the enzymatic nucleic acid molecule is preferably targeted to a highly conserved sequence region of target RNAs encoding target proteins such that specific treatment of a disease or condition can be provided with either one or several nucleic acid molecules of the invention. Such nucleic acid molecules can be delivered exogenously to specific tissue or cellular targets as required. Alternatively, the nucleic acid molecules (e.g., DNA
enzymes) can be expressed from single stranded DNA expression vectors that are delivered to specific cells.
In a preferred embodiment, an expression vector comprising a nucleic acid sequence encoding at least one of the nucleic acid catalysts of the instant invention is disclosed. The nucleic acid sequence encoding the nucleic acid catalyst of the instant invention is operable linked in a manner which allows expression of that nucleic acid molecule.
In one embodiment, the expression vector comprises: a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); c) a nucleic acid sequence encoding at least one of the nucleic acid catalyst of the instant invention; and wherein said sequence is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. The vector may optionally include'an open reading frame (ORF) for a protein operably linked on the S' side or the 3'-side of the sequence encoding the nucleic acid catalyst of the invention; and/or an intron (intervening sequences).
5 Another means of accumulating high concentrations of a ribozyme(s) within cells is to incorporate the ribozyme-encoding sequences into a DNA or RNA expression vector. Transcription of the ribozyme sequences are driven from a promoter for eukaryotic RNA
polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III
promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given 10 cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990 Proc. Natl. Acad. Sci. U S A, 87, 6743-7; Gao and Huang 1993 Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993 Methods Enzymol., 217, 47-66; Zhou et al., 1990 Mol.
Cell. Biol., 10, 4529-15 37). Several investigators have demonstrated that ribozymes expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992 Antisense Res.
Dev., 2, 3-15; Ojwang et al., 1992 Proc. Natl. Acad. Sci. U S A, 89, 10802-6; Chen et al., 1992 Nucleic Acids Res., 20, 4581-9; Yu et al., 1993 Proc. Natl. Acad. Sci. U S A, 90, 6340-4; L'Huillier et al., 1992 EMBO J.
11, 4411-8; Lisziewicz et al., 1993 Proc. Natl. Acad. Sci. U. S. A., 90, 8000-4;Thompson et al., 1995 Nucleic Acids Res. 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566).
The above ribozyme transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).
By "highly conserved sequence region" is meant, a nucleotide sequence of one or more regions in a target gene does not vary significantly from one generation to the other or from one biological system to the other.
The nucleic acid-based inhibitors of the invention are added directly, or can be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complexes can be locally administered to relevant tissues ex vivo, or in vivo through injection, infusion pump or stmt, with or without their incorporation in biopolymers.
In another aspect, the invention provides mammalian cells containing one or more nucleic acid molecules and/or expression vectors of this invention. The one or more nucleic acid molecules can independently be targeted to the same or different sites.
By "comprising" is meant including, but not limited to, whatever follows the word "comprising". Thus, use of the term "comprising" indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present.
By "consisting of is meant including, and limited to, whatever follows the phrase "consisting of'. Thus, the phrase "consisting of indicates that the listed elements are required or mandatory, and that no other elements may be present.
Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.
Description of the Preferred Embodiments The drawings will first briefly be described.
Drawings:
Figure 1 is a diagram that shows the construct on which the DNA enzyme selection is based.
Capital letters indicate the four standard DNA bases and RNA bases (reverse type) in regions of the molecular library which were constant among all molecules. These regions provided the RNA
substrate, positioned the random region adjacent to the substrate by base-pairing and allowed manipulation of the library during selection using standard methods. Catalytic sequences were derived from the region of 50 nucleotides, imbedded between the constant regions, synthesized to contain random DNA sequences. Molecules were selected on the basis of their ability to self cleave at an RNA residue. Molecules were reacted in solution in a buffer which approximated the composition of Escherichia coli cytoplasm with respect to conditions expected to be relevant to RNA cleavage Figure 2 is a diagram that shows a non-limiting secondary-structure model for Clone 27 of a class I DNA enzyme of the instant invention. The secondary structure shown in Figure 2a is based on the region of conserved nucleotides underlined in Table 2 with base pairing restored at the 3' end of the catalyst. The Ka for this enzyme interacting with substrate is 5 pM.
The enzyme does not require glutathione but does lose 10-fold activity in the absence of putrescine. Its pKa is ~ 7.9, reaching a maximum pseudo first order rate constant in 0.5 mM Mg2+ of 0.06 miri'. The enzyme also cleaves the in vitro transcribed target shown in Figure 2b, demonstrating that it does not require DNA residues in the substrate and can be generalized by changing the substrate binding arms.
Figure 3 is a diagram showing a non-limiting secondary structure model for clone 37 of a class II DNA enzyme of the instant invention.
Figure 4 is a diagram that shows a selection scheme for the isolation of self cleaving DNA
enzymes from a random-sequence DNA population.
Figure 5 is a diagram that shows the substrate sequence requirements of Class I motif nucleozymes of the invention.
Figure 6 is a diagram that shows the kinetic parameters of a Class I motif nucleozyme of the invention.
Figure 7 is a diagram showing proposed secondary structures of Class IV and Class V trans-cleaving nucleozymes of the invention.
Figure 8A is a diagram that shows a selection scheme for the isolation of self cleaving ribozymes from a random-sequence RNA population. (I) RNAs are incubated under permissive reaction conditions. (II) The 5' fragments of cleaved RNAs are separated from uncleaved precursors by denaturing 10% PAGE and recovered by crush/soaking from the appropriate gel section. (III) The recovered RNA fragments are amplified by RT-PCR, which introduces a T7 promoter sequence and restores the nucleotides that were lost upon ribozyme cleavage. The resulting double-stranded DNAs are transcribed by T7 RNAP to generate the subsequent population of RNAs.
Figure 8B is a diagram of the RNA construct used to initiate the in vitro selection process. N4°
depicts 40 random-sequence positions. Underlined nucleotides identify the region that represents all 16 possible nearest neighbor combinations.

Figure 9 is a diagram that shows non-limiting secondary-structure models for different classes of self cleaving ribozymes of this invention. For each class (I-XII), the generation of its first appearance in the selection process (see Figure 8) is encircled. In addition, the cleavage sites (arrowheads) and observed rate constants are given for all RNA constructs as depicted. In some cases, secondary-structure models are based on artificial phylogenetic data (e.g. see Table 11) or otherwise reflect the most stable structure predicted by the Zuker RNA mfold program that is accessible on the Internet (www.ibc.wustl.edu/~mfold/rna/forml.c~i ). Putative Watson/Crick base pairing interactions are represented by dashes and putative G~U wobble interactions are represented by dots. Note that classes VI and VII were examined as unimolecular constructs. No reasonable secondary-structure model was established for class VII ribozymes. In this case, the boxed regions identify variable (shaded) or conserved nucleotides that reside in the original random-sequence domain. The nucleotides of the hammerhead ribozyme (class VIII) are numbered according to the system suggested by Hertel et al. (Hertel et al., 1992, Nucleic Acids Research, 20, 3252).
Figure 10A is a diagram showing cleavage reaction profiles for bimolecular class I (open circles) and class II (filled circles) ribozymes as depicted in Figure 9 under the permissive reaction conditions. Observed rate constants for class I and class II ribozymes are 0.01 and 0.05 miri', respectively, as determined by the negative slope of the lines. Figure lOB
shows a compilation of the cleavage sites of the 12 classes of ribozymes. Numbers identify the nucleotides within the nearest-neighbor domain depicted in Figure 8B.
Figure 11 shows a comparison of the secondary structures of two hammerhead ribozymes and the dominant X motif. Figure 11A is a diagram of two distinct versions (i and ii) of the hammerhead ribozyme which were isolated and examined for catalytic activity with S21 substrate. Both variants retain the highly conserved catalytic core, which is known to tolerate sequence variation only at position 7 (Tang and Breaker, 1997, RNA, 3, 914-925). Stem elements and nucleotides in (~ are numbered according to the nomenclature defined by Hertel et al. (Hertel et al., supra). Figure 11B
shows the dominant unimolecular construct isolated after a total of 25 rounds of in vitro selection conforms to the X-motif (class I) class of self cleaving ribozymes. This self cleaving ribozyme can be reorganized into a bimolecular format wherein separate substrate RNAs (S21) are cleaved by a 43-nt enzyme domain, the latter which encompasses all highly conserved nucleotides that were identified during reselection (Table 11). Enzyme-substrate interactions result from the formation of two (stems I and IV) of the four putative helical regions that define the motif. Arrowheads identify the sites of ribozyme-mediated cleavage.
Figure 12 is a demonstration of cleavage site versatility of the X motif ribozyme. Figure 12 shows three different 43-nt RNAs carrying the conserved core of the X motif class of ribozymes were generated by in vitro transcription such that each differed in the base pairing potential of binding arms I and IV. Specifically, ribozyme X-E1 is engineered to form eight base pairs that flank both the 5' and 3' sides of an unpaired G reside. The lines represent nucleotides within binding arms I and IV that are complementary to the X-E1 target site (depicted by the arrow). Similarly, ribozymes X-E2 and X-E3 carry the corresponding binding arm sequences that allow base pairing only with their corresponding target sites. Base pairing interactions are depicted by dashes.
Figure 13 is a representative diagram of a Class V ribozyme motif which shows the effect of sequential 2'-O-methyl substitutions on Kobs in the ribozyme core. Figure 13 also shows a typical site of substrate cleavage for the Class V ribozyme as well as the numbering system used in this application for describing modifications to this class of ribozyme as described in Tables VI-IX.
Figure 14 is a representative diagram of structural similarities between Class I (SEQ ID NO
146), (substrate SEQ ID NO 147) and Class VIII (SEQ ID NO 148), (substrate SEQ
m NO 149) enzymatic nucleic acid molecules of the invention.
Figure 15 is a comparison of the kinetic characteristics of the Class I and Class VIII
enzymatic nucleic acid molecules of the invention. (A) Saturation of substrate with enzymes based on Class I motif and Class VIII motif enzymes, respectively. (B) Influence of monovalent ions on ribozyme activity. (C) Magnesium dependence of each ribozyme. Reactions were conducted in 50 mM Tris-HC1 (pH 7.5 at 23°C), and 20 mM magnesium chloride unless otherwise indicated.
Nucleic Acid Catalysts The invention provides nucleic acid catalysts and methods for producing a class of enzymatic nucleic acid cleaving agents which exhibit a high degree of specificity for the nucleic acid sequence of a desired target. The enzymatic nucleic acid molecule is preferably targeted to a highly conserved sequence region of a target such that specific diagnosis and/or treatment of a disease or condition in a variety of biological systems can be provided with a single enzymatic nucleic acid. Such enzymatic nucleic acid molecules can be delivered exogenously to specific cells as required. In the preferred Class I and II motifs, the small size (less than 60 nucleotides, preferably between 25-40 nucleotides in length) of the molecule allows the cost of treatment to be reduced.
By "nucleic acid catalyst" as used herein is meant a nucleic acid molecule (e.g., the molecules of formulae I, II, III and IV), capable of catalyzing (altering the velocity and/or rate of) a variety of 5 reactions including the ability to repeatedly cleave other separate nucleic acid molecules (endonuclease activity) in a nucleotide base sequence-specific manner. Such a molecule with endonuclease activity may have complementarity in a substrate binding region (e.g. X and Y in formulae I, II, III, and IV) to a specified gene target, and also has an enzymatic activity that specifically cleaves RNA or DNA in that target. That is, the nucleic acid molecule with 10 endonuclease activity is able to intramolecularly or intermolecularly cleave RNA or DNA and thereby inactivate a target RNA or DNA molecule. This complementarity functions to allow sufficient hybridization of the enzymatic RNA molecule to the target RNA or DNA to allow the cleavage to occur. 100% complementarity is preferred, but complementarity as low as 50-75% may also be useful in this invention. The nucleic acids may be modified at the base, sugar, and/or 15 phosphate groups. The term enzymatic nucleic acid is used interchangeably with phrases such as ribozymes, catalytic RNA, enzymatic RNA, catalytic DNA, nucleozyme, RNA
enzyme, endoribonuclease, endonuclease, minizyme, oligozyme, finderon or nucleic acid catalyst. All of these terminologies describe nucleic acid molecules with enzymatic activity.
The specific examples of enzymatic nucleic acid molecules described in the instant application are not limiting in the 20 invention and those skilled in the art will recognize that all that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target nucleic acid regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart a nucleic acid cleaving activity to the molecule.
In preferred embodiments of the present invention, an enzymatic nucleic acid molecule, is 13 to 100 nucleotides in length, e.g., in specific embodiments 35, 36, 37, or 38 nucleotides in length (e.g., for particular DNA enzymes). In particular embodiments, the nucleic acid molecule is 15-100, 17-100, 20-100, 21-100, 23-100, 25-100, 27-100, 30-100, 32-100, 35-100, 40-100, 50-100, 60-100, 70-100, or 80-100 nucleotides in length. Instead of 100 nucleotides being the upper limit on the length ranges specified above, the upper limit of the length range can be, for example, 30, 40, 50, 60, 70, or 80 nucleotides. Thus, for any of the length ranges, the length range for particular embodiments has lower limit as specified, with an upper limit as specified which is greater than the lower limit. For example, in a particular embodiment, the length range can be 35-50 nucleotides in length. All such ranges are expressly included. Also in particular embodiments, a nucleic acid molecule can have a length which is any of the lengths specified above, for example, a catalytic core of 21 conserved nucleotides in length with variable length binding arms and/or variable regions.
The enzymatic nucleic acid molecules of Formulae 1, II, III and IV can independently comprise a cap structure which can independently be present or absent.
By "chimeric nucleic acid molecule" or "mixed polymer" is meant that, the molecule can be comprised of both modified or unmodified nucleotides.
By "cap structure" is meant chemical modifications, which have been incorporated at either terminus of the oligonucleotide. These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and can help in delivery and/or localization within a cell. The cap can be present at the 5'-terminus (S'-cap) or at the 3'-terminus (3'-cap) or can be present on both termini.
In non-limiting examples the S'-cap is selected from the group consisting of the following: inverted abasic residue (moiety); 4',5'-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide, 4'-thio nucleotide, carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides;
modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3'-3'-inverted nucleotide moiety; 3'-3'-inverted abasic moiety; 3'-2'-inverted nucleotide moiety; 3'-2'-inverted abasic moiety; 1,4-butanediol phosphate; 3'-phosphoramidate;
hexylphosphate; aminohexyl phosphate; 3'-phosphate; 3'-phosphorothioate; phosphorodithioate; or bridging or non-bridging methylphosphonate moiety (for more details, see Beigelman et al., International PCT publication No. WO 97/26270, incorporated by reference herein).
In yet another preferred embodiment, the 3'-cap is selected from a group consisting of the following: 4',5'-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide;
4'-thio nucleotide;
carbocyclic nucleotide; 5'-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate, 3-aminopropyl phosphate; G-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide;
phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3',4'-seco.
nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide; 5'-5'-inverted nucleotide moiety; 5'-S'-inverted abasic moiety; S'-phosphoramidate; 5'-phosphorothioate; 1,4-butanediol phosphate; S'-amino; bridging and/or non-bridging S'-phosphoramidate; phosphorothioate and/or phosphorodithioate; bridging or non bridging methylphosphonate; and 5'-mercapto moieties (for more details see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).
By "oligonucleotide" as used herein, is meant a molecule comprising two or more nucleotides.
The specific enzymatic nucleic acid molecules described in the instant application are not limiting in the invention and those skilled in the art will recognize that all that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site (e.g., X and Y of Formulae I, II, III and IV above) which is complementary to one or more of the target nucleic acid regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart a nucleic acid cleaving activity to the molecule.
The determination of whether the V or L regions can be deleted or changed can be determined by experimentation and tested in vitro using the methods described herein.
Similarly, when the V
region is present the determination or whether its length can be increased or decreased can be evaluated using the selection protocols described herein.
By "enzymatic portion" is meant that part of the enzymatic nucleic acid molecule essential for cleavage of an RNA substrate.
By "substrate binding arm" or "substrate binding domain" is meant that portion of a enzymatic nucleic acid molecule which is complementary to (i.e., able to base-pair with) a portion of its substrate. Generally, such complementarity is 100%, but can be less if desired. For example, as few as 10 nucleotides out of a total of 14 can be base-paired. Such arms are shown generally in Figures 2, 3, 7, 9, and 11 and as X and Y in Formulae I - IV. That is, these arms contain sequences within an enzymatic nucleic acid molecule which are intended to bring enzymatic nucleic acid molecule and target RNA together through complementary base-pairing interactions. The enzymatic nucleic acid molecules such as ribozymes and DNAzymes of the invention can have binding arms that are contiguous or non-contiguous and can be of varying lengths. The length of the binding arms) are preferably greater than or equal to four nucleotides; specifically 12-100 nucleotides; more specifically 14-24 nucleotides long. The two binding arms are chosen, such that the length of the binding arms are symmetrical (i.e., each of the binding arms is of the same length; e.g., five and five nucleotides, six and six nucleotides or seven and seven nucleotides long) or asymmetrical (i.e., the binding arms are of different length; e.g., six and three nucleotides; three and six nucleotides long;

four and five nucleotides long; four and six nucleotides long; four and seven nucleotides long; and the like).
Catalytic activity of the enzymatic nucleic acid molecule described in the instant invention can be optimized as described by Usman et al., US Patent No. 5,807,718. The methods described by Draper et al., supra, for nucleic acid catalysts can readily be applied for use in the optimization of the nucleic acid molecules of the instant invention. Specific details will not be repeated here, but include altering the length of the enzymatic nucleic acid molecule binding arms, or chemically synthesizing enzymatic nucleic acid molecules with modifications (base, sugar and/or phosphate) that prevent their degradation by serum ribonucleases and/or enhance their enzymatic activity (see e.g., Eckstein et al., International Publication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991 Science 253, 314; Usman and Cedergren, 1992 Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO 93/15187; Rossi et al., International Publication No. WO 91/03162; Sproat, US Patent No. 5,334,711; and Burgin et al., supra; all of these describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of enzymatic DNA and/or RNA molecules). All these publications are hereby incorporated by reference herein. Modifications which enhance their efficacy in cells, and removal of bases from stem loop structures to shorten enzymatic nucleic acid molecule synthesis times and reduce chemical requirements are desired. The enzymatic nucleic acid molecules can be synthesized entirely of deoxyribonucleotides, or other 2'-modified nucleotides (e.g.; 2'-O-methyl, 2'-O-allyl, 2'-C-allyl, 2'-deoxy-2'-amino, 2'-deoxy-2'-fluoro, 2'-O-amino etc.), individually or in combination, so long as the nucleic acid catalyst is functional.
Therapeutic enzymatic nucleic acid molecules should remain stable within cells until translation of the target RNA has been inhibited long enough to reduce the levels of the undesirable protein. This period of time varies between hours to days depending upon the disease state. In particular, DNAzymes should be resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of DNA and RNA
(Wincott et al., 1995 Nucleic Acids Res. 23, 2677; incorporated by reference herein) have expanded the ability to modify DNA enzymes to enhance their nuclease stability.
By "nucleotide" is meant a heterocyclic nitrogenous base in N-glycosidic linkage with a phosphorylated sugar. Nucleotides are recognized in the art to include natural bases (standard), and modified bases well known in the art. Such bases are generally located at the 1' position of a nucleotide sugar moiety. Nucleotides generally comprise a base, sugar and a phosphate group. The nucleotides can be unmodified or modif ed at the sugar, phosphate and/or base moiety, (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides and other; see for example, Usman and McSwiggen, supra;
Eckstein et al., International PCT Publication No. WO 92/07065; Usman et al., International PCT
Publication No.
WO 93/15187; Uhlman & Peyman, supra all are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art as summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183. Some of the non-limiting examples of chemically modified and other natural nucleic acid bases that can be introduced into nucleic acids include, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2, 4, 6-trimethoxy benzene, 3-methyl uracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), S-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6-methyluridine), propyne, quesosine, 2-thiouridine, 4-thiouridine, wybutosine, wybutoxosine, 4-acetylcytidine, 5-(carboxyhydroxymethyl)uridine, S'-carboxymethylaminomethyl-2-thiouridine, S-carboxymethylaminomethyluridine, beta-D-galactosylqueosine, 1-methyladenosine, 1-methylinosine, 2,2-dimethylguanosine, 3-methylcytidine, 2-methyladenosine, 2-methylguanosine, N6-methyladenosine, 7-methylguanosine, 5-methoxyaminomethyl-2-thiouridine, 5-methylaminomethyluridine, 5-methylcarbonylmethyluridine, 5-methyloxyuridine, 5-methyl-2-thiouridine, 2-methylthio-N6-isopentenyladenosine, ?-D-mannosylqueosine, uridine-5-oxyacetic acid, 2-thiocytidine, threonine derivatives and others (Burgin et al., 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). By "modified bases" in this aspect is meant nucleotide bases other than adenine, guanine, cytosine and uracil at 1' position or their equivalents; such bases can be used at any position, for example, within the catalytic core of an enzymatic nucleic acid molecule and/or in the substrate-binding regions of the nucleic acid molecule.
In a preferred embodiment, the invention features modified DNAzymes with phosphate backbone modifications comprising one or more phosphorothioate, phosphorodithioate, methylphosphonate, morpholino, amidate carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and/or alkylsilyl, substitutions. For a review of oligonucleotide backbone modifications see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417, and Mesmaeker et al., 1994, Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39.
In a further preferred embodiment of the instant invention, an inverted deoxy abasic moiety is utilized at the 3' end of the enzymatic nucleic acid molecule.
5 In particular, the invention features modified enzymatic nucleic acid molecules having a base substitution selected from pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2, 4, 6-trimethoxy benzene, 3-methyluracil, dihydrouracil, naphthyl, 6-methyl-uracil and aminophenyl.
There are several examples in the art describing sugar and phosphate modifications that can be introduced into enzymatic nucleic acid molecules without significantly effecting catalysis and with 10 significant enhancement in their nuclease stability and efficacy. Enzymatic nucleic acid molecules are modified to enhance stability and/or enhance catalytic activity by modification with nuclease resistant groups, for example, 2'-amino, 2'-C-allyl, 2'-flouro, 2'-O-methyl, nucleotide base modifications (for a review see Usman and Cedergren, 1992 TIES 17, 34; Usman et al., 1994 Nucleic Acids Symp. Ser. 31, 163; Burgin et al., 1996 Biochemistry 35, 14090).
Sugar modifications 15 of enzymatic nucleic acid molecules have been extensively described in the art (see Eckstein et al., International Publication PCT No. WO 92/07065; Perrault et al. Nature 1990, 344, 565-568;
Pieken et al. Science 1991, 253, 314-317; Usman and Cedergren, Trends in Biochem. Sci. 1992, 17, 334-339; Usman et al. International Publication PCT No. WO 93/15187; Sproat, US Patent No.
5,334,711 and Beigelman et al., 1995 J. Biol. Chem. 270, 25702).
20 Additionally, the enzymatic nucleic acid molecules can be linked to various chemical moieties and/or ligands to enhance stability, localization, and/or efficacy. Such moieties and ligands include but are not limited to polyethylene glycol (PEG), cholesterol, cytofectins (such as DOPE, DDAB, DOGS, DOTMA and DOTMA analogues including DOTAP, DMRIE, DOSPA, DORIE, DORI, and GAP-DLRIE), glucose, galactose, spermine, spermidine, C-dextran, polyacrylamide, biotin, retinoic 25 acid, peptide nucleic acids, antigens (such as CD40, CD44, carcinoembryonic, endoglin, and prostate-specific antigens), receptors (such as VEGF, HER2/neu), and other fatty acids, steroids, cationic lipids, polyamines, polyamides, glucocorticoids, integrins, histones, protamines, toxins, viroids, virusoids, amino acids, peptides, proteins, sugars, polysaccharides, glycoconjugates, oligonucleotides, metals, small molecules, macromolecules and combinations thereof. For a review of non-limiting carbohydrate modifications including 2'-conjugates, see Manoharan, 1999, Biochim.

Biophys. Acta., 1489(1), 117-130. For a review of non-limiting drug macromolecule conjugates, see Takakura et al., 1996, Advan. Drug, Delivery Rev., 19(3), 377-399. Such publications describe general methods and strategies to determine the location of incorporation of sugar, base and/or phosphate modifications and the like into nucleic acid molecules without inhibiting catalysis, and are incorporated by reference herein. In view of such teachings, similar modifications can be used as described herein to modify the nucleic acid catalysts of the instant invention.
As the term is used in this application, non-nucleotide-containing enzymatic nucleic acid means a nucleic acid molecule that contains at least one non-nucleotide component which replaces a portion of an enzymatic nucleic acid molecule, e.g., but not limited to, a double-stranded stem, a single-stranded "catalytic core" sequence, a single-stranded loop or a single-stranded recognition sequence. These molecules are able to cleave (preferably, repeatedly cleave through multiple turnover) separate RNA or DNA molecules in a nucleotide base sequence specific manner. Such molecules can also act to cleave intramolecularly if that is desired. Such enzymatic molecules can be targeted to virtually any RNA transcript.
The sequences of enzymatic nucleic acid molecules that are chemically synthesized, useful in this invention, are shown in the Tables and Figures. Those in the art will recognize that these sequences are representative only of many more such sequences where the enzymatic portion of the enzymatic nucleic acid molecule (all but the binding arms) is altered to affect activity. The enzymatic nucleic acid molecule sequences listed in the tables and figures can be formed of deoxyribonucleotides or other nucleotides or non-nucleotides. Such enzymatic nucleic acid molecules with enzymatic activity are equivalent to the enzymatic nucleic acid molecules described specifically in the tables and figures.
Synthesis of Nucleic Acid Molecules Synthesis of nucleic acids greater than 100 nucleotides in length can be difficult using automated methods, and the therapeutic cost of such molecules can be prohibitive. In this invention, small nucleic acid motifs ("small" refers to nucleic acid motifs no more than 100 nucleotides in length, preferably no more than 80 nucleotides in length, and most preferably no more than SO
nucleotides in length; e.g., antisense oligonucleotides, hammerhead or the Inozyme enzymatic nucleic acids) are preferably used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of RNA
structure. Exemplary molecules of the instant invention are chemically synthesized, and others can similarly be synthesized.
The nucleic acid molecules of the invention, including certain enzymatic nucleic acid molecules, can be synthesized using the methods described in Usman et al., 1987, J. Am. Chem.
Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684 Wincott et al., 1997, Methods Mol. Bio., 74, 59. Such methods make use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 ~mol scale protocol with a 7.5 min coupling step for alkylsilyl protected nucleotides and a 2.5 min coupling step for 2'-O-methylated nucleotides. Table 1 outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 ~mol scale can be done on a 96-well plate synthesizer, such as the PG2100 instrument produced by Protogene (Palo Alto, CA) with minimal modification to the cycle. A 33-fold excess (60 ~,L of 0.11 M = 6.6 ~,mol) of 2'-O-methyl phosphoramidite and a 75-fold excess of S-ethyl tetrazole (60 pL of 0.25 M =
15 ~mol) can be used in each coupling cycle of 2'-O-methyl residues relative to polymer-bound S'-hydroxyl. A 66-fold excess (120 ~L of 0.11 M = 13.2 pmol) of alkylsilyl (ribo) protected phosphoramidite and a 150-fold excess of S-ethyl tetrazole (120 pL of 0.25 M = 30 pmol) can be used in each coupling cycle of ribo residues relative to polymer-bound 5'-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc.
synthesizer include; detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution is 16.9 mM I2, 49 mM pyridine, 9% water in THF
(PERSEPTIVETM). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide 0.05 M in acetonitrile) is used.
Cleavage from the solid support and deprotection of the oligonucleotide is typically performed using either a two-pot or one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40%
aq. methylamine (1 mL) at 65 °C for 10 min. After cooling to -20 °C, the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H20/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder. The base deprotected oligoribonucleotide is resuspended in anhydrous TEA/HF/NMP
solution (300 pL of a solution of 1.5 mL N-methylpyrrolidinone, 750 ~L TEA and 1 mL TEA~3HF to provide a 1.4 M HF
concentration) and heated to 65 °C. After 1.5 h, the oligomer is quenched with 1.5 M NH4HC03.
Alternatively, for the one-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 33%
ethanolic methylamine/DMSO: 1/1 (0.8 mL) at 65°C for 15 min. The vial is brought to r.t. TEA~3HF (0.1 mL) is added and the vial is heated at 65 °C for 1 S min. The sample is cooled at -20 °C and then quenched with 1.5 M NH4HC03. An alternative deprotection cocktail for use in the one pot protocol comprises the use of aqueous methylamine (0.5 ml) at 65°C for 15 min followed by DMSO
(0.8 ml) and TEA~3HF (0.3 ml) at 65°C for 15 min. A similar methodology can be employed with 96-well plate synthesis formats by using a Robbins Scientific Flex Chem block, in which the reagents are added for cleavage and deprotection of the oligonucleotide.
For anion exchange desalting of the deprotected oligomer, the TEAB solution is loaded onto a Qiagen 500~ anion exchange cartridge (Qiagen Inc.) that is prewashed with 50 mM TEAB (10 mL).
After washing the loaded cartridge with 50 mM TEAB (10 mL), the RNA is eluted with 2 M TEAB
( 10 mL) and dried down to a white powder.
For purification of the trityl-on oligomers, the quenched NH4HC03 solution is loaded onto a C-18 containing cartridge that had been prewashed with acetonitrile followed by 50 mM TEAA.
After washing the loaded cartridge with water, the RNA is detritylated with 0.5% TFA for 13 min.
The cartridge is then washed again with water, salt exchanged with 1 M NaCI
and washed with water again. The oligonucleotide is then eluted with 30% acetonitrile.
Alternatively, for oligonucleotides synthesized in a 96-well format, the crude trityl-on oligonucleotide is purified using a 96-well solid phase extraction block packed with C 18 material, on a Bohdan Automation workstation.
The average stepwise coupling yields are typically >98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). Those of ordinary skill in the art will recognize that the scale of synthesis can be adapted as larger or smaller than the example described above including but not limited to 96 well format, all that is important is the ratio of chemicals used in the reaction.
To ensure the quality of synthesis of nucleic acid molecules of the invention, quality control measures are utilized for the analysis of nucleic acid material. Capillary Gel Electrophoresis, for example using a Beckman MDQ CGE instrument, can be ulitized for rapid analysis of nucleic acid molecules, by introducing sample on the short end of the capillary. In addition, mass spectrometry, for example using a PE Biosystems Voyager-DE MALDI instrument, in combination with the Bohdan workstation, can be utilized in the analysis of oligonucleotides, including oligonucleotides synthesized in the 96-well format.
Enzymatic nucleic acids can also be synthesized in two parts and annealed to reconstruct the active enzymatic nucleic acid (Chowrira and Burke, 1992 Nucleic Acids Res., 20, 2835-2840).
Enzymatic nucleic acids are also synthesized from DNA templates using bacteriophage T7 RNA
polymerase (Milligan and Uhlenbeck, 1989, Methods Enzymol. 180, 51).
Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together post-synthetically, for example by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO
93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides &
Nucleotides, 16, 951;
Bellon et al., 1997, Bioconjugate Chem. 8, 204).
The nucleic acid molecules of the present invention are preferably modified to enhance stability by modification with nuclease resistant groups, for example, 2'-amino, 2'-C-allyl, 2'-flouro, 2'-O-methyl, 2'-H (for a review see Usman and Cedergren, 1992, TIBS 17, 34;
Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163). Enzymatic nucleic acids are purified by gel electrophoresis using known methods or are purified by high pressure liquid chromatography (HPLC; See Wincott et al., Supra, the totality of which is hereby incorporated herein by reference) and are re-suspended in water.
Administration of Nucleic Acid Molecules Sullivan et al., PCT WO 94/02595, describe the general methods for delivery of enzymatic nucleic acid molecules. DNAzymes can be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres. For some indications, DNAzymes can be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles.
Alternatively, the DNAzymes/vehicle combination is locally delivered by direct injection or by use 5 of a catheter, infusion pump or stmt. Other routes of delivery include, but are not limited to, intravascular, intramuscular, subcutaneous or joint injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery.
More detailed descriptions of nucleic acid molecule delivery and administration are provided in Sullivan et al., supra and Draper et al., PCT W093/23569 which have been incorporated by reference herein.
10 The molecules of the instant invention can be used as pharmaceutical agents. Pharmaceutical agents prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state in a patient.
The negatively charged polynucleotides of the invention can be administered (e.g., RNA, DNA or protein) and introduced into a patient by any standard means, with or without stabilizers, 15 buffers, and the like, to form a pharmaceutical composition. When it is desired to use a liposome delivery mechanism, standard protocols for formation of liposomes can be followed. The compositions of the present invention may also be formulated and used as tablets, capsules or elixirs for oral administration, suppositories for rectal administration, sterile solutions, suspensions for injectable administration, and other compositions known in the art.
20 The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., acid addition salts, including salts of hydrochloric, hydrobromic, acetic acid, and benzene sulfonic acid.
A pharmacological composition or formulation refers to a composition or formulation in a form suitable for administration, e.g., systemic administration, into a cell or patient, preferably a human.
25 Suitable forms, in part, depend upon the use or the route of entry, for example, oral, transdermal, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged polymer is desired to be delivered to). For example, pharmacological compositions injected into the blood stream should be soluble.
Other factors are known in the art, and include considerations such as toxicity and forms which prevent the 30 composition or formulation from exerting its effect.

By "systemic administration" is meant in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body.
Administration routes which lead to systemic absorption include, without limitations: intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary and intramuscular. Each of these administration routes expose the desired negatively charged polymers, e.g., nucleic acids, to an accessible diseased tissue. The rate of entry of a drug into the circulation has been shown to be a function of molecular weight or size.
The use of a liposome or other drug carrier comprising the compounds of the instant invention can potentially localize the drug, for example, in certain tissue types, such as the tissues of the reticular endothelial system (RES). A liposome formulation which can facilitate the association of drug with the surface of cells, such as, lymphocytes and macrophages is also useful.
This approach can provide enhanced delivery of the drug to target cells by taking advantage of the specificity of macrophage and lymphocyte immune recognition of abnormal cells, such as cancer cells.
The invention also features the use of a composition comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem.
1995, 42, 24864-24870; Choi et al., International PCT Publication No. WO
96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No.
WO 96/10392; all of which are incorporated by reference herein). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen. Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et a1.,1995, Biochim. Biophys. Acta, 1238, 86-90).
The present invention also includes compositions prepared for storage or administration which include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A.R. Gennaro edit. 1985) hereby incorporated by reference herein. For example, preservatives, stabilizers, dyes and flavoring agents can be added to the compositions. Id.
at 1449. Suitable examples include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents can be added to the compositions.
A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical characteristics of the specific mammal under consideration, concurrent medication, and other factors which those skilled in the medical arts will recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer. In a one aspect, the invention provides enzymatic nucleic acid molecules that can be delivered exogenously to specific cells as required. The enzymatic nucleic acid molecules are added directly, or can be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to smooth muscle cells. The RNA or RNA complexes can be locally administered to relevant tissues through the use of a catheter, infusion pump or stmt, with or without their incorporation in biopolymers. Using the methods described herein, other enzymatic nucleic acid molecules that cleave target nucleic acid may be derived and used as described above. Specific examples of nucleic acid catalysts of the instant invention are provided below in the Tables and Figures.
Alternatively, the enzymatic nucleic acid molecules of the instant invention can be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985 Science 229, 345; McGarry and Lindquist, 1986 Proc. Natl. Acad. Sci. USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci.
USA, 88, 10591-S; Kashani-Sabet et al., 1992 Antisense Res. Dev., 2, 3-15;
Dropulic et al., 1992 J.
Virol, 66, 1432-41; Weerasinghe et al., 1991 J. Virol, 65, 5531-4; Ojwang et al., 1992 Proc. Natl.
Acad. Sci. USA 89, 10802-6; Chen et al., 1992 Nucleic Acids Res., 20, 4581-9;
Sarver et al., 1990 Science 247, 1222-1225; Thompson et al., 1995 Nucleic Acids Res. 23, 2259; Good et al., 1997, Gene Therapy, 4, 45; all of the references are hereby incorporated in their totality by reference herein). Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a enzymatic nucleic acid (Draper et al., PCT WO

93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., 1992 Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al., 1993 Nucleic Acids Res., 21, 3249-55; Chowrira et al., 1994 J. Biol. Chem. 269, 25856; all of the references are hereby incorporated in their totality by reference herein).
In another aspect of the invention, enzymatic nucleic acid molecules that cleave target molecules are expressed from transcription units (see for example Couture et al., 1996, TIG., 12, S 10) inserted into DNA or RNA vectors. The recombinant vectors are preferably DNA plasmids or viral vectors. Enzymatic nucleic acid expressing viral vectors could be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus.
Preferably, the recombinant vectors capable of expressing the enzymatic nucleic acids are delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of enzymatic nucleic acids. Such vectors can be repeatedly administered as necessary. Once expressed, the enzymatic nucleic acids cleave the target mRNA. The active enzymatic nucleic acid contains an enzymatic center or core equivalent to those in the examples, and binding arms able to bind target nucleic acid molecules such that cleavage at the target site occurs. Other sequences can be present which do not interfere with such cleavage. Delivery of enzymatic nucleic acid expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that allows for introduction into the desired target cell (for a review see Couture et al., 1996, TIG., 12, 510).
In one aspect the invention features, an expression vector comprising nucleic acid sequence encoding at least one of the nucleic acid catalyst of the instant invention is disclosed. The nucleic acid sequence encoding the nucleic acid catalyst of the instant invention is operably linked in a manner which allows expression of that nucleic acid molecule.
In another aspect the invention features an expression vector comprising: a) a transcription initiation region (e.g., eukaryotic pol 1, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); c) a nucleic acid sequence encoding at least one of the nucleic acid catalyst of the instant invention; and wherein said sequence is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. The vector may optionally include an open reading frame (ORF) for a protein operably linked on the 5' side or the 3'-side of the sequence encoding the nucleic acid catalyst of the invention; and/or an intron (intervening sequences).
Transcription of the nucleic acid molecule sequences can be driven from a promoter for eukaryotic RNA polymerise I (pol I), RNA polymerise II (pol II), or RNA
polymerise III (pol III).
Transcripts from pol II or pol III promoters are generally expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA
polymerise promoters can be also used, providing that the prokaryotic RNA polymerise enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acid. Sci. U S A, 87, 6743-7;
Gao and Huang 1993, Nucleic Acids Res.., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). All of these references are incorporated by reference herein.
Several investigators have demonstrated that nucleic acid molecules, such as enzymatic nucleic acids, expressed from such promoters function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acid. Sci. U S
A, 89, 10802-6;
Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc.
Natl. Acid. Sci. U S A, 90, 6340-4; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl.
Acid. Sci. U. S. A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger &
Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA
are useful in generating high concentrations of desired RNA molecules such as enzymatic nucleic acids in cells (Thompson et al., supra; Couture and Stinchcomb, 1996, supra;
Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., US Patent No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736;
all of these publications are incorporated by reference herein. The above enzymatic nucleic acid transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).
In yet another aspect the invention features an expression vector comprising nucleic acid sequence encoding at least one of the nucleic acid molecules of the invention, in a manner which allows expression of that nucleic acid molecule. The expression vector comprises in one embodiment; a) a transcription initiation region; b) a transcription termination region; c) a nucleic acid sequence encoding at least one said nucleic acid molecule; and wherein said sequence is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In another preferred embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination 5 region; c) an open reading frame; d) a nucleic acid sequence encoding at least one said nucleic acid molecule, wherein said sequence is operably linked to the 3'-end of said open reading frame; and wherein said sequence is operably linked to said initiation region, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In yet another embodiment the expression vector comprises: a) a transcription initiation 10 region; b) a transcription termination region; c) an intron; d) a nucleic acid sequence encoding at least one said nucleic acid molecule; and wherein said sequence is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading 15 frame; e) a nucleic acid sequence encoding at least one said nucleic acid molecule, wherein said sequence is operably linked to the 3'-end of said open reading frame; and wherein said sequence is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.
Alternatively, the enzymatic nucleic acid molecules of the instant invention can be expressed 20 from single stranded DNA expression vectors.
The invention also features a method for enhancing the effect of the nucleic acid catalyst of the instant invention in vivo. The method includes the step of causing the nucleic acid catalyst to be localized in vivo with its target. In a related aspect, the invention features nucleic acid catalysts which are adapted for localization with the viral target of the agent in vivo.
25 Those in the art will recognize that many methods can be used for modification of nucleic acid catalyst such that they are caused to be localized in an appropriate compartment with a target.
Examples of these methods follow but are not limiting in the invention. Thus, for example, the nucleic acid catalysts of the invention can be synthesized in vivo from vectors (or formed in vitro) such that they are covalently or noncovalently bonded with a targeting agent, examples of which are 30 well known in the art (Sullenger et al., US Patent No. 5,854,038;
Castanotto et al., Methods Enzymol 2000;313:401-20; Rossi et al., Science 1999, 285,1685). These targeting agents are termed "localization signals". In addition, nucleic acid catalysts can be synthesized in vitro and administered in any one of many standard methods to cause the nucleic acid catalysts to be targeted to an appropriate cellular compartment within a patient.
By "enhancing" the effect of a nucleic acid catalysts in vivo is meant that a localization signal targets that nucleic acid catalysts to a specific site within a cell and thereby causes that nucleic acid catalysts to act more efficiently. Thus, a lower concentration of nucleic acid catalysts administered to a cell in vivo can have an equal effect to a larger concentration of non-localized nucleic acid catalysts. Such increased efficiency of the targeted or localized nucleic acid catalysts can be measured by any standard procedure well-known to those of ordinary skill in the art. In general, the effect of the nucleic acid catalyst is enhanced by placing the nucleic acid catalyst in a closer proximity with the target, so that it may have its desired effect on that target. This may be achieved by causing the nucleic acid catalysts to be located in a small defined compartment with the target (e.g., within a viral particle), or to be located in the same space within a compartment, e.g., in a nucleus at the location of synthesis of the target.
Localization signals include any proteinaceous or nucleic acid component which naturally becomes localized in the desired compartment, for example, a viral packaging signal, or its equivalent. Localization signals can be identified by those in the art as those signals which cause the nucleic acid catalysts to which they are associated with to become localized in certain compartments, and can be readily discovered using standard methodology (Sullenger et al., US
Patent No. 5,854,038; Shaji et al., US Patent No. 5,834,186). These localization signals can be tethered to the nucleic acid catalysts by any desired procedure, for example, by construction of a DNA template which produces both the localization signal and nucleic acid catalysts as part of the same molecule, or by covalent or ionic bond formation between two moieties.
All that is essential in the invention is that the nucleic acid catalysts be able to have its inhibitory effect when localized in the target site, and that the localization signal be able to localize that nucleic acid catalysts to that target site. For example, localization signals such as HIV's Rev response element can be linked to the DNA enzyme to sort in some unique way. Those skilled in the art will recognize that other nucleic acid localization elements may be attached to the DNAzymes of the instant invention using methods known in the art.

Other examples include any cellular RNA/DNA localization signal which causes RNA/DNA
containing the signal to be sorted into a pathway which does not contain large numbers of incorrect targets; viral protein localization/assembly signals, e.g., Rev or gag proteins.
Increasing the concentration of a viral inhibitor at an intracellular site important for viral replication or assembly is a general way to increase the effectiveness of nucleic acid catalysts. The above-described co-localization strategy can make use of, for example, a viral packaging signal to co-localize nucleic acid catalysts with a target responsible for viral replication. In this way viral replication can be reduced or prevented. This method can be employed to enhance the effectiveness of nucleic acid catalysts by tethering them to an appropriate localization signal to sort them to the therapeutically important intracellular and viral location where the viral replication machinery is active.
Such co-localization or regulation of enzymatic nucleic acid molecule strategies are not limited to using naturally occurnng localization and regulation signals.
Nucleic acid catalysts can be targeted to important intracellular locations by use of artificially evolved DNA/RNAs and/or protein decoys (Szostak, 17 TIBS 89, 1992). These evolved molecules are selected, for example, to bind to a viral protein and can be used to co-localize nucleic acid catalysts with a viral target by tethering the inhibitor to such a decoy.
By "consists essentially of ' is meant that the active enzymatic nucleic acid molecule contains an enzymatic center or core equivalent to those in the examples, and binding arms able to bind target nucleic acid molecules such that cleavage at the target site occurs.
Other sequences can be present which do not interfere with such cleavage.
The nucleic acid catalyst of the instant invention can be used to inhibit expression of foreign or endogenous genes, in vitro or in vivo, in prokaryotic cells or in eukaryotic cells, in bacteria, fungi, mycoplasma, archebacteria, algae, plants or any other biological system.
By "endogenous" gene is meant a gene normally found in a cell in its natural location in the genome.

By "foreign" or "heterologous" gene is meant a gene not normally found in the host cell, but that is introduced by standard gene transfer techniques or acquired as result of an infection (e.g., bacterial, viral or fungal infection).
By a "plant" is meant a photosynthetic organism, either eukaryotic and prokaryotic.
Examples The following are non-limiting examples showing the selection, isolation, synthesis and activity of enzymatic nucleic acids of the instant invention.
Applicant employed in vitro selection to isolate populations of Mgz+-dependent self cleaving DNA enzymes from a pool of random-sequence molecules. Characterization of a small number of individual DNAzymes from various populations revealed the emergence of at least six classes of DNA enzymes that adopt distinct secondary structure motifs. None of the six classes corresponds to a previously known folding pattern. Each prototypic DNA enzyme promotes self cleavage with a chemical rate enhancement of at least 1000-fold above the corresponding uncatalyzed rate.
Example 1: In vitro selection of catalytic DNAs from a random pool The initial random population was created by ligating a pool of molecules, R19 (5'-ACGTGTGCAGCTTTC-3') (SEQ ID NO 111) connected by a random region [N50]
followed by (5'-TTATTACGGTAACGTTGGCAC-3') (SEQ ID NO 112), where N50 indicates the random region of 50 nucleotides) to a synthetic RNA/DNA chimeric substrate, 2.26 (5'-GGCACACCACAAGAGUAAUAAUGAAAGAAGCGACGCT-3') (SEQ ID NO 113), where underlined type indicates the RNA region) using T4 DNA ligase and the oligo 1.30 (5'-TGCACACGTAGCGTCGCT-3') (SEQ ID NO 114) to template the ligation. The pool of synthetic R19 molecules had first been phosphorylated and end-labeled with (y-3zP]ATP
using T4 polynucleotide kinase to provide the S' phosphate necessary for T4 ligase. The full-length population was separated from unligated components by denaturing PAGE. Following elution from the gel, the full-length molecules were ethanol precipitated and resuspended either in 0.001% SDS (early rounds) or directly in 1X selection buffer (later rounds). The population was then reacted at 37°C in the selection buffer and successful catalysts were separated from unreacted molecules by denaturing PAGE. A zone of gel was excised to encompass all possible RNA cleavage events.
Eluted catalysts were amplified by PCR using Taq DNA polymerase and primers 1.1 (5'-GTGCCAACGTTACCG-3') (SEQ ID NO 115) and 2.29 (5'-ACGTGTGCAGCTTC-3') (SEQ ID NO 116) to create multiple copies of the successful catalysts. A portion of the reaction was then amplified with PCR using primers 1.1r (5'-GTGCCAACGTTACCG-3', which terminates with a ribose) (SEQ ID
NO 117) and 2.29 to produce molecules with a ribose imbedded in the negative strand. The negative strand was cleaved at this ribose with alkali and heat. The positive strand was then separated from the negative strand fragments by denaturing PAGE. The positive strand was phosphorylated and ligated to the substrate 2.26 as for the initial population. The new pool was then purified from un-incorporated substrate and ligation template by denaturing PAGE for the next round of selection. Figure 4 is a schematic representation of the selection process described above.
Generation 0 composed of the initial random pool was reacted at 37°C
for 12 hours in a buffer that was 50 mM magnesium chloride, 20 mM for amino acids with pKa's nearest neutral (arg, asn, cys, gln, glu, his, lys, met, phe, ser), 1 mM for tyrosine (due to its low solubility), and 2 mM for the remaining natural amino acids. The selection buffer also contained, in every round, 150 mM
potassium chloride, 7 mM putrescine (to potentially assist in folding), and 10 mM reduced glutathione and was adjusted to pH 7.6 ~ 0.1 at 37°C after addition of all components. Both the reaction time and the concentrations of magnesium and the amino acids were reduced over the course of selection to final values of 10 minutes reaction time and 0.5 mM of both magnesium and each amino acid. When the amino acid content was reduced, HEPES was added at 50 mM to compensate for the loss in buffering.
During the selection process, the times allowed for ligation and for elution of the pool from the ligation acrylamide gel were reduced to prevent RNA cleavage during these processes.
Glutathione was included in the selection buffer at a cytoplasm-like concentration to keep the components, especially cysteine, reduced. As an additional precaution, the cysteine and glutathione were resuspended and added fresh to the selection buffer just before use (early rounds) or the freshly prepared solution was frozen in single-use aliquots and thawed just before use (later rounds).
Additionally, arginine was included in the cysteine/glutathione mix because arginine is also somewhat volatile in that its solutions absorb cardon dioxide from air, thus potentially changing the pH.
In vitro selection was performed for the purpose of discovering novel deoxyribozymes ideally suited for cleaving RNA in cells. Several new classes of magnesium dependent RNA-cleaving DNA
sequences have been recovered. These enzymes show no primary sequence similarity to known deoxyribozymes performing the same chemical reaction. Prototypic unimolecular representatives from each of these classes self cleave at imbedded RNA moieties with observed rate constants of 10-Z miri' in 0.5 mM MgCl2, with 150 mM KCI, 7 mM putrescine, 10 mM reduced glutathione, and SO mM HEPES pH 7.6 at 37°C. A shortened version of the sequence of the dominant class, class I, 5 has a catalytic core of 20 nucleotides. This deoxyribozyme can be made to cleave the target in trans with a pseudo first order rate constant of at least 0.06 miri', can be generalized to cleave an in vitro transcribed RNA target of a different sequence, and has a pKa for a catalytically critical functional group of ~7.9. Its kinetic rate increases in higher concentrations of magnesium but its maximum rate has yet to be determined.
10 The construct on which the library was based is shown in Figure 1 and the selection scheme utilized is shown in Figure 4. Capitol letters indicate the four standard DNA
bases and RNA bases (reverse type) in regions of the molecular library which were constant among all molecules. These regions provided the RNA substrate, positioned the random region adjacent to the substrate by base-pairing and allowed manipulation of the library during selection using standard methods. Catalytic 15 sequences were derived from the region of 50 nucleotides, imbedded between the constant regions, synthesized to contain random DNA sequences.
Molecules were selected on the basis of their ability to self cleave at an RNA
residue.
Molecules were reacted in solution in a buffer which approximated the composition of Escherichia coli cytoplasm with respect to conditions expected to be relevant to RNA
cleavage (Figure 1, 20 legend). Incubations were performed at 37°C. Magnesium ions and amino acids were initially included in the selection buffer at concentrations well above cytoplasmic levels in order to favor RNA cleavage so as to increase the copy number of deoxyribozymes from the random library.
Active catalysts were isolated from the remainder of the pool by size separation for all possible cleavage events within the RNA region with denaturing PAGE. Once a catalytic population had 25 been established, the conditions of the selection were made increasingly more stringent by decreasing the time the molecules were allowed to react and by decreasing the concentration of all buffer components to physiologic levels.
No known DNAzyme motif has been identified amongst the six classes of DNAs examined from the current selection. Instead entirely new catalytic motifs have been discovered (Table 2) that 30 have no detectable primary or secondary sequence similarity to known RNA-cleaving deoxyribozymes. Representative clones from each class were tested in their unimolecular format to determine catalytic rate and cleavage site (Table 3). These new sequences may represent unique tertiary structures having altered kinetic properties. Studies are in progress to assess each class individually.
Clone 27 of class I was studied in a minimized, bimolecular format (Figure 2).
The secondary structure shown in Figure 2a is based on the region of conserved nucleotides underlined in Table 2 with base-pairing restored at the 3' end of the catalyst. The Kd for this enzyme interacting with substrate is 5 ~M, which may reflect poor binding due to the A-U rich nature of the putative substrate binding arms. The enzyme does not require glutathione but does lose 10-fold activity in the absence of putrescine. Its pKa is ~ 7.9, reaching a maximum pseudo first order rate constant in 0.5 mM Mg2+ of 0.06 miri'. The enzyme also cleaves the in vitro transcribed target shown in Figure 2b, demonstrating that it does not require DNA residues in the substrate and can be generalized by changing the substrate binding arms. The relative cleavage rates of the Class I motif on various substrates shown in Figure 6 are presented in Table 4. Under single-turnover conditions, the rate of each enzyme is limited by binding a single magnesium ion with a Kd of 1 mM
(Figure 6).
Therefore, the catalytic core is well adapted to the magnesium and pH levels in cells. The pseudo first order rate constant for RNA cleavage under simulated physiologic conditions (pH 7.6, 2 mM
Mgz+, 150 mM K+, 7 mM putrescine, 37°C) is 0.060 miri'. The maximum rate constant at room temperature with MgZ+ increased to 8 mM and pH at 8.9 is 0.22 miri'.
The Class I motif has been targeted to cleave a variety of RNA substrates under simulated physiologic, single-turnover conditions by altering the putative substrate binding regions to be complementary to new targets. Additional cleavage sites are shown in Figure 5.
The cleavage rates relative to the model substrate from Figure 2 are summarized in Table 4 and show wide variation.
This variation is not due to an inability to recognize an all-RNA substrate over an RNA/DNA
chimera, as was present in the original selection but is most likely a result of intramolecular structure of the RNA targets. The substrate in Figure SA corresponds to a portion of the 5' UTR and ORF of an mRNA of a bacterial protein while the substrate in Figure SB was specifically designed for this test. The suitability of the latter substrate was checked by the secondary structure prediction program mfold (Mathews et al., 1999, J. Mol. Biol., 288, 911-940) version 3.1 such that: (1) the substrate was predicted not to have significant intramolecular structure; (2) each deoxyribozyme would interact with only one site on the RNA; (3) and each deoxyribozyme/substrate base-pairing interaction would 4 to 8 kcal/mole more stable than the model substrate interaction indicated in Figure 2.

Nevertheless, tertiary and non-standard interactions that may have significant effects, especially intramolecularly, may not be predicted.
Class IV and class V motifs can also cleave substrates in trans (Figure 7).
The class IV clone sequences from in vitro selection contained an extended stem-loop in the core that has been truncated, making the core size no more than 29 nucleotides. Likewise, class V
has been truncated to a core size of 28 nucleotides. The Class IV motif can be targeted to cleave an in vitro transcribed RNA with a pseudo first order rate constant of 0.002 min-1 in 0.5 mM Mg2+, 150 mM K+, 7 mM
putrescine, pH 7.6, 37°C. With this substrate, the Kd is approximately 1 pM in the same buffer. The motif has been shown to have no requirement for glutathione. The rate constant of the class V motif is estimated to be approximately 0.006 min-1 when tested in a similar buffer as above but with 10 mM glutathione included.
Studies were performed on clones 27 and 37 of class II. As for clone 27, an attempt was made to synthesize a molecule thought to be the minimal catalytically active sequence but with perfect substrate recognition sites (Figure 3). There is a dramatic loss of activity with this construct. An unligated bimolecular assay on the original clone 37 where the entire sequence of the full-length molecule was present but the molecule was severed in the connecting loop region was also inactive.
The other motifs have been studied unimolecularly, cleaving RNA in cis. The class III clone, 21, does cleave in an unligated bimolecular assay. However, the poor procession of the unimolecular reaction (only 7% processed, Table 3) indicates an interference of some sort, possibly one that might be solved by truncation if more structural data were available. Clone 34 does show activity but apparently activates during elution from the purification gel following preparation. Clone 34 reactions show significant cleavage at time zero but no additional cleavage under several buffer conditions, including those designed to mimic the elution buffer. An isolated class VI motif has been shown to be a magnesium dependent catalyst with an estimated cleavage rate constant of 0.002 min-1 (0.5 mM Mgz+, 150 mM K+, 7 mM putrescine, 10 mM glutathione pH 7.6, 37°C).
DNAzyme Engineering Sequence, chemical and structural variants of DNAzymes of the present invention can be engineered using the techniques shown above and known in the art to cleave a separate target RNA
or DNA in traps. DNAzymes can be reduced or increased in size using techniques known in the art.
Techniques described for engineering molecules containing 2'-hydroxyl (2'-OH) groups can be applied to the DNA enzymes of the instant invention (for example, see Zaug et al., 1986, Nature, 324, 429; Ruffner et al., 1990, Biochem., 29, 10695; Beaudry et al., 1990, Biochem., 29, 6534;
McCall et al., 1992, Proc. Natl. Acad. Sci., USA., 89, 5710; Long et al., 1994, supra; Hendry et al., 1994, BBA 1219, 405; Benseler et al., 1993, JACS, 115, 8483; Thompson et al., 1996, Nucl. Acids Res., 24, 4401;Michels et al., 1995, Biochem., 34, 2965; Been et al., 1992, Biochem., 31, 11843;
Guo et al., 1995, EMBO. .1., 14, 368; Pan et al., 1994, Biochem., 33, 9561;
Cech, 1992, Curr. Op.
Struc. Bio., 2, 605; Sugiyama et al., 1996, FEBS Lett., 392, 215; Beigelman et al., 1994, Bioorg.
Med. Chem., 4, 1715; all of these references are incorporated in their totality by reference herein).
For example, the stem-loop domains of the DNAzymes may not be essential for catalytic activity and hence can be systematically reduced in size using a variety of methods known in the art, to the extent that the overall catalytic activity of the DNAzyme is not significantly decreased. In addition, the introduction of variant stem-loop structures via site directed mutagenesis and/or chemical modification can be employed to develop DNAzymes with improved catalysis, increased stability, or both.
Further rounds of in vitro selection strategies described herein and variations thereof can be readily used by a person skilled in the art to evolve additional nucleic acid catalysts and such new catalysts are within the scope of the instant invention. Additionally, "Mutagenic PCR" (Cadwell RC, Joyce GF PCR Methods Appl 1994 Jun 3:6 S136-40) can be used to further optimize the sequences described in Formulae I and II. In addition, the optimization of these variant DNAzyme constructs by modification of stem-loop structures as is known in the art can provide for species with improved cleavage activity.
Target sequence requirements for DNAzymes can be determined and evaluated using methods known in the art.
New ribozvme motifs An extensive array of site-directed mutagenesis studies have been conducted with the hammerhead ribozyme to probe relationships between nucleotide sequence and catalytic activity..
These systematic studies have made clear that most nucleotides in the conserved core of the hammerhead ribozyme (Forster & Symons, 1987, Cell, 49, 211) cannot be mutated without significant loss of catalytic activity. In contrast, a combinatorial strategy that simultaneously screens a large pool of mutagenized ribozymes for RNAs that retain catalytic activity can be used more efficiently to define immutable sequences and to identify new ribozyme variants (Breaker, 1997, supra). For example, Joseph and Burke (1993; J. Biol. Chem., 268, 24515) have used an in vitro selection approach to rapidly screen for sequence variants of the 'hairpin' self cleaving RNA that show improved catalytic activity. This approach was successful in identifying two mutations in the hairpin ribozyme that together give a 10-fold improvement in catalytic rate.
Applicant employed in vitro selection to isolate populations of Mg2+-dependent self cleaving ribozymes from a pool of random-sequence molecules. Characterization of a small number of individual ribozymes from various populations revealed the emergence of at least 12 classes of ribozymes that adopt distinct secondary structure motifs. Only one of the 12 classes corresponds to a previously known folding pattern - that of the natural hammerhead ribozyme.
Each prototypic ribozyme promotes self cleavage via an internal phosphoester transfer reaction involving the adjacent 2'-hydroxyl group with a chemical rate enhancement of at least 1000-fold above the con-esponding uncatalyzed rate.
In vitro selection of self cleaving RNAs from a random pool Isolation of new ribozymes from a population of 10'4 different RNAs was performed using the selective-amplification scheme depicted in Figure 8A. Each RNA construct used for in vitro selection includes a 40-nt random-sequence region flanked both on its S'- and 3' sides by domains of defined nucleotide sequence (Figure 8B). The 3'-flanking domain was designed to serve as the target site for ribozyme cleavage. Due to its extended length, the 3'-flanking domain can experience the loss of nucleotides via ribozyme action, yet still function as a primer-binding site for amplification by RT-PCR. Moreover, the nucleotide sequence of this domain was designed to represent all 16 possible nearest neighbor combinations in order to favor the isolation of ribozymes that might have necessity for a particular dinucleotide identity at their cleavage site.
In each round of selection, the RNAs were transcribed in vitro using T7 RNAP
and the uncleaved RNA precursors were isolated by PAGE. The Mg2+ concentration and the incubation time used for in vitro transcription were minimized in order to reduce the likelihood that efficient Mg2+-dependent ribozymes would be cleaved during enzymatic synthesis and thereby lost upon isolation of the uncleaved RNA precursors. In addition, the incubation time used for crush/soak isolation of RNA precursors from polyacrylamide gel was minimized to preclude the isolation of self cleaving ribozymes that react in the absence of Mg2+. For selection, the purified RNA
precursors were incubated under permissive reaction conditions (50 mM Tris-HC1 [pH 7.5 at 23°C], 250 mM KC1, 20 mM MgClz) at 23°C for 4 hr. RNAs that cleaved in the 3' domain during this incubation were isolated by PAGE. Specifically, the zone that contains RNA cleavage fragments that are between ~10 to ~30 nucleotides shorter than the precursor RNAs was excised and the recovered RNAs were 5 amplified by RT-PCR.
The population of RNAs isolated after six rounds of selection (G6) exhibits a significant level of self cleavage activity in the presence of Mg2+. At this stage, the major 5'-cleavage products were isolated and the RT-PCR products of the isolated RNAs were cloned and sequenced. The remainder of the zone typically excised, which presumably contains 5'-cleavage fragments of different lengths, 10 was used to continue the selective-amplification process. This isolation strategy serves two purposes. First, the ribozymes that produce the major cleavage products observed in Fig. 1 C, and which presumably dominate the population at G6, can be examined in greater detail. Second, these more commonly represented sequences are largely excluded from the subsequent rounds of selection and thus are less likely to dominate the RNA population in future rounds. This allows ribozymes 15 that are less frequently represented to increase in frequency in later populations. In a similar fashion, the main product bands representing the 5'-cleavage fragments at G9, G12 and G15 were selectively recovered from the gel and subjected to RT-PCR amplification followed by cloning and sequencing.
This strategy offers an effective means by which many different self cleaving RNA motifs can be isolated.
20 By "random sequence region" is meant a region of completely random sequence and/or partially random sequence. By completely random sequence is meant a sequence wherein theoretically there is equal representation of A, T, G and C nucleotides or modified derivatives thereof, at each position in the sequence. By partially random sequence is meant a sequence wherein there is an unequal representation of A, T, G and C nucleotides or modified derivatives thereof, at 25 each position in the sequence. A partially random sequence can therefore have one or more positions of complete randomness and one or more positions with defined nucleotides.
Characterization of New self cleavin, riboz, m~quences Sequence analysis of greater than 100 clones representing self cleaving ribozymes from the G6, G9, G 12 and G1 S populations revealed as many as 20 distinct sequence classes of RNAs. In 30 some cases, numerous RNAs conformed to a single class of self cleaving ribozyme based on sequence elements that are common among the related variants. For example, ~30 clones were identified that can form a common secondary structure with similar core nucleotides that we defined as "class I" ribozymes. In other instances, RNAs were isolated that were entirely unique in sequence compared to all other clones. These "orphan" sequences were classified independently, for example, as was done with the "class II" ribozyme. Ultimately, these 20 different sequence classes were grouped into twelve distinct structural classes of self cleaving ribozymes that were identified based on the presence of distinctive sequence elements, secondary structures and cleavage sites (Figure 9).
Only one of the twelve classes (class IX) corresponds to a naturally-occurring RNA - the self cleaving hammerhead ribozyme. The distinctions between the different structural classes of ribozymes were established as described for class I and class II ribozymes below.
For each of the 20 putative sequence classes into which the ribozymes were originally grouped, applicant conducted three to five rounds of reselection (Figure 8A) for self cleavage activity beginning with a population of ribozyme variants based on the nucleotide sequence of a representative clone. As expected, the introduction of random mutations (d =
0.21; see Fedor and Uhlenbeck, 1992, Biochemistry, 31, 12042-12054) into the original N4o domain of each clone decreases the catalytic activity of the population significantly. However, after three to five rounds of reselection, the mutagenized populations recovered significant levels of self cleavage activity. Once the catalytic activity of a particular population became near equal to that of its parent clone, representative ribozyme variants were identified by cloning and sequencing.
The nucleotide sequences corresponding to the variant ribozyme domains of cloned RNAs for each class were aligned to provide an artificial phylogeny. Table 11 shows artificial phylogenetic analysis of class I, class II, and class V ribozymes. Sequence variations are depicted for the 40 nucleotides corresponding to the original random-sequence domain of each parental sequence (numbered). Dots indicate no change from the parental sequence listed first.
The asterisk identifies a class I ribozyme variant that carries mutations at positions 18 and 26 that retain the ability to base pair. For example, applicant observed that the parental sequences of both class I and class II
ribozymes undergo substantial mutation without complete disruption of catalytic activity (Table 11).
However, the pattern of mutation acquisition in each case is indicative of the presence of conserved primary and secondary structures that presumably are important for ribozyme function. Among the ribozyme variants obtained for class I, all retain the prototypic nucleotide sequence at positions 12-16 (Figure 9 and Table 11), suggesting that these nucleotides are critical for self cleavage activity.
Nucleotides 8-14, which overlap with the conserved 12-16 nt region exhibit complementarity to nucleotides within the 3' primer-binding domain. Moreover, the nucleotides at positions 17-19 and 25-27 are both mutually complementary and highly conserved. This indicates that these latter two sequence elements also might form a hairpin structure with intervening nucleotides 20-24 serving as a connecting loop. Consistent with this interpretation is the observation that mutations within positions 17-19 and 25-27 acquired by a class I ribozyme variant (Table 11;
asterisk) allows retention of base complementarity. In addition, the putative loop sequence spanning nucleotides 20-24 tolerates significant mutation as would be expected if the nucleotides in the loop were unimportant for stem formation and ultimately for ribozyme action.
Similar characteristics of structure formation and conserved sequences are evident in the artificial phylogeny for class II ribozymes (Table 11). However, the data indicate that class II
ribozymes form a catalytic structure that is distinct from that of class I.
For example, complementary segments of the original random-sequence domain also are consistent with the formation of two separate stem elements. However, if present, these stems would be arranged differently from those predicted to form in class I ribozymes. At this time only one stem, that formed between nucleotides 8: 11 and 16-19, appears to be present as judged by the emergence of sequence variants in the artificial phylogeny of class II. Moreover, two conserved regions (nucleotides 1-7 and 22-30) (Figure 9 and Table 11) of class II RNAs are different from the conserved sequences found in class I RNAs, indicating that the two classes of ribozymes are indeed distinct.
Likewise, by analysis of the artificial phylogenetic data for the remaining 18 clones, applicant identified as many as 12 distinct classes of ribozymes (Figure 9). In many instances, obscure sequence and structural similarities were revealed between the different sequence classes upon examination of each artificial phylogeny that was generated by reselection.
Such unforeseen similarities were identified typically among representative RNAs that conform to a structural class placing very little demand on sequence conservation in the core of the ribozyme domain (e.g. classes V and VIII). It also is important to note that the structural models depicted in Figure 9 are not intended to represent confirmed secondary structures. In most cases, limited artificial phylogenetic data coupled with preliminary analyses using a secondary-structure prediction algorithm (Zuker, 1989, Science, 244, 48-52) were used to derive the models.
Characterization of Bimolecular Ribozvme Reactions Based on preliminary sequence analysis, class I self cleaving ribozymes form an X-shaped secondary structure (Figure 9). In this model, a separate ribozyme domain base pairs to its corresponding substrate domain with duplex formation occurring both 5' and 3' relative to an unpaired G residue that resides within the nearest neighbor sequence of the original RNA construct (position 4 of the nearest neighbor domain, Figure 8B; position 9 of a 21-nt substrate "S21", Figure 9). This secondary structure arrangement also locates the conserved nucleotides and the putative hairpin structures near this unpaired G residue.
Phosphodiester linkages of residues that reside outside of helical structures are most likely to be targets for ribozyme action. While stable RNA helices restrict conformational freedom of phosphodiester bonds, linkages joining unpaired nucleotides can more easily adopt the "in-line"
geometry that is necessary for internal transesterification (Soukup, 1999, RNA, 5, 1308-1325).
Therefore, the structural model indicates that cleavage of S21 should occur at the G residue residing at position 9 (Figure 9). Consistent with the proposed "X-motif ' model is the observation that a bimolecular construct comprised of S21 and a 46-nt RNA corresponding to the enzyme domain of a minimized X motif variant (Figure 9) exhibits Mgz+-dependent cleavage activity. Furthermore, the RNA cleavage was determined to occur at the phosphodiester linkage that resides 3' relative to the unpaired G (between nucleotides 9 and 10) of 521.
Applicant also examined the cleavage activity of a 44-nt construct that carnes the conserved sequence and structural elements identified in class II ribozymes. This RNA
forms a bimolecular interaction with S21 that presumably leaves unpaired the substrate nucleotides G and A at positions 6 and 7 (Table 11). Consistent with this structural model, we find that the complex is cleaved within S21 between nucleotides 6 and 7 when MgZ+ is included in the reaction mixture.
In a similar fashion, bimolecular structures were tested for eight of the remaining 10 classes. In most instances, ribozyme activity and cleavage patterns are consistent with the proposed secondary structures depicted in Figure 9.
Rate Constants for Prototypic Constructs Representing the 12 Ribozyme Classes Rate constants for RNA transesterification were determined for each of the 12 constructs depicted in Figure 9. For example, both class I and class II constructs produce linear cleavage kinetics through more than one half life of the substrate RNA (Figure 10A).
The representative class I and class II constructs examined herein exhibit rate constants of 0.01 and 0.05 miri', respectively.
Similar examinations of the remaining ribozyme constructs reveal that the rate constants for RNA
cleavage in nearly all cases are below 0.05 miri'. In contrast, rate constants for the natural self cleaving RNAs such as the hammerhead and HDV ribozymes typically range between 1 miri' and 100 miri' (Fedor and Uhlenbeck, 1999, Biochemistry, 31, 12042-12054). For comparison, the uncatalyzed rate of internal RNA transesterification under the selection conditions used is ~10-' miri ' (Li and Breaker, 1999, J. Am. Chem. Soc., 121, 5364-5372). Therefore, even the slowest of constructs depicted in Figure 9 accelerate the chemical step of RNA cleavage by at least 1,000 fold.
The most active prototype construct (class VIII, kobs - 0.1 miri') provides an overall chemical rate enhancement of ~1 million fold over the corresponding uncatalyzed rate.
It is important to note, however, that the original selection and the 20 independent reselections were conducted such that even very slow ribozymes were allowed to persist in the population. The isolation of ribozymes from random sequence employed ribozyme incubation times of 4 hr. Under these selection conditions, RNAs that self cleave with a rate constant greater than 10-3 miri' experience little or no selective disadvantage compared to ribozymes that cleave with infinitely faster cleavage rates. Similarly, the goal of the reselections was to create variant ribozymes that retained activity so that an artificial phylogeny could be created for each representative RNA. The ribozyme incubations during reselection were typically carried out for 30-60 min. Therefore, the selective pressure applied at this stage also was not sufficient to favor the isolation of ribozymes with rates that rival those of naturally occurnng ribozymes.
Ribozyme Cleava a Ribozymes and deoxyribozymes that catalyze the cleavage of RNA via a cyclizing mechanism typically require a specific consensus sequence at the site of cleavage. In most cases, substrate binding specificity is determined by Watson/Crick base pairing between enzyme and substrate domains, and this specificity can easily be engineered by the user. However, the hammerhead ribozyme favors cleavage of the phosphodiester linkage at UH sites, where H
represents A, U or C
(Vaish et al., 1998, PNAS USA, 95, 2158-2162). To maximize the diversity of ribozymes that could be isolated by applicant's selection scheme, applicant included the nearest neighbor domain depicted in Figure 8B. This domain provides a comprehensive sampling of all 16 dinucleotides, thereby offering a greater diversity of cleavage sites than would be present in most substrate domains of arbitrary sequence composition. Applicant found that the 12 classes of ribozymes examined in this study cleave at five different locations within the nearest neighbor domain (Figure 10B). As predicted from RNA cleavage patterns, ribozymes isolated from the G6 population (classes I-IV) cleave at two sites - both near the 5' end of this domain. Similar correspondence between cleavage patterns and cleavage site selection are observed with ribozymes isolated from subsequent rounds.
However, ribozymes from G12 and G15 that generate the largest 5'-cleavage fragments are not representative of new cleavage sites near the 3' end of the nearest neighbor domain. Applicant fords that several ribozymes accumulated insertions in the original NQ°
domain that yield longer 5'-5 cleavage fragments despite processing at sites that are also used by other ribozymes. The most frequently used cleavage site is the linkage between the initial GA
dinucleotide at the 5' end of the nearest neighbor domain, (Figure 10B). However, it is not clear whether or not this dinucleotide sequence is intrinsically favorable to the formation of structures that self cleave.
Class I "X motif' 10 Nearly all ribozyme constructs derived from the reselections (Figure 9) exhibit rate constants for RNA cleavage that are far below the maximum values obtained for the natural self cleaving ribozymes. This observation brings into question whether new RNA-cleaving motifs can even approach the catalytic efficiency of motifs that currently exist in nature.
Until this point, applicant's in vitro selection and reselection efforts have been directed towards the identification and 15 confirmation of new structural motifs for self cleaving ribozymes.
Therefore, the selection reactions intentionally were conducted under exceedingly permissive conditions such that even highly defective variants of new motifs could be enriched in the RNA population and ultimately be identified by cloning and sequencing. Likewise, reselections were conducted under almost equally permissive conditions in order to identify variants that could contribute to the assembly of artificial 20 phylogenies, and not necessarily to produce superior catalysts. Indeed, none of the 20 reselections conducted, including one that was carried out using a mutagenized population derived from hammerhead i, provided variant ribozymes that exhibit kinetic characteristics like those displayed by natural self cleaving ribozymes.
Therefore applicant set out to enrich for ribozyme variants whose rate constants were 25 significantly higher than that of the general population. To this end, applicant pooled RNA samples from G6, G9, G12 and G15. This combined starting population was then subjected to additional rounds of in vitro selection as described in Figure 8A, but where decreasing incubation times (as low as 5 sec) for the selection reaction were used to favor the isolation of the fastest ribozymes.
After 10 additional rounds of selection, applicant found that the resulting RNA population 30 undergoes ~6% cleavage upon incubation for S sec under the permissive reaction conditions.
Surprisingly, only a single 5'-cleavage fragment is observed despite the fact that ribozymes cleaving at multiple sites within the nearest neighbor domain were selectively amplified. These results indicated that a single class of relatively fast ribozymes (kobs ~0.7 miri') has come to dominate the RNA population. Indeed, cloning and sequencing revealed that the population is comprised primarily of a single RNA sequence (Figure 11B) that corresponds to a variation of the original X
motif ribozyme (Figure 9, class I).
A bimolecular construct based on the dominant self cleaving RNA (Figure 11B) exhibits a kobs of ~0.2 miri' under single turn-over conditions, which corresponds to a 20-fold improvement over the corresponding class I construct depicted in Figure 9. This finding suggests that further improvements in catalytic performance might be made to the remaining classes of ribozymes, as the initial constructs examined likely reflect non-optimal variants.
Interestingly, the maximum rate constant expected for optimal hammerhead ribozymes (~1 miri') remains several fold greater than that measured for the bimolecular version of the improved X motif depicted in Figure 11B.
Nevertheless, applicant concludes from these findings that other small RNA
motifs can form RNA-cleaving structures that compare favorably in catalytic rate enhancement with that of natural ribozymes.
Ribozyme Engineering Sequence, chemical and structural variants of ribozymes of the present invention can be engineered using the techniques shown above and known in the art to cleave a separate target RNA
or DNA in traps. For example, the size of ribozymes can be reduced or increased using techniques known in the art (Zaug et al., 1986, Nature, 324, 429; Ruffner et al., 1990, Biochem., 29, 10695;
Beaudry et al., 1990, Biochem., 29, 6534; McCall et al., 1992, Proc. Natl.
Acad. Sci., USA., 89, 5710; Long et al., 1994, Supra; Hendry et al., 1994, BBA 1219, 405; Benseler et al., 1993, JACS, 115, 8483; Thompson et al., 1996, Nucl. Acids Res., 24, 4401;Michels et al., 1995, Biochem., 34, 2965; Been et al., 1992, Biochem., 31, 11843; Guo et al., 1995, EMBO. J., 14, 368; Pan et al., 1994, Biochem., 33, 9561; Cech, 1992, Curr. Op. Struc. Bio., 2, 605; Sugiyama et al., 1996, FEBSLett., 392, 21 S; Beigelman et al., 1994, Bioorg. Med. Chem., 4, 1715; all are incorporated in their totality by reference herein). For example, the stem-loop domains of the ribozymes may not be essential for catalytic activity and hence could be systematically reduced in size using a variety of methods known in the art, to the extent that the overall catalytic activity of the ribozyme is not significantly decreased. In addition, the introduction of variant stem-loop structures via site directed mutagenesis and/or chemical modification may be employed to develop ribozymes with improved catalysis, increased stability, or both.
Further rounds of in vitro selection strategies described herein and variations thereof can be readily used by a person skilled in the art to evolve additional nucleic acid catalysts and such new catalysts are within the scope of the instant invention. In addition, the optimization of these variant ribozyme constructs by modification of stem-loop structures as is known in the art may provide for species with improved cleavage activity.
Example 2: Oligonucleotide synthesis Synthetic DNAs and the 21 nucleotide (nt) RNA substrate (S21) were prepared by standard solid phase methods (Keck Biotechnology Resource Laboratory, Yale University) and purified by denaturing (8 M urea) polyacrylamide gel electrophoresis (PAGE). The 2'-TBDMS
groups of the synthetic RNA were removed by 24 hr treatment with triethylamine trihydrofluoride (15 p1 per AU26° crude RNA). Molecules that were radiolabeled using T4 polynucleotide kinase (T4 PNK, New England Biolabs) and [y-32P]ATP according to the manufacturer's directions were subsequently purified by denaturing 20% PAGE and isolated from the gel by crush-soaking in 10 mM Tris-HCl (pH 7.5 at 23°C), 200 mM NaCI and 1 mM ethylenediaminetetraacetic acid (EDTA) followed by precipitation with ethanol as described below.
Example 3: In vitro Selection The initial population of RNA for in vitro selection was created by first generating a double-stranded DNA template for in vitro transcription. SuperScript~ II reverse transcriptase (RT, GibcoBRL) was used to extend 280 pmoles of the DNA oligonucleotide "primer 1"
(5'-GAAATAAACTCGCTTGGAGTAACCATCAGGAC-AGCGACCGTA-3') (SEQ ID NO 118);
region representing 16 possible nearest neighbor combinations is underlined) using 270 pmoles of the template DNA (5'- TCTAATACGACTCACTATAGGAAGACGTAGCCAA-3') (SEQ ID NO
119) followed by a random region (NQ°) followed by (S'-TACGGTCGCTGTCCTG-3') (SEQ ID NO
120); T7 promoter is underlined and N represents an equal mixture of the four standard nucleotides).
The extension reaction was conducted in a total of 50 p1 containing 50 mM Tris-HCl (pH 8.3 at 23°C), 75 mM KCI, 3 mM MgCl2, 10 mM dithiothreitol (DTT), 0.2 mM each of the four deoxyribonucleoside-5' triphosphates (dNTPs), and 10 U p1-' RT by incubation at 37°C for 1 hr. The resulting double-stranded DNA was precipitated by the addition of S p1 3 M
sodium acetate (pH 5.5) and 140 p1 100% ethanol and pelleted by centrifugation. This extension reaction provides 10'4 different template sequences.
The DNA templates were transcribed in a total volume of 100 p1 containing 50 mM Tris-HCl (pH 7.5 at 23°C), 10 mM MgClz, 50 mM DTT, 20 mM spermidine, 2 mM each of the four ribonucleoside-5' triphosphates (NTPs), and 35 U p1-' T7 RNA polymerise (T7 RNAP) by incubation at 37°C for 1 hr. [a-'zP]UTP was added to the transcription reaction to produce internally ~ZP-labeled RNAs when necessary. The reaction was terminated by the addition of 50 p l 40 mM
EDTA and precipitated by the addition of the appropriate amounts of sodium acetate and ethanol.
The uncleaved precursor RNAs were isolated by denaturing 10% PAGE, recovered from the gel as described above and stored in deionized water (dHzO) at -20°C until use. In subsequent rounds of selection, double-stranded DNA from the polymerise chain reaction (PCR) was transcribed as described above, but for shorter periods of time (e.g. 10 min) to minimize the loss of ribozymes that efficiently cleave during transcription.
The initial selection reaction (GO) contained 2000 pmoles of RNA in a total of 400 p1 reaction buffer (SO mM HEPES [pH 7.5 at 23°C], 250 mM KCl and 20 mM MgClz) and was incubated at 23°C for 4 hr. The reaction was terminated by the addition of EDTA and the RNA was recovered by precipitation with ethanol. RNA cleavage products were separated by denaturing 10% PAGE, visualized and quantified using a Molecular Dynamics PhosphorImager~, and the gel region corresponding to the location of the desired RNA cleavage products was excised. The RNA was recovered from the excised gel by crush-soak elution followed by precipitation with ethanol. The selected RNAs were amplified by RT-PCR as described previously (10) using primers l and 2 (5'-GAATTCTAATACGACTCACTATAGGAA-GACGTAGCCAA-3') (SEQ ID NO 121); T7 promoter is underlined). The resulting double-stranded DNA from each round of in vitro selection was used to transcribe the RNA population for the subsequent round, in which all steps were conducted at ~1/10'h the scale of G0. All other parameters of the selection process were maintained as in G0. Representative ribozymes from the populations derived from 6, 9, 12 and 15 rounds of selection were examined by cloning (TOPO~-TA cloning kit; Invitrogen) and sequencing (ThermoSequenase~ kit; Amersham Pharmacia).

Example 4: Artificial Phylo~y Generation To confirm the self cleaving activity of various clones, internally 'ZP-labeled ribozyme precursors were incubated under the selection reaction conditions for up to several hours to detect cleavage products upon separation by denaturing 10% PAGE. Artificial phylogenies for active clones each representing one of ~20 different sequence classes were generated by conducting reselections after the introduction of mutations. Reselections were conducted by first synthesizing a DNA construct for each individual that corresponds to the template strand for in vitro transcription.
In each case, the nucleotides corresponding to the original random-sequence domain were synthesized with a degeneracy (d) of 0.21 per position, such that all possible variants with six or fewer mutations relative to the original sequence are represented. Typically, three to five rounds of selective amplification as described above (using selection reaction incubations of 1 hr or less) were required for each population to exhibit a level of catalytic activity that corresponded to that of the original clone. When this occurred, the population was cloned and sequenced.
Example 5: Characterization of Ribozyme Catalytic Function In most cases, more detailed kinetic and structural characterizations of ribozymes from different structural classes were conducted with a variant from the corresponding artificial phylogeny that contains the mutations most commonly acquired during reselection. Initial rate constants for self cleavage (classes VI and VII) were determined by incubating internally 3zP-labeled ribozyme precursors in selection buffer for various times, separating the products by PAGE, and quantifying the yields by PhosphorImager~. Rate constants were derived as previously described (Soukup and Breaker, 1999, Proc. Natl. Acad. Sci. USA, 96, 3584-3589). Rate constants for bimolecular ribozyme function were established using a similar strategy, except that the reactions were allowed to proceed through at least two half lives of the substrate. To achieve single turnover conditions, trace amounts of 32P-labeled substrate were incubated with S00 nM
ribozyme.
Cleavage sites for unimolecular reactions were determined by incubating 5' 3ZP-labeled precursor RNA in selection buffer, separating the products by denaturing 10%
PAGE and comparing the gel mobility of the S' cleavage fragment to that of each cleavage fragment generated by partial RNA digestion using RNase T1 or alkali as described previously (Soukup and Breaker, 1999, RNA, 5, 1308-1325). Similarly, the cleavage site for each bimolecular ribozyme reaction was established by incubating trace amounts of S' 3ZP-labeled substrate RNA with S00 nM
ribozyme and comparing the products of ribozyme cleavage, RNase T1 digestion, and alkaline digestion using denaturing 20% PAGE.
Example 6: Chemical stabilization of ribozyme motif (Class V) Examples of stabilized Class V ribozymes and control ribozymes useful in this study are 5 shown in Table 10. Initially, ribozymes (Class V) were designed with varying combinations of 2'-O-methyl nucleotides. The ribozymes were chemically synthesized. Cleavage reactions were carried out with 500 nM final ribozyme concentration, single turnover kinetics in SO mM Tris-Cl pH
7.5, 150 mM KCI, 20 mM Mg2+, 37C and trace substrate. Results are summarized in Table 5. The all ribo wild type V ribozyme used as a control (RPI No. 14189) resulted in a cleavage rate (Kobs) of 10 0.044 mint . Two of the 2'-O-methyl constructs (RPI No. 14880 with 6 and 7 substituted 2'-O-Me arms, and RPI No. 14881 with 5 and 7 substituted 2'-O-Me arms), both resulted in improved cleavage activity with Kobs values of 0.066 min-1. RPI construct No 14880 was subsequently used as a control for a study to determine the effect of 2'-O-methyl substitution in the Class V ribozyme motif core via a 2'-O-methyl "walk" experiment using the same cleavage reaction conditions as 15 above. The results of this study are summarized in Figure 13 with Kobs and Kre~ values summarized in Table 6. The effect of various combinations of 2'-O-methyl substitutions in the Class V ribozyme core was investigated under the same conditions. Table 7 outlines the results of this study in which a "seven ribose" core motif emerged with a Kobs value of 0.127 min-1. This seven ribose motif of the Class V ribozyme (RPI No. 15705) was used as the base motif for further 20 core stabilization studies. Additional experiments focused on stabilization of the core pyrimidine residues of the Class V motif. Table 8 summarizes data from an experiment determining the cleavage activity Class V motif ribozymes with modified core pyrimidines with phosphorodithioate, 2'-fluoro, 2'-amino, and 2'-deoxy substitutions. This study indicates that the C7 position (Figure 13) is the most tolerant to modifications while the U4 position is the least tolerant to modification.
25 Further reductions in ribo core residues resulted in ribozymes with decreased activity relative to the "seven ribo" core version of the Class V motif, however, these further stabilized versions retained activity. Testing of the further reduced ribo constructs in conjunction with additional chemical modifications is summarized in Table 9.

Example 7: Similarity between Class I and Class VIII ribozymes Two strategies were used to examine whether the Class I and Class VIII
ribozymes share sequence and structural similarities. First, a series of fourteen variant constructs were generated that examined the importance of various structural features of Class VIII
ribozymes. For example, the 5'-leader sequence of Class VIII is essential, only when the extra bulge immediately preceding the stem II element is present. If this bulge and putative stem II element is replaced by a more convincing stem II structure like that present in the Class I motif structure (Figure 14), then the leader sequence of Class VIII can be eliminated. In a similar fashion, other elements of Class VIII
ribozymes when examined, show similarity to those of Class I ribozymes. A
series of kinetic analyses were used to compare the characteristics of the Class I and Class VIII motifs. In each case, the bimolecular constructs depicted in Figure 14 were used for comparison.
Each of these substrates (trace) can be saturated with ribozyme as depicted in Figure 15a.
Furthermore, each motif has near identical characteristics upon variation of monovalent salt (Figure 15b), pH (Figure 15c), and divalent magnesium (Figure 15d). These results support the view that, at their respective core, the Class I and Class VIII motifs are similar.
Diagnostic uses Enzymatic nucleic acids of this invention can be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of target RNA in a cell. The close relationship between enzymatic nucleic acid activity and the structure of the target RNA allows the detection of mutations in any region of the molecule which alters the base-pairing and three-dimensional structure of the target RNA. By using multiple enzymatic nucleic acids described in this invention, one can map nucleotide changes which are important to RNA
structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with enzymatic nucleic acids can be used to inhibit gene expression and define the role (essentially) of specified gene products in the progression of disease. In this manner, other genetic targets can be defined as important mediators of the disease. These experiments can lead to better treatment of the disease progression by affording the possibility of combinational therapies (e.g., multiple enzymatic nucleic acids targeted to different genes, enzymatic nucleic acids coupled with known small molecule inhibitors, or intermittent treatment with combinations of enzymatic nucleic acids and/or other chemical or biological molecules). Other in vitro uses of enzymatic nucleic acids of this invention are well known in the art, and include detection of the presence of mRNAs associated with disease condition. Such RNA is detected by determining the presence of a cleavage product after treatment with a Enzymatic nucleic acid using standard methodology.
In a specific example, enzymatic nucleic acids which can cleave only wild-type or mutant forms of the target RNA are used for the assay. The first enzymatic nucleic acid is used to identify wild-type RNA present in the sample and the second enzymatic nucleic acid can be used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNA can be cleaved by both enzymatic nucleic acids to demonstrate the relative enzymatic nucleic acid efficiencies in the reactions and the absence of cleavage of the "non-targeted" RNA species.
The cleavage products from the synthetic substrates will also serve to generate size markers for the analysis of wild-type and mutant RNAs in the sample population. Thus each analysis can involve two enzymatic nucleic acids, two substrates and one unknown sample which can be combined into six reactions. The presence of cleavage products can be determined using an RNAse protection assay so that full-length and cleavage fragments of each RNA can be analyzed in one lane of a polyacrylamide gel. It is not absolutely required to quantify the results to gain insight into the expression of mutant RNAs and putative risk of the desired phenotypic changes in target cells. The expression of mRNA whose protein product is implicated in the development of the phenotype is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels will be adequate and will decrease the cost of the initial diagnosis. Higher mutant form to wild-type ratios will be correlated with higher risk whether RNA
levels are compared qualitatively or quantitatively.
Additional Uses Potential uses of sequence-specific enzymatic nucleic acid molecules of the instant invention include many of the same applications for the study of RNA that DNA
restriction endonucleases have for the study of DNA (Nathans et al., 1975 Ann. Rev. Biochem. 44:273).
For example, the pattern of restriction fragments can be used to establish sequence relationships between two related RNAs, and large RNAs can be specifically cleaved to fragments of a size more useful for study. The ability to engineer sequence specificity of the enzymatic nucleic acid is ideal for cleavage of RNAs of unknown sequence.
The nucleic acid catalysts of the instant invention can be used to specifically cleave an RNA
sequence for which an appropriately engineered nucleic acid catalyst base pairs at the designated flanking regions (e.g., X and Y in Formulae I - IV). Suitable target RNA
substrates include viral, messenger, transfer, ribosomal, nuclear, organellar, other cellular RNA, or any other natural RNA
having a cleavage sequence, as well as RNAs, which have been engineered to contain an appropriate cleavage sequence. The nucleic acid catalysts are useful in vivo in prokaryotes or eukaryotes of plant or animal origin for controlling viral infections or for regulating the expression of specific genes.
Once introduced into the cell, the nucleic acid catalyst binds to and cleaves the target RNA
sequence or sequences for which it has been designed, inactivating the RNA. If the RNA is necessary for the life cycle of a virus, the virus will be eliminated and if the RNA is the product of a specific gene, the expression of that gene will thus be regulated. The nucleic acid catalyst can be designed to work in prokaryotes and within the nucleus (without poly(A) tail) or in the cytoplasm of a eukaryotic cell (with polyadenylation signals in place) for plants and animals.
All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.
One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The methods and compositions described herein as presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention.
Changes therein and other uses will occur to those skilled in the art, which are encompassed within the spirit of the invention, are defined by the scope of the claims.
It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. Thus, such additional embodiments are within the scope of the present invention and the following claims.
The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. Thus, for example, in each instance herein any of the terms "comprising", "consisting essentially of", and "consisting of may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments, optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the description and the appended claims.
In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.
Thus, additional embodiments are within the scope of the invention and within the claims that follow.

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Table 3: Kinetic unimolecular parameters of selected clones Observed Amount CIaSS Clone Cleavage site rate constant Processed I 23 nt 4 nd Nd 27 nt 4 0.024 80%
51 nt 4 0.0048 nd~
II 37 nt 6 0.0074 70%
47 nt 6 nd Nd 53 nt 6 nd Nd III 21 nt 4 0.014 7%
IV 32 nt 7 0.093 50%
V 52 nt 1 0.014 70%
VI 33 Inactive nd nd 34 nt 7~ nd nd Reaction conditions: 0.5 mM MgCl2, 7 mM putrescine, 10 mM glutathione, SO
mM HEPES pH 7.6, 37°C.
Cleavage site: enzyme cleaves after the indicated nucleotide, numbered 1 to 13 (Figure 1) within the RNA region.
Observed rate constant is in units of mine.
Amount processed is the amount of cleavage at which the reaction plateaus.
*Reaction kinetics changed during the time course such the new reaction did not asymptotically approach a minimum.
~Enzyme had reacted prior to assay and did not react further. Presumably it reacted during elution from the purification gel but these conditions could not be duplicated.

Table 4: Relative cleavage rates of Class I DNAzyme motif on various substrates Substrate Substrate sequence Relative SEQ ID NO
name rate of cleavage*

Model, FigureaagagUAA-UAA-UGAAAGCag1 44 Figure Sa, GAGGGUAU-UAA-UAAUGAAAG0.18 45 site 1 Figure Sa, GGUAUUAA-UAA-UGAAAGCUA0.30 46 site 2 Figure Sb, GGGAAUGC-UAA-UCUACUACG0.0057 47 site 1 Figure Sb, CUACUACG-UAA-UCAGCAACG0 48 site 2 Figure 5b, CAGCAACG-UAA-UGCUCUGUA0.011 49 site 3 Figure Sb, GCUCUGUA-UAA-UGACGACUG0 I 50 site 4 I I

Legend: The catalytic core from G1 to T19 shown in Figure 2 was synthesized between arms that base-pair to the substrate sequence such that the U immediately 3' to the cleavage site is engaged in a wobble pair with G1 of the catalytic core and the UAA separately by hyphens is bulged. Cleavage site is 3' to the U of the bulged UAA. Substrates are RNA except for the model substrate where DNA is indicated by lowercase.
Assay conditions: 50 ~tM enzyme, trace (<5) nM substrate, 2 mM Mg2+, 150 mM K+, 7 mM putrescine, pH 7.6, 37°C
* This data is meant for comparison only. Assays for the substrate sites in Figure 5B are not multiple-point rate assays and the rate constant is estimated from a single time point. For this reason, the actual rate constants or estimated rate constants have been normalized to the rate for the model substrate so that the actual values will not be emphasized.

Table 5: Class V ribozyme 2'-O- methyl arm optimization RPI No. DESCRIPTION ~ obs min. I) % in 1s' exponential 14880 6 7 2'-O-Me arms0.066 82.3 14881 5 ,7 2'-O-Me 0.066 81.0 arms 14189 WT all ribose 0.044 72.5 "bulged U"

14882 S G 2'-O-Me arms0.043 76.6 14883 5 5 2'O-Me arms 0.037 75.4 14885 4 4 2'-O-Me arms0.031 84.0 14884 4 5 2'-O-Me arms0.030 82.8 14879 6 8 2'-O-Me arms0.0009 60.0 Table 6: Class V ribozyme motif 2'-O-methyl core "wal k"
RPI No. DESCRIPTION k obs ~min.-~)Krel to .20672 14189 WT All Ribose 0.036 0.64 Assa Control 14880 6 7 2'-OMe Arms 0.061 1.09 e1- urified 15297 6 7 2'-OMe Arms 0.056 / 0.058 1.00 crude s nthesis 15305 G 7 2'-OMe Arms 0.072 1.29 +

Core 2'-OMe A6 15310 7 7 2'-OMe Arms 0.070 1.25 ribo core 15309 6 7 2'-OMe Arms 0.069 1.23 +

Core 2'-OMe G2 15299 6 7 2'-OMe Arms 0.068 1.21 +

Core 2'-OMe A12 15300 G c 7 2'-OMe Arms0.060 1.07 +

Core 2'-OMe All 15306 6 7 2'-OMe Arms 0.057 1.02 +

Core 2'-OMe A5 15301 6 7 2'-OMe Arms 0.050 0.89 +

Core 2'-OMe G10 15298 6 7 2'-OMe Arms 0.030 0.54 +

Core 2'-OMe G13 15303 6 7 2'-OMe Arms 0.029 0.52 +

Core 2'-OMe G8 15304 6 7 2'-OMe Arms 0.017 0.30 +

Core 2'-OMe C7 - 15308 6 7 2'-OMe Arms 0.010 0.17 +

Core 2'-OMe A3 15302 6 7 2'-OMe Arms 0.0004 0.007 +

Core 2'-OMe U9 15307 G 7 2'-OMe Arms 0.0001 0.002 +

Core 2'-OMe U4 15311 All 2'-OMe 0.00008 0.001 A14.1 = Ribo Table 7: Class V ribozyme motif combination core RPI No. DESCRIPTION k o6, (min:') k,e, to .20672 (all other residues All Ribo Core = 2'-O-Meth 1 15705 7 RIBO CORE 0.127 2.31 A3, U4, C7, G8, U9, G13, A14.1 = ribo 15297 ALL RIBO "CORE" 0.055 1.00 G2 - A14.1 = ribo 15702 6 RIBO CORE 0.036 0.65 U4, C7, G8, U9, G13, A14.1 = ribo 15700 4 RIBO "CORE" 0.0019 0.03 U4, C7, U9, A14.1 = ribo 15701 5 RIBO "CORE" 0.0012 0.02 U4, C7, G8, U9, A14.1 = ribo 15703 3 RIBO CORE 0.0006 0.01 U4, U9, A14.1 =
ribo 15704 3 RIBO CORE 0.0006 0.01 U4, U9, A14.1 =
ribo Table 8: Class V ribozyme motif with pyrimidine stabilized core RPI NO. DESCRIPTION k abs (min.-')k~~i to .21422k~ei to .20b (7 Ribo Core)(All Ribo C

15705 7 RIBO CORE 0.113 1.00 2.05 A3, U4, C7, G8, U9, G13, A14.1 = ribo 16188 "7 ribo" 0.144 1.28 2.62 U4 = PS2 16191 "6 ribo" 0.121 1.07 2.2 C7 = 2'F-C

16197 "6 ribo" 0.063 0.56 1.15 C7 = 2-NH2-C

16186 "7 ribo" 0.063 0.56 1.15 U9 = PS2 16194 "6 ribo" 0.030 0.27 0.55 C7 = 2-deoxy-C

16196 "6 ribo" 0.025 0.22 0.45 U9 = 2-NH2-U

16192 "6 ribo" 0.015 0.13 0.27 U9 = 2'F-U

16195 "6 ribo" 0.011 0.10 0.20 U9 = 2-deoxy-U

16198 "6 ribo" 0.001 0.009 0.02 U4 = 2-NH2-U

16190 "6 ribo" 0.0005 0.004 0.009 U4 = 2'F-U

16193 "6 ribo" 0.0002 0.002 0.004 U4 = 2'-deoxy-U

PS2 = phosphorodithioate linkage 2'-F-U = 2'-deoxy-2'-fluoro uridine 2'-F-C = 2'-deoxy-2'-fluoro cytidine 2'-NH2-U = 2'-deoxy-2'-amino uridine 2'-NH2-C = 2'-deoxy-2'-amino cytidine Table 9: Class V ribozyme motif with reduced ribo content RPI NO DESCRIPTION k obs kr~~ to .21422kre~ to .20672 (min.-') (7 Ribo Core)(All Ribo Core;

A3, U4, C7, G8, 0.117 1.00 2.13 U9, G13, A14.1 = ribo U4, G8, U9, A14.1 0.041 0.35 0.75 =

ribo U4, U9 = PS 0.0008 0.007 0.02 C7 = 2'-OMe U4, U9 = PS 0.0018 0.02 0.03 C7 = 2'-OMe U4 = PS, U9 = NH2 0.0003 0.003 0.005 C7 = 2'-OMe U4 = PS, U9 = NH2 0.0006 0.005 0.01 C7 = 2'-OMe U4 = PS, U9 = NH2 0.0021 0.02 0.04 C7 = 2'-F

C7 = PS 0.105 0.90 1.91 U4, U9 = PS 0.022 0.19 0.40 C7 = 2'-OMe U4, U9 = PS 0.012 0.10 0.22 C7=2'F

PS = phosphorothioate linkage 2'-F = 2'-deoxy-2'-fluoro Table 10: Class V ribozymes Synth . SEQ RPI Ribozyme No. ID No.
#

19984 51 14880 gga guaA GA CGUGAAG Au caggacB
UAA

19985 52 14881 gga guAA GA CGUGAAG Au caggacB
UAA

UAA G

19986 54 14882 gga guAA GA CGUGAA AU caggacB
UAA G

19987 55 14883 gga guAA GA CGUGAAG AU CaggacB
UAA

19989 56 14885 gga gUAA GA CGU AU CAggacB
UAA GAA
G

19988 57 14884 gga gUAA GA CGUGAAG AU CaggacB
UAA

19983 58 14879 gga guaA GA CGUGAAG au caggacB
UAA

20672 59 15297 gga guaA GA CGUGAAG Au caggacB
UAA

20680 60 15305 gga guaA GA CGUGAAG Au caggacB
UAa 20685 61 15310 gga guaa GA CGUGAAG Au caggacB
UAA

20684 62 15309 gga guaA GA CGUGAAG Au caggacB
UAA

20674 63 15299 gga guaA GA CGUGAaG Au caggacB
UAA

20675 64 15300 gga guaA GA CGU Au caggacB
UAA GaA
G

20681 65 15306 gga guaA GA CGUgAA Au caggacB
UaA G

20676 66 15301 gga guaA GA CGUGAAG Au caggacB
UAA

20673 67 15298 gga guaA GA CGUGAAg Au caggacB
UAA

20678 68 15303 gga guaA GA CgUGAAG Au caggacB
UAA

20679 69 15304 gga guaA GA cGUGAA Au caggacB
UAA G

21076 70 15308 gga guaA GA CGUGAAG Au caggacB
UAA

20677 71 15302 gga guaA GA CGuGAAG Au caggacB
UAA

21075 72 15307 gga guaA GA CGUGAAG Au caggacB
uAA

20686 73 15311 gga guaa ga cgugaag Au caggacB
uaa 21422 74 15705 gga guaa gA CGUgaaG Au caggacB
Uaa 21577 75 15702 gga guaa ga CGUgaaG Au caggacB
Uaa 21417 76 15700 gga guaa ga CgUgaag Au caggacB
Uaa 21418 77 15701 gga guaa ga CGUgaag Au caggacB
Uaa 21420 78 15703 gga guaa ga cgUgaag Au caggacB
Uaa 21421 79 15704 gga guaa ga cgUgaag Au caggacB
Uaa 22128 80 16188 gga guaa CGU cag gA US2aa gaa gacB
G
Au 22131 81 16191 gga guaa gA CGUgaaG Au caggacB
Uaa 22137 82 16197 gga guaa gA CGUgaaG caggacB
Uaa Au 22126 83 16186 gga guaa gaa cag gA Uaa G gacB
CGUS2 Au 22134 84 16194 gga guaa gA CGUgaaG Au caggacB
Uaa 22136 85 16196 gga guaa gA CGUgaaG Au caggacB
Uaa 22132 86 16192 gga guaa gA CGUgaaG Au caggacB
Uaa 22135 87 16195 gga guaa gA CGUgaaG Au caggacB
Uaa 22138 88 16198 gga guaa gA CGUgaaG Au caggacB
Vaa 22130 89 16190 gga guaa gA CGUgaaG Au caggacB
Uaa 22133 90 16193 gga guaa gA CGUgaaG Au caggacB
Uaa 21818 91 16013 gga guaa ga cGUgaag Au caggacB
Uaa 23786 92 17584 gga guaa cGUSgaa caggacB
ga Usaa g Au 23787 93 17585 gga guaa cGUSgaa caggacB
ga Usaa G
Au 23788 94 17586 gga guaaga UsaacGU gaag AucaggacB

23789 95 17587 gga guaaga UsaacGU gaaG AucaggacB

23791 96 17589 gga guaaga UsaaCGU gaaG AucaggacB

23792 97 17590 gga guaaga Uaa gaaG caggacB
CSGU Au 23793 98 17591 gga guaaga UsaacGUSgaaG AucaggacB

24021 99 17588 gga guaaga UgaaCGUggaag AucaggacB
I

U, C = 2'-deoxy-2'-fluoro Uridine, Cytidine U, C = 2'-deoxy Uridine, Cytidine U, C = 2'-deoxy-2'-amino Uridine, Cytidine UPPER CASE = RIBO
lower case = 2'-O-Methyl S = phosphorothioate linkage S2 - phosphorodithioate linkage B = 3',3'-inverted deoxyabasic moiety

Claims (96)

Claims What is claimed is:

1. A nucleic acid molecule with endonuclease activity having the formula I:
wherein, X and Y are independently oligonucleotides of lengths sufficient to stably interact with a target nucleic acid molecule, and Z is independently a nucleotide sequence comprising 5'-GATGCAGCTGGGGAGGCGTTT-3' (SEQ ID NO 51).

2. A nucleic acid molecule with endonuclease activity having the formula II:
wherein, X and Y are independently oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule, R is independently a nucleotide sequence comprising 5'-GGGGA-3', V represents a nucleotide or non-nucleotide linker, which may be present or absent;
and W is independently an oligonucleotide comprising a nucleotide sequence selected from the group consisting of 5'-TGGGGAAGCACAGGGT-3' (SEQ ID NO 52), 5'-TGGGGAAGCTCTGGGT-3' (SEQ ID NO 53), 5'-TGGGGAAGCACAGGGT-3' (SEQ ID NO
54), and 5'-TGGGGAAGCACAGGGT-3' (SEQ ID NO 55).

3. The nucleic acid molecule of claim 2, wherein V is a nucleotide linker.

4. The nucleic acid molecule of claim 2, wherein V is a non-nucleotide linker.

5. The nucleic acid molecule of claim 3, wherein said nucleotide linker is a sequence selected from the group consisting of 5'-ACCTGAGGG-3', 5'-GCGTTAG-3' and 5'-AGGAAGCATCTTATGCGACC-3' (SEQ ID NO 56).

6. The nucleic acid molecule of claim 3, wherein said nucleotide linker is a nucleic acid aptamer.

7. The nucleic acid molecule of claim 6, wherein said aptamer is an ATP
aptamer.

8. The nucleic acid molecule of claim 1 or claim 2, wherein said chemical linkage is independently or in combination selected from the group consisting of phosphate ester , amide , phosphorothioate, phosphorodithioate, methylphosphonate, arabino, and arabinofluoro linkages.

9. The nucleic acid molecule of claim 1 or claim 2, wherein said nucleic acid molecule is chemically synthesized.

10. The nucleic acid molecule of claim 1 or claim 2, wherein said nucleic acid molecule comprises at least one sugar modification.

11. The nucleic acid molecule of claim 1 or claim 2, wherein said nucleic acid molecule comprises at least one nucleic acid base modification.

12. The nucleic acid molecule of claim 1 or claim 2, wherein said nucleic acid molecule comprises at least one phosphate backbone modification.

13. The nucleic acid molecule of claim 10, wherein said sugar modification is a 2'-modification.

14. The nucleic acid molecule of claim 13, wherein said sugar modification is selected from the group consisting of 2'-O-methyl, 2'-O-allyl, 2'-C-allyl, 2'-deoxy-2'-fluoro, 2'-deoxy-2'-arabinofluoro, 2'-deoxy-2'-amino, and 2'-O-amino modifications.

15. The nucleic acid molecule of claim 12, wherein said phosphate backbone modification is selected from the group consisting of phosphorothioate, phosphorodithioate, methylphosphonate, and amide modifications.

16. The nucleic acid molecule of claim 1 or claim 2, wherein said nucleic acid molecule comprises a 5'-cap, a 3'-cap, or both a 5'-cap and a 3'-cap.

17. The nucleic acid molecule of claim 16, wherein said 5'-cap is a phosphorothioate modification of at least one 5'-terminal nucleotide in said nucleic acid molecule.

18. The nucleic acid molecule of claim 16, wherein said 5'-cap is a phosphorothioate modification of at least two 5'-terminal nucleotides in said nucleic acid molecule.

19. The nucleic acid molecule of claim 16, wherein said 5'-cap is a phosphorothioate modification of at least three 5'-terminal nucleotides in said nucleic acid molecule.

20. The nucleic acid molecule of claim 16, wherein said 5'-cap is a phosphorothioate modification of at least four 5'-terminal nucleotides in said nucleic acid molecule.

21. The nucleic acid molecule of claim 16, wherein said 3'-cap is a 3'-3' inverted riboabasic moiety.

22. The nucleic acid molecule of claim 16, wherein said 3'-cap is a 3'-3' inverted deoxyriboabasic moiety.

23. The nucleic acid molecule of any of claims 1 and 2, wherein said nucleic acid cleaves a separate nucleic acid molecule.

24. The nucleic acid molecule of claim 23, wherein said separate nucleic acid molecule is RNA.

25. The nucleic acid molecule of claim 23, wherein said nucleic acid comprises between 12 and 100 bases complementary to said separate nucleic acid molecule.

26. The nucleic acid molecule of claim 23, wherein said nucleic acid comprises between 14 and 24 bases complementary to said separate nucleic acid molecule.

27. The nucleic acid molecule of claim 1 or claim 2, wherein said X and Y are independently lengths selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, and 20 nucleotides.

28. The nucleic acid molecule of claim 1 or claim 2, wherein the length of said X is equal to the length of said Y.

29. The nucleic acid molecule of claim 1 or claim 2, wherein the length of said X is not equal to the length of said Y.

30. A cell including the nucleic acid molecule of claim 1 or claim 2.

31. The cell of claim 30, wherein said cell is a prokaryotic cell.

32. The cell of claim 30, wherein said cell is a eukaryotic cell.

33. The cell of claim 30, wherein said cell is a mammalian cell.

34. The cell of claim 33, wherein said cell is a human cell.

35. The cell of claim 30, wherein said cell is a plant cell.

36. An expression vector comprising a nucleic acid sequence encoding at least one of the nucleic acid molecules of claim 1 or claim 2, in a manner which allows expression of the nucleic acid molecule.

37. A cell including the expression vector of claim 36.

38. The cell of claim 37, wherein said cell is a mammalian cell.

39. The cell of claim 38, wherein said cell is a human cell.

40. A pharmaceutical composition comprising the nucleic acid molecule of claim 1 or claim 2.

41. A method for modulating expression of a gene in a plant cell by administering to said cell the nucleic acid molecule of claim1 or claim 2.

42. A method for modulating expression of gene in a mammalian cell by administering to said cell the nucleic acid molecule of claim 1 or claim 2.

43. A method for modulating expression of gene in a bacterial cell by administering to said cell the nucleic acid molecule of claim 1 or claim 2.

44. A method for modulating expression of gene in a fungal cell by administering to said cell the nucleic acid molecule of claim 1 or claim 2.

45. A method of cleaving a separate nucleic acid comprising, contacting the nucleic acid molecule of claim 1 or claim 2 with said separate nucleic acid molecule under conditions suitable for the cleavage of said separate nucleic acid molecule.

46. The method of claim 45, wherein said cleavage is carried out in the presence of a divalent cation.

47. The method of claim 46, wherein said divalent cation is Mg2+

48. A nucleic acid molecule with endonuclease activity having the formula III:
wherein, each N represents independently a nucleotide or a non-nucleotide linker, which may be same or different; X and Y are independently oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule; m, n, o, and p are integers independently greater than or equal to 1, wherein if (N)m and (N)n and/or (N)o and (N)p are nucleotides, (N)m and (N)n and/or (N)o and (N)p are optionally able to interact by hydrogen bond interaction; D is U, G or A; and L1 and L2 are independently linkers, which may be the same or different and which may be present or absent, but when present, are nucleotide and/or a non-nucleotide linkers which may be a single-stranded and/or double-stranded region.

49. A nucleic acid molecule with endonuclease activity having the formula IV:
wherein, N represents a nucleotide or a non-nucleotide linker; X and Y are independently oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule; and Z
is an oligonucleotide having a nucleotide sequence selected from the group consisting of 5'-AGAUAACGUGAAGAU-3' (SEQ ID NO 53) and 5'-AAUGGCCUAUCGGUGCGA-3' (SEQ
ID NO 54).

50. The nucleic acid molecule of claim 48, wherein said (N)m is selected from the group consisting of 5'-AC-3', 5'-GC-3', and 5'-CG-3' and (N)n is selected from the group consisting of 5'-GU-3', 5'-GC-3', and 5'-CG-3'.

51. The nucleic acid molecule of claim 48, wherein said (N)o is selected from the group consisting of 5'-AUUG-3', 5'-UUG-3', 5'-UUC-3', and 5'-UAG-3' and (N)p is selected from the group consisting of 5'-CAAU-3', 5'-CAA-3', 5'-GAA-3', and 5'-CUA-3'.

52. The nucleic acid molecule of claim 48, wherein L1 is a nucleotide linker.

53. The nucleic acid molecule of claim 48, wherein L2 is a nucleotide linker.

54. The nucleic acid molecule of claim 52, wherein said nucleotide linker is a sequence consisting of 5'-CUUAA-3'or 5'-CUAAA-3'.

55. The nucleic acid molecule of claim 53, wherein said nucleotide linker is a sequence consisting of 5'-UGUGAA-3'or 5'-GUGA-3'.

56. The nucleic acid molecule of claim 52 or claim 53, wherein said nucleotide linker is a nucleic acid aptamer.

57. The nucleic acid molecule of claim 56, wherein said aptamer is an ATP
aptamer.

58. The nucleic acid molecule of claim 48, wherein L1, L2 or L1 and L2 is a non-nucleotide linker.

59. The nucleic acid molecule of claim 48 or claim 49, wherein said chemical linkage is independently or in combination selected from the group consisting of phosphate ester linkage, amide linkage, phosphorothioate, phosphorodithioate, arabino, and arabinofluoro linkages.

60. The nucleic acid molecule of claim 48 or claim 49, wherein said nucleic acid molecule is chemically synthesized.

61. The nucleic acid molecule of claim 48 or claim 49, wherein said nucleic acid molecule comprises at least one sugar modification.

62. The nucleic acid molecule of claim 48 or claim 49, wherein said nucleic acid molecule comprises at least one nucleic acid base modification.

63. The nucleic acid molecule of claim 48 or claim 49, wherein said nucleic acid molecule comprises at least one phosphate backbone modification.

64. The nucleic acid molecule of claim 61, wherein said sugar modification is selected from the group consisting of 2'-H, 2'-O-methyl, 2'-O-allyl, 2'-C-allyl, 2'-deoxy-2'-fluoro, and 2'-deoxy-2'-amino modifications.

65. The nucleic acid molecule of claim 63, wherein said phosphate backbone modification is selected from the group consisting of phosphorothioate, phosphorodithioate, and amide modifications.

66. The nucleic acid molecule of claim 48 or claim 49, wherein said nucleic acid molecule comprises a 5'-cap, a 3'-cap, or both a 5'-cap and a 3'-cap.

67. The nucleic acid molecule of claim 66, wherein said 5'-cap is a phosphorothioate modification of at least one 5'-terminal nucleotide in said nucleic acid molecule.

68. The nucleic acid molecule of claim 66, wherein said 5'-cap is a phosphorothioate modification of at least two 5'-terminal nucleotides in said nucleic acid molecule.

69. The nucleic acid molecule of claim 66, wherein said 5'-cap is a phosphorothioate modification of at least three 5'-terminal nucleotides in said nucleic acid molecule.

70. The nucleic acid molecule of claim 66, wherein said 5'-cap is a phosphorothioate modification of at least four 5'-terminal nucleotides in said nucleic acid molecule.

71. The nucleic acid molecule of claim 66, wherein said 3'-cap is a 3'-3' inverted riboabasic moiety.

72. The nucleic acid molecule of claim 66, wherein said 3'-cap is a 3'-3' inverted deoxyriboabasic moiety.

73. The nucleic acid molecule of any of claims 48 and 49, wherein said nucleic acid cleaves a separate nucleic acid molecule.

74. The nucleic acid molecule of claim 73, wherein said separate nucleic acid molecule is RNA.

75. The nucleic acid molecule of claim 73, wherein said nucleic acid comprises between 12 and 100 bases complementary to said separate nucleic acid molecule.

76. The nucleic acid molecule of claim 73, wherein said nucleic acid comprises between 14 and 24 bases complementary to said separate nucleic acid molecule.

77. The nucleic acid molecule of claim 48 or claim 49, wherein said X and Y
are independently of length selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, and 20 nucleotides.

78. The nucleic acid molecule of claim 48 or claim 49, wherein the length of X
is equal to the length of Y.

79. The nucleic acid molecule of claim 48 or claim 49, wherein the length of X
is not equal to the length of Y.

80. A cell including the nucleic acid molecule of claim 48 or claim 49.

81. The cell of claim 80, wherein said cell is a mammalian cell.

82. The cell of claim 81, wherein said cell is a human cell.

83. An expression vector comprising nucleic acid sequence encoding at least one of the nucleic acid molecule of claim 48 or claim 49, in a manner which allows expression of the nucleic acid molecule.

84. A cell including the expression vector of claim 83.

85. The cell of claim 84, wherein said cell is a mammalian cell.

86. The cell of claim 85, wherein said cell is a human cell

87. A pharmaceutical composition comprising the nucleic acid molecule of claim 48 or claim 49.

88. A method for modulating expression of a gene in a plant cell by administering to said cell the nucleic acid molecule of claim 48 or claim 49.

89. A method for modulating expression of gene in a mammalian cell by administering to said cell the nucleic acid molecule of claim 48 or claim 49.

90. A method of cleaving a target nucleic acid comprising, contacting the nucleic acid molecule of claim 48 or claim 49 with said target nucleic acid molecule under conditions suitable for the cleavage of said target nucleic acid molecule.

91. The method of claim 90, wherein said cleavage is carried out in the presence of a divalent cation.

92. The method of claim 91, wherein said divalent cation is Mg2+.

93. The expression vector of claim 83, wherein said vector comprises:
a) a transcription initiation region;
b) a transcription termination region;
c) a nucleic acid sequence encoding at least one nucleic acid molecule of claim 48 or claim 49; and wherein said sequence is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

94. The expression vector of claim 83, wherein said vector comprises:
a) a transcription initiation region;
b) a transcription termination region;
c) an open reading frame;
d) a nucleic acid sequence encoding at least one nucleic acid molecule of claim 48 or claim 49, wherein said sequence is operably linked to the 3'-end of said open reading frame; and wherein said sequence is operably linked to said initiation region, said open reading frame; and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

95. The expression vector of claim 83, wherein said vector comprises:
a) a transcription initiation region;
b) a transcription termination region;
c) an intron;
d) a nucleic acid sequence encoding at least one nucleic acid molecule of claim 48 or claim 49; and wherein said sequence is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

96. The expression vector of claim 83, wherein said vector comprises:
a) a transcription initiation region;
b) a transcription termination region;
c) an intron;
d) an open reading frame;
e) a nucleic acid sequence encoding at least one nucleic acid molecule of claim 48 or claim 49, wherein said sequence is operably linked to the 3'-end of said open reading frame; and wherein said sequence is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.