EP1019497A1 - Ribozymes en tete de marteau a fonction de clivage etendue - Google Patents

Ribozymes en tete de marteau a fonction de clivage etendue

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Publication number
EP1019497A1
EP1019497A1 EP98930352A EP98930352A EP1019497A1 EP 1019497 A1 EP1019497 A1 EP 1019497A1 EP 98930352 A EP98930352 A EP 98930352A EP 98930352 A EP98930352 A EP 98930352A EP 1019497 A1 EP1019497 A1 EP 1019497A1
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Prior art keywords
composition
rna
seq
straight chain
branched
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English (en)
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Janos Ludwig
Brian S. Sproat
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Sirna Therapeutics Inc
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Ribozyme Pharmaceuticals Inc
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    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C12N15/1136—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against growth factors, growth regulators, cytokines, lymphokines or hormones
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    • C12N15/1138—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against receptors or cell surface proteins
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    • C12N2310/10—Type of nucleic acid
    • C12N2310/12—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes
    • C12N2310/121—Hammerhead
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    • C12N2310/33—Chemical structure of the base

Definitions

  • the present invention is in the field of compositions having RNA- cleavage activity.
  • Hammerhead ribozymes are an example of catalytic RNA molecules which are able to recognize and cleave a given specific RNA substrate (Hotchins et al., Nucleic Acids Res. 14:3627 (1986); Keese and Symons, in Viroids and viroid - like pathogens (J . Semanchik, publ. , CRC-Press, Boca Raton, Florida, 1987), pages 1-47).
  • the catalytic center of hammerhead ribozymes is flanked by three stems and can be formed by adjacent sequence regions of the RNA or also by regions which are separated from one another by many nucleotides.
  • Figure 1 shows a diagram of such a catalytically active hammerhead structure.
  • the stems have been denoted I, II and III.
  • the nucleotides are numbered according to the standard nomenclature for hammerhead ribozymes (Hertel et al. , Nucleic Acids Res. 20:3252 (1992)).
  • bases are denoted by a number which relates their position relative to the 5' side of the cleavage site.
  • each base that is involved in a stem or loop region has an additional designation (which is denoted by a decimal point and then another number) that defines the position of that base within the stem or loop.
  • N u 3 A designation of N u 3 would indicate that this base is involved in a paired region and that it is the third base in that stem going away from the core region.
  • This accepted convention for describing hammerhead derived ribozymes allows for the nucleotides involved in the core of the enzyme to always have the same number relative to all of the other nucleotides.
  • the size of the stems involved in substrate binding or core formation can be any size and of any sequence, and the position of A 9 , for example, will remain the same relative to all of the other core nucleotides.
  • Nucleotides designated, for example, N ⁇ 12 or N 9 ⁇ represent an inserted nucleotide where the position of the caret 7) relative to the number denotes whether the insertion is before or after the indicated nucleotide.
  • N A12 represents a nucleotide inserted before nucleotide position 12
  • N 9 ⁇ represents a nucleotide inserted after nucleotide position 9.
  • hammerhead ribozymes Possible uses include, for example, generation of RNA restriction enzymes and the specific inactivation of the expression of genes in, for example, animal, human or plant cells and prokaryotes, yeasts and plasmodia.
  • a particular biomedical interest is based on the fact that many diseases, including many forms of tumors, are related to the overexpression of specific genes. Inactivating such genes by cleaving the associated mRNA represents a possible way to control and eventually treat such diseases.
  • Ribozymes have potential as such anti-infective agents since RNA molecules vital to the survival of the organism can be selectively destroyed.
  • N 16 - 2 U 16 'H 17 where N can be any nucleotide, U is uridine, and H is either adenosine, cytidine, or uridine (Koizumi et al. , FEBS Lett. 228, 228-230 (1988); Ruffner et al.
  • Efficient catalytic molecules with reduced or altered requirements in the cleavage region are highly desirable because their isolation would greatly increase the number of available target sequences that molecules of this type could cleave. For example, it would be desirable to have a ribozyme variant that could efficiently cleave substrates containing triplets other than N 16 - 2 U 16 1 H 17 since this would increase the number of potential target cleavage sites.
  • oligonucleotides which contain a block of deoxyribonucleotides in the middle region of the molecule have potential as pharmaceutical agents for the specific inactivation of the expression of genes (Giles et al. , Nucleic Acids Res. 20:763-770 (1992)). These oligonucleotides can form a hybrid DNA-RNA duplex in which the DNA bound RNA strand is degraded by RNase H. Such oligonucleotides are considered to promote cleavage of the RNA and so cannot be characterized as having an RNA- cleaving activity nor as cleaving an RNA molecule (the RNase H is cleaving).
  • RNA molecules A significant disadvantage of these oligonucleotides for in vivo applications is their low specificity, since hybrid formation, and thus cleavage, can also take place at undesired positions on the RNA molecules.
  • Previous attempts to recombinantly express catalytically active RNA molecules in the cell by transfecting the cell with an appropriate gene have not proven to be very effective since a very high expression was necessary to inactivate specific RNA substrates.
  • the vector systems which are available now cannot generally be applied.
  • unmodified ribozymes cannot be administered directly due to the sensitivity of RNA to degradation by RNases and their interactions with proteins.
  • 5,334,711 describes such chemically modified active substances based on synthetic catalytic oligonucleotide structures with a length of 35 to 40 nucleotides which are suitable for cleaving a nucleic acid target sequence and contain modified nucleotides that contain an optionally substituted alkyl, alkenyl or alkynyl group with 1 - 10 carbon atoms at the 2'-O atom of the ribose. These oligonucleotides contain modified nucleotide building blocks and form a structure resembling a hammerhead structure. These oligonucleotides are able to cleave specific RNA substrates.
  • compositions that cleave RNA and in particular to provide RNA-cleaving oligomers which at the same time have a high stability, activity, and specificity.
  • compositions having an RNA-cleavage activity as well as their use for cleaving RNA substrates in vitro and in vivo.
  • the compositions contain an active center, the subunits of which are selected from nucleotides and/or nucleotide analogues, as well as flanking regions contributing to the formation of a specific hybridization with an RNA substrate.
  • Preferred compositions form, in combination with an RNA substrate, a structure resembling a hammerhead structure.
  • the active center of the disclosed compositions is characterized by the presence of I 15 - 1 which allows cleavage of RNA substrates having C 16 1 .
  • Figure 1 is a diagram of a hammerhead structure and the corresponding nomenclature (SEQ ID NO: l). Cleavage occurs between H 17 and N to generate the 2', 3 '-cyclic phosphate at H 17 .
  • Figure 2 is a diagram of an RNA substrate (SEQ ID NO: 3) in association with an example of an oligomer (SEQ ID NO:2) that cleaves the RNA substrate.
  • the structure formed by the oligomer and the substrate resembles the structure of a hammerhead ribozyme. In this case, the substrate makes up half of stems I and III, and loops I and III are not present. Cleavage occurs 3' of H 17 .
  • Figure 3 is a diagram showing the interaction of the A 15,1 -U 16,1 base pair in hammerhead ribozymes (top), and the predicted isostructural interaction of a I 15 '-C 16 ' base pair (bottom) that replaces the A 15 '-U 16 ' base pair.
  • Figure 4A is a graph of fraction of cleavage product versus time (in minutes) for the cleavage of a short 5'-fluorescein labelled oligoribonucleotide substrate (SEQ ID NO: 8) containing a GCA site by four variants of 2'-0-allylated 5-ribo catalytic oligomers each containing a different nucleobase at position N 7 (U, C, A and G; SEQ ID NOS: 18, 22, 23, and 24, respectively).
  • Figure 4B is a graph of fraction of cleavage product versus time (in minutes) for the cleavage of a short 5'-fluorescein labelled oligoribonucleotide substrate of SEQ ID NO: 8 contaimng a GCA site by four variants of 2'-0-allylated 5-ribo catalytic oligomers each containing a different nucleobase or base analogue at position N 7 (U, 5-nitroindole, I, and quinazoline-2, 4-dione; SEQ ID NOS: 18, 27, 25, and 26, respectively).
  • compositions having an RNA-cleavage activity as well as their use for cleaving RNA-substrates in vitro and in vivo.
  • the compositions contain an active center, the subunits of which are selected from nucleotides and/or nucleotide analogues, as well as flanking regions contributing to the formation of a specific hybridization with an RNA substrate.
  • Preferred compositions form, in combination with an RNA substrate, a structure resembling a hammerhead structure.
  • the active center of the disclosed compositions is characterized by the presence of I 15 ' which allows cleavage of RNA substrates having C 16 1 . All naturally occurring hammerhead ribozymes have an A 15 '-U 16 ' base pair.
  • substrates for ribozymes based on the consensus hammerhead sequence strongly prefer a substrate that contains an N 16 - 2 U 16 'H 17 triplet in which H 17 is not a guanosine (Koizumi et al , FEBS Lett. 228, 228-230 (1988); Ruffner et al , Biochemistry 29, 10695-10702 (1990); Perriman et al , Gene 113, 157-163 (1992)).
  • Gerlach type ribozyme analogues containing an inosine at position 15.1 readily cleave RNA substrates containing an N 16 2 C 16 1 H 17 triplet.
  • compositions preferably synthetic oligomers, which cleave a nucleic acid target sequence containing the triplet N 16 2 C 16 ⁇ 17 .
  • H 17 is not guanosine.
  • the ability to cleave substrates having N 16 2 C 16 1 X 17 triplets effectively doubles the number of targets available for cleavage by compositions of the type disclosed.
  • compositions Having an RNA-cleavage Activity Specifically disclosed is a composition that cleaves an RNA substrate, where the composition includes components (a) and (b), where component (a) includes a structure 5'-Z r Z 2 -3' and component (b) includes a structure 5'-Z 3 -Z 4 -3' .
  • Components (a) and (b) can either be separate molecules or can be covalently coupled.
  • Elements Z, and Z 4 in components (a) and (b) are each oligomeric sequences which are made up of nucleotides, nucleotide analogues, or a combination of both, or are oligonucleotide analogues.
  • the oligomeric sequences of elements Z[ and Z 4 specifically interact with the RNA substrate, preferably by hybridization.
  • element Z j has a structure of 5'-X 3 X 4 X 5 X 6 X 7 X 8 X 9 -3 ⁇ or 5 '-X X 4 X 5 X 6 X 7 X 8 X 9 X 9 "-3 '
  • element Z 3 has a structure of
  • Elements Z 2 and Z 3 in these preferred compositions are made up of nucleotides, nucleotide analogues, or a combination of both.
  • the nucleotides and nucleotide analogues in elements Z 2 and Z 3 each have the structure
  • each B can be adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-l-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5- propynylcytosin-1-yl, 5-propynyluracil-l-yl, isoguanin-9-yl, 2-aminopurin-9- yl, 6-methyluracil-l-yl, 4-thiouracil-l-yl, 2-pyrimidone-l-yl, quinazoline-2,4- dione-1-yl, xanthin-9-yl, N 2 -dimethylguanin-9-yl or a functional
  • Each V can be an O, S, NH, or CH 2 group.
  • Each W can be -H, -OH, -COOH, -CONH 2 , -CONHR 1 , -CONR'R 2 , -NH 2 , -NHR 1 , -NR'R 2 , -NHCOR 1 , -SH, SR 1 , -F, -ONH 2 , -ONHR 1 , - ONR'R 2 , -NHOH, -NHOR', -NR 2 OH, -NR 2 OR ⁇ substituted or unsubstituted C,-C 10 straight chain or branched alkyl, substituted or unsubstituted C 2 -C 10 straight chain or branched alkenyl, substituted or unsubstituted C 2 -C 10 straight chain or branched alkynyl, substituted or unsubstituted C r C 10 straight chain or branched alkoxy, substituted or unsubstituted C 2 -C ⁇ 0 straight chain or branched al
  • the substituents for W groups are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.
  • R 1 and R 2 can be substituted or unsubstituted alkyl, alkenyl, or alkynyl groups, where the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.
  • D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleoside analogues or together form an analogue of an internucleosidic bond.
  • B is hypoxanthin-9-yl, or a functional equivalent thereof, in X 15 1 ;
  • B can be guanin-9-yl, hypoxanthin-9-yl or 7-deazaguanin-9-yl in X 5 , X 8 , and X 12 ;
  • B can be adenin-9-yl, 2,6-diaminopurin-9-yl, purin-9-yl or 7-deazaa- denin-9-yl in X 6 , X 9 , X 13 , and X 14 ;
  • B can be uracil-1-yl, uracil-5-yl, thymin- 1-yl or 5-propynyluracil-l-yl in X 4 ;
  • B can be cytosin-1-yl, 5-methylcytosin- 1-yl or 5-propynylcytosin-l-yl in X 3 ; and B can be adenin-9-yl
  • B of X 15 1 is preferably hypoxanthin-9-yl or an analog where no hydrogen bond can form between any group at the 2 position of the base and the 2-oxo group of C 16 1 .
  • B is not guanin-9-yl in X 15 '.
  • B in X 3 , X 4 , X 5 , X 6 , X 8 , X 9 , X 12 , X 13 , and X 14 can also be a functionally equivalent nucleobase within the context of the catalytic core of a hammerhead ribozyme.
  • C 3 , U ⁇ G 5 , and A 6 in hammerhead ribozymes form a structure closely resembling a uridine turn in a tRNA (Pley et al , Nature 372:68-74 1994).
  • nucleotides X 3 , X 4 , X 5 , X 6 may be replaced as a group with nucleotides or nucleotide analogues that have the potential to form a structure resembling a uridine turn.
  • the sheared base pairs in the catalytic core of hammerhead ribozymes have interactions that may be similar to interactions of other non-canonical base pairs.
  • oligomer refers to oligomeric molecules composed of subunits where the subunits can be of the same class (such as nucleotides) or a mixture of classes (such as nucleotides and ethylene glycol). It is preferred that the disclosed oligomers be oligomeric sequences, non- nucleotide linkers, or a combination of oligomeric sequences and non-nucleotide linkers. It is more preferred that the disclosed oligomers be oligomeric sequences.
  • Oligomeric sequences are oligomeric molecules where each of the subunits includes a nucleobase (that is, the base portion of a nucleotide or nucleotide analogue) which can interact with other oligomeric sequences in a base- specific manner.
  • the hybridization of nucleic acid strands is a preferred example of such base-specific interactions.
  • Oligomeric sequences preferably are comprised of nucleotides, nucleotide analogues, or both, or are oligonucleotide analogues.
  • Non-nucleotide linkers can be any molecule, which is not an oligomeric sequence, that can be covalently coupled to an oligomeric sequence.
  • Preferred non-nucleotide linkers are oligomeric molecules formed of non-nucleotide subunits. Examples of such non-nucleotide linkers are described by Letsinger and Wu, (/. Am. Chem. Soc. 117:7323-7328 (1995)), Benseler et al, (J. Am. Chem. Soc. 115:8483-8484 (1993)) and Fu et al. , (/. Am. Chem. Soc. 116:4591-4598 (1994)).
  • Preferred non-nucleotide linkers, or subunits for non-nucleotide linkers include substituted or unsubstituted C r C 10 straight chain or branched alkyl, substituted or unsubstituted C 2 -C 10 straight chain or branched alkenyl, substituted or unsubstituted C 2 -C 10 straight chain or branched alkynyl, substituted or unsubstituted C r C 10 straight chain or branched alkoxy, substituted or unsubstituted C 2 -C 10 straight chain or branched alkenyloxy, and substituted or unsubstituted C 2 -C 10 straight chain or branched alkynyloxy.
  • the substituents for these preferred non-nucleotide linkers (or subunits) can be halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.
  • nucleoside refers to adenosine, guanosine, cytidine, uridine, 2'-deoxyadenosine, 2 '-deoxy guanosine, 2'- deoxycytidine, or thymidine.
  • a nucleoside analogue is a chemically modified form of nucleoside containing a chemical modification at any position on the base or sugar portion of the nucleoside.
  • nucleoside analogue encompasses, for example, both nucleoside analogues based on naturally occurring modified nucleosides, such as inosine and pseudouridine, and nucleoside analogues having other modifications, such as modifications to the 2' position of the sugar.
  • nucleotide refers to a phosphate derivative of nucleosides as described above
  • a nucleotide analogue is a phosphate derivative of nucleoside analogues as described above.
  • the subunits of oligonucleotide analogues, such as peptide nucleic acids, are also considered to be nucleotide analogues.
  • a ribonucleotide is a nucleotide having a 2' hydroxy 1 function.
  • a 2'-deoxyribonucleotide is a nucleotide having only 2' hydrogens.
  • ribonucleotides and deoxyribonucleotides as used herein refer to naturally occurring nucleotides having nucleoside components adenosine, guanosine, cytidine, and uridine, or 2'-deoxyadenosine, 2'- deoxy guanosine, 2 '-deoxycytidine, and thymidine, respectively, without any chemical modification.
  • Ribonucleosides, deoxyribonucleosides, ribonucleoside analogues and deoxyribonucleoside analogues are similarly defined except that they lack the phosphate group, or an analogue of the phosphate group, found in nucleotides and nucleotide analogues.
  • oligonucleotide analogues are polymers of nucleic acid-like material with nucleic acid-like properties, such as sequence dependent hybridization, that contain at one or more positions, a modification away from a standard RNA or DNA nucleotide.
  • a preferred example of an oligonucleotide analogue is peptide nucleic acid.
  • base pair refers to a pair of nucleotides or nucleotide analogues which interact through one or more hydrogen bonds.
  • the term base pair is not limited to interactions generally characterized as Watson- Crick base pairs, but includes non-canonical or sheared base pair interactions (Topal and Fresco, Nature 263:285 (1976); Lomant and Fresco, Prog. Nucl. Acid Res. Mol. Biol. 15: 185 (1975)).
  • nucleotides A 15 - 1 and U 16 ! form a base pair in hammerhead ribozymes (see Figure 1) but the base pair is non- canonical (see Figure 3).
  • the internucleosidic linkage between two nucleosides can be achieved by phosphodiester bonds or by modified phospho bonds such as by phosphorothioate groups or other bonds such as, for example, those described in U.S. Pat. No. 5,334,711.
  • the monomeric subunits of elements ⁇ and Z 4 which flank the active center are preferably nucleotides and/or nucleotide analogues.
  • Elements Z, and Z 4 are designed so that they specifically interact, preferably by hybridization, with a given RNA substrate and, together with the active center Z 2 and Z 3 , form a structure (preferably a structure resembling that of a hammerhead ribozyme) which specifically cleaves the RNA substrate.
  • the subunits of elements Z and Z 4 can, on the one hand, be ribonucleotides. However, it is preferred that the number of ribonucleotides be as small as possible since the presence of ribonucleotides reduces the in vivo stability of the oligomers.
  • Elements Z ⁇ and Z 4 (and also the active center Z 2 and Z 3 ) preferably do not contain any ribonucleotides at the positions containing pyrimidine nucleobases. Such positions preferably contain nucleotide analogues.
  • elements Z, and Z 4 each preferably contain (1) no ribonucleotides, and (2) no sequences of more man 3 consecutive deoxyribonucleotides.
  • the subunits of elements Z x and Z 4 are preferably nucleotides, nucleotide analogues, or a combination.
  • the nucleotides and nucleotide analogues in elements Z x and Z 4 each have the structure
  • each B can be adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-l-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5- propynylcytosin-1-yl, 5-propynyluracil-l-yl, isoguanin-9-yl, 2-aminopurin-9- yl, 6-methyluracil-l-yl, 4-thiouracil-l-yl, 2-pyrimidone-l-yl, quinazoline-2,4- dione-1-yl, xanthin-9-yl, N 2 -dimethylguanin-9-yl or a functional
  • Each V can be an O, S, NH, or CH, group.
  • Each W can be -H, -OH, -COOH, -CONH 2 , -CONHR 1 , -CONR'R 2 , -NH 2 , -NHR 1 , -NR'R 2 , -NHCOR 1 , -SH, SR 1 , -F, -ONH 2 , -ONHR 1 , - ONR'R 2 , -NHOH, -NHOR 1 , -NR 2 OH, -NR 2 OR', substituted or unsubstituted C,-C 10 straight chain or branched alkyl, substimted or unsubstituted C 2 -C ]0 straight chain or branched alkenyl, substimted or unsubstituted C 2 -C 10 straight chain or branched alkynyl, substituted or unsubstituted C r C 10 straight chain or branched alkoxy, substituted or unsubstituted C 2 -C 10 straight
  • the substituents for W groups are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.
  • R 1 and R 2 can be substimted or unsubstituted alkyl, alkenyl, or alkynyl groups, where the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.
  • D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleoside analogues or together form an analogue of an internucleosidic bond.
  • each W is substituted or unsubstituted C r C 10 straight chain or branched alkoxy, C 2 -C 10 straight chain or branched alkenyloxy, or C 2 -C 10 straight chain or branched alkynyloxy.
  • the flanking elements Z, and Z 4 can also contain nucleotide analogues such as peptide nucleic acids (also referred to as peptidic nucleic acids; see for example Nielsen et al, Science 254: 1497-1500 (1991), and Dueholm et al , J. Org. Chem.
  • Elements Z x and Z 4 when based on peptide nucleic acids, can be coupled to elements Z 2 and Z 3 , based on nucleotides or nucleotide analogues, using either suitable linkers (see, for example, Petersen et al , BioMed. Chem. Lett. 5: 1119-1121 (1995)) or direct coupling (Bergmann et al, Tetrahedron Lett. 36:6823-6826 (1995)). Where elements Z x and Z 4 contain a combination of nucleotides (and/or nucleotide analogues) and peptide nucleic acid, similar linkages can be used to couple the different parts.
  • the subunits of the flanking elements Z ⁇ and Z 4 contain nucleobases or nucleobase analogues which can hybridize or interact with nucleobases that occur naturally in RNA molecules.
  • the nucleobases are preferably selected from naturally occurring bases (that is, adenine, guanine, cytosine, thymine and uracil) as well as nucleobase analogues, such as 2,6-diaminopurine, hypoxanthine, 5-methylcytosine, pseudouracil, 5-propynyluracil, and 5- propynylcytosine, which enable a specific binding to the target RNA.
  • nucleobase analogues be used in oligomeric sequences of elements Z and Z 4 in place of the standard nucleobases: 2,6- diaminopurine instead of adenine; thymine or 5-propynyluracil instead of uracil; and 5-methylcytosine or 5-propynylcytosine instead of cytosine.
  • 2- Amino-2'-0-alkyladenosines are also preferred (Lamm et al, Nucleic Acids Res. 19:3193-3198 (1991)).
  • aromatic systems can be linked to positions 4 and 5 of uracil to produce nucleobase analogues such as phenoxazine, which can improve the stability of the double-strand (Lin et al , J. Am. Chem. Soc. 117:3873-3874 (1995)).
  • RNA substrates for cleavage by the disclosed compositions have the structure
  • X 17 is adenosine, cytidine, or uridine, more preferably X 17 is adenosine or cytidine, and most preferably X 17 is adenosine.
  • X 162 (that is, the 3' nucleoside in Z 4 ') is adenosine or guanosine.
  • the target sites in substrates which can be cleaved by the disclosed compositions are distinct from target sites for previous hammerhead ribozymes since previous hammerhead ribozymes require a uridine in position 16.1 of the substrate.
  • Position N 16 2 which is the 3' most position present in Z 4 ', can be either a guanosine, adenosine, cytidine, or uridine. It is preferred that N 16 2 is either a guanosine, adenosine, or cytidine. It is more preferred that N 16 2 is either guanosine or adenosine. It is most preferred that N 16 2 is guanosine. Preferred substrates for cleavage by the disclosed compounds are those where N 16 2 is guanosine, adenosine, or cytidine and X 17 is adenosine.
  • More preferred substrates for cleavage by the disclosed compounds are those where N 16 2 is guanosine or adenosine and X 17 is adenosine. Most preferred substrates for cleavage by the disclosed compounds are those where N 16 2 is guanosine and X 17 is adenosine.
  • Flanking elements Z x and Z 4 preferably contain, independently of each other, from 3 to 40, and more preferably from 5 to 10, nucleotides or nucleotide analogues. It is preferred that Z and Z,' interact to form a stem of at least three base pairs, and that Z 4 and Z 4 ' interact to form a stem of at least three base pairs. It is more preferred that these stems are adjacent to Z 2 and Z 3 , respectively. It is most preferable that Z, and Z x interact to form a stem of more than three base pairs, and that Z 4 and Z 4 ' interact to form a stem of more than three base pairs.
  • RNA substrates are those that have little inhibitory secondary structure associated with the target region of the RNA.
  • Preferred methods for determining regions of single- stranded RNA are those that map the single-stranded regions of RNA by selectively reacting with or recognizing these regions.
  • chemicals dimenthyl sulfate (DMS), diethylpyrocarbonate (DEPC), cathoxal (CMCT), carbodumides which react with nitrogens at the Watson-Crick face of nucleotides.
  • Nucleotides involved in Watson-Crick base pairing show less reactivity with these chemicals than nucleotides which are not.
  • Enzymatic reactions using reverse transcriptase, RNase Tl, cobra venom nuclease, nuclease SI, nuclease VI
  • RNA create shortened oligonucleotides whose length is dependant on the base where the chemical reaction occurred. Since chemical reactions occur preferentially at the single stranded regions of the RNA, these techniques indicate where the secondary strucmre of the RNA is. For example, methods such as dimethyl sulfate and reverse transcription mapping indicate regions of double-stranded RNA.
  • Reverse transcriptase under the appropriate conditions is unable to process through regions of double-stranded RNA, and therefore, there are abortive transcripts which when analyzed by polyacrylamide gel electrophoresis (PAGE) indicate where in the RNA regions of strong secondary strucmre exist. Examples of these methods are described by Kumar et al. ,
  • RNase H mapping Another method which assesses which regions of RNA are single- stranded is RNase H mapping.
  • short, random DNA oligonucleotides are synthesized and mixed with the target RNA. Regions of easy accessibility are hybridized with the short DNA molecules.
  • the DNA- RNA hybrid regions are then cleaved by RNase H.
  • the labeled RNA molecule can then be analyzed by PAGE. By comparing the cleaved molecules with a sequencing ladder, the regions of single-stranded DNA can be inferred. Examples of this method are described by Ho et al , Nature Biotechnology 16:59-63 (1998), and in U.S. Patent No. 5,525,468 to McSwiggen.
  • RNA selection experiments can also be performed to determine the accessible single-stranded regions of RNA.
  • the target RNA can be mixed with random DNA oligonucleotides that contain primer binding regions which can be used for PCR amplification. Amplification and reselection in an iterative manner will allow for enrichment of those DNA sequences which are capable of binding the RNA. This identifies the regions of the RNA which are accessible for oligonucleotide hybridization.
  • the selection or enrichment step can be any size selection or double-stranded nucleic acid separation technique. For example, Sephadex column chromotagraphy will separate the large, bound DNA: RNA complexes and the small unbound DNA molecules, or nitrocellulose filtration will retain the bound RNA while the unbound DNA molecules will flow through.
  • position N 7 of the oligomers which has no specific sequence requirements, can be changed to help minimize the possibility of unwanted secondary structure in the oligomers designed for a given target sequence.
  • specific base modifications such as 7-deaza- guanosine or 7-deaza-adenosine, can be utilized in regions having a number of guanosines or adenosines to prevent unwanted purine:purine interactions. Similar substitutions can be accomplished by introducing inosine into guanosine rich regions, that may be present for example in regions Z 1 or Z 4 of the catalytic oligomer.
  • Catalytic Core Elements Z 2 and Z 3 are considered to form the catalytic core of the disclosed compositions, and are preferably made up of nucleotide analogues and a small number of ribonucleotides.
  • each W in structure (I) is C r C 5 straight chain or branched alkyl, C 2 -C 5 straight chain or branched alkenyl, C 2 -C 5 straight chain or branched alkynyl, C r C 5 straight chain or branched alkoxy, C 2 -C 5 straight chain or branched alkenyloxy, and C 2 -C 5 straight chain or branched C 2 -C 5 alkynyloxy.
  • W is NH 2 , OH-substituted C r C 4 alkyl, OH-substituted C 2 -C 4 alkenyl, OH-substituted C r C 4 alkoxy or OH- substituted C 2 -C 4 alkenyloxy. It is more preferred that in each X 3 , X 4 , X 7 and X A ' 2 , W is NH 2 , methoxy, 2-hydroxyethoxy, allyloxy or allyl. It is also preferred that in X 12 , W is -H or -OH.
  • W is C r C 4 alkyl, C 2 -C 4 alkenyl, C r C 4 alkoxy, C 2 -C 4 alkenyloxy, OH-substituted C r C 4 alkyl, OH-substituted C 2 -C 4 alkenyl, OH-substituted C r C 4 alkoxy, or OH-substituted C 2 -C 4 alkenyloxy. It is more preferred that in each X 13 and X 14 , W is methoxy, 2-hydroxyethoxy or allyloxy.
  • the subunits in elements Z 2 and Z 3 are preferably nucleotide analogues which can only hybridize weakly with ribonucleotides.
  • Examples of such subunits are nucleotide analogues that contain a substituted or unsubstituted alkyl, alkenyl, alkynyl, alkoxy, alkenyloxy or alkynyloxy group, with preferably 1 to 5 carbon atoms, at the 2' position of ribose.
  • Preferred nucleobases which can be used in elements Z 2 and Z 3 for this purpose are adenin-9-yl, purin-9-yl, uracil- 1-yl, cytosin-1-yl, guanin-9-yl and hypoxanthin-9-yl.
  • B guanin-9-yl
  • Elements Z 2 and Z 3 interact in a way that allows for the formation of a catalytic strucmre.
  • Z 2 and Z 3 interact in a way that allows for the formation of a catalytic structure resembling a hammerhead catalytic strucmre.
  • One way Z 2 and Z 3 can interact to form a catalytic strucmre is through the interaction of the nucleotides and/or nucleotide analogues making up Z 2 and Z 3 .
  • the disclosed compositions have an RNA cleaving activity independent of RNase H. That is, the disclosed compositions are able to cause cleavage of an RNA substrate without involving RNase H. Although the disclosed compositions may also be capable of promoting cleavage of RNA by RNase H, it is preferred that they do not.
  • Desired interaction between Z 2 and Z 3 is preferably enhanced by coupling elements to the 3 '-end of Z 2 and/or the 5 '-end of Z 3 .
  • a single element (referred to herein as Z 5 ) can be used in this way to covalently couple elements Z 2 and Z 3 .
  • the structure of such a form of the disclosed compositions would be 5'-Z r Z 2 -Z 5 -Z 3 -Z 4 -3'.
  • Separate elements referred to herein as Z 6 and Z 7
  • Z 2 and Z 3 which preferably interact (non-covalently) to stabilize or otherwise enhance the interaction of elements Z 2 and Z 3 .
  • Component (a) of a composition of this form would have the strucmre 5'-Z r Z 2 -Z 6 -3', and component (b) would have the strucmre 5'-Z 7 -
  • elements Z 5 , Z 6 and Z 7 are oligomeric sequences, non-nucleotide linkers, or a combination of oligomeric sequences and non- nucleotide linkers. It is more preferred that elements Z 5 , Z 6 and Z 7 are oligomeric sequences. It is most preferred that these oligomeric sequences interact to form an intramolecular stem (in the case of Z 5 ) or an intermolecular stem (in the case of Z 6 and Z 7 ). Such stems preferably contain from 2 to 30 base pairs, and are preferably continuous (that is, lacking unpaired bases).
  • Elements Z 5 , Z 6 and Z 7 preferably are comprised of nucleotides, nucleotide analogues, or both, or are oligonucleotide analogues. It is preferred that Z 5 interacts with itself in such a way as to stabilize the interactions between Z 2 and Z 3 . Similarly, it is preferred that Z 6 interact with Z 7 in such a way as to stabilize the interactions between Z 2 and Z 3 . It is preferred that elements are oligomeric sequences made up of nucleotides and/or nucleotide analogues, oligonucleotide analogues, or a combination, which are able to hybridize with each other.
  • Element Z 5 can serve as a covalent linker coupling the 3 ' end of Z 2 to the 5' end of Z 3 .
  • Element Z 5 is preferably made up of either non-nucleotide molecules such as polyethylene glycol, or oligomeric sequences, including nucleotides, nucleotide analogues and oligonucleotide analogues, or a combination of nucleotides, nucleotide analogues and oligonucleotide analogues.
  • a preferred form of element Z 5 is made up of nucleotides, nucleotide analogues, oligonucleotide analogues, or a combination of nucleotides and nucleotide analogues which are able to interact intramolecularly to form a stem-loop strucmre.
  • a preferred stem-loop strucmre for element Z 5 is one containing from 2 to 30 base pairs.
  • a preferred form of the disclosed composition is one in which there is a G added to the 3' end of Z 2 .
  • Taira and co-workers (Amontov and Taira, J. Am. Chem. Soc. 118: 1624-1628 (1996)) have shown that the stacking energy gained from a guanosine juxtaposed to R 9 of a hammerhead-like ribozyme stabilizes the formation of a catalytic structure.
  • the 5' nucleotide of Z 6 is G.
  • compositions can be protected against degradation by exonucleases by, for example, using a nucleotide analogue that is modified at the 3' position of the ribose sugar (for example, by including a substimted or unsubstituted alkyl, alkoxy, alkenyl, alkenyloxy, alkynyl or alkynyloxy group as defined above).
  • a nucleotide analogue that is modified at the 3' position of the ribose sugar (for example, by including a substimted or unsubstituted alkyl, alkoxy, alkenyl, alkenyloxy, alkynyl or alkynyloxy group as defined above).
  • compositions can also be stabilized against degradation at the 3 ' end by exonucleases by including a 3 '-3 '-linked dinucleotide structure (Ortigao et al , Antisense Research and Development 2: 129-146 (1992)) and/or two modified phospho bonds, such as two phosphorothioate bonds.
  • compositions can also be linked to a prosthetic group in order to improve their cellular uptake and/or to enable a specific cellular localization.
  • prosthetic groups are polyamino acids (for example, polylysine), lipids, hormones or peptides. These prosthetic groups are usually linked via the 3' or 5' end of the oligomer either directly or by means of suitable linkers (for example, linkers based on 6-aminohexanol or 6-mercaptohexanol). These linkers are commercially available and techniques suitable for linking prosthetic groups to the oligomer are known to a person skilled in the art.
  • Increasing the rate of hybridization can be important for the biological activity of the disclosed compositions since in this way it is possible to achieve a higher activity at low concentrations of the composition. This is important for short-lived RNA substrates or RNA substrates that occur less often.
  • a substantial acceleration of the hybridization can be achieved by, for example, coupling positively charged peptides (containing, for example, several lysine residues) to the end of an oligonucleotide (Corey J. Am. Chem. Soc. 117:9373-9374 (1995)).
  • the disclosed compositions can be simply modified in this manner using the linkers described above.
  • the rate of hybridization can also be increased by incorporation of subunits which contain sperminyl residues (Schmid and Behr, Tetrahedron Lett. 36: 1447- 1450 (1995)).
  • Such modifications of the disclosed compositions also improve the ability to bind to RNA substrates having secondary structures.
  • compositions can be synthesized using any suitable method. Many synthesis methods are known. The following techniques are preferred for synthesis of the disclosed compositions. 2'-0-Allyl modified oligomers that contain residual purine ribonucleotides, and bearing a suitable 3 '-terminus such as an inverted thymidine residue (Ortigao et al. , Antisense Research and Development 2: 129-146 (1992)) or two phosphorothioate linkages at the 3 '-terminus to prevent eventual degradation by 3'- exonucleases, can be synthesized by solid phase ⁇ -cyanoethyl phosphoramidite chemistry (Sinha et al , Nucleic Acids Res.
  • Fluorescein can be added to the 5 '-end of a substrate RNA during the synthesis by using commercially available fluorescein phosphoramidites.
  • a desired oligomer can be synthesized using a standard RNA cycle.
  • all base labile protecting groups are removed by an 8 hour treatment at 55 °C with concentrated aqueous ammonia/ ethanol (3: 1 v/v) in a sealed vial.
  • the ethanol suppresses premature removal of the 2'-O-TBDMS groups which would otherwise lead to appreciable strand cleavage at the resulting ribonucleotide positions under the basic conditions of the deprotection (Usman et al. , J. Am. Chem.
  • Purification can be performed either by denaturing polyacrylamide gel electrophoresis or by a combination of ion-exchange HPLC (Sproat et al , Nucleosides and Nucleotides 14:255-273 (1995)) and reversed phase HPLC.
  • synthesized oligomers be converted to their sodium salts by precipitation with sodium perchlorate in acetone. Traces of residual salts are then preferably removed using small disposable gel filtration columns that are commercially available.
  • the authenticity of the isolated oligomers is checked by matrix assisted laser desorption mass spectrometry (Pieles et al. , Nucleic Acids Res. 21:3191-3196 (1993)) and by nucleoside base composition analysis.
  • a functional cleavage test with the oligomer on the corresponding chemically synthesized short oligoribonucleotide substrate is also preferred.
  • the disclosed compositions have a very high in vivo activity since the RNA cleavage is promoted by protein factors that are present in the nucleus or cytoplasm of the cell.
  • protein factors which can increase the activity of hammerhead ribozymes are, for example, the nucleocapsid protein NCp7 of HIV1 (Muller et al. , J. Mol. Biol. 242:422- 429 (1994)) and the heterogeneous nuclear ribonucleoprotein Al (Heidenreich et al , Nucleic Acids Res. 23:2223-2228 (1995)).
  • compositions can be used in pharmaceutical compositions that contain one or several oligomers as the active substance, and, optionally, pharmaceutically acceptable auxiliary substances, additives and carriers.
  • Such pharmaceutical compositions are suitable for the production of an agent to specifically inactivate the expression of genes in eukary- otes, prokaryotes and viruses, especially of human genes such as tumor genes or viral genes or RNA molecules in a cell. Further areas of application are the inactivation of the expression of plant genes or insect genes.
  • the disclosed compositions can be used as drugs for humans and animals as well as a pesticide for plants.
  • microparticles include liposomes, virosomes, microspheres and microcapsules formed of synthetic and/or natural polymers.
  • Methods for making microcapsules and microspheres are known to those skilled in the art and include solvent evaporation, solvent casting, spray drying and solvent extension.
  • useful polymers which can be incorporated into various microparticles include polysaccharides, polyanhydrides, polyorthoesters, polyhydroxides and proteins and peptides.
  • Liposomes can be produced by standard methods such as those reported by Kim et al , Biochim. Biophys. Acta, 728:339-348 (1983); Liu et al , Biochim. Biophys. Acta, 1104:95-101 (1992); and Lee et al. , Biochim. Biophys. Acta., 1103: 185-197 (1992); Wang et al , Biochem. , 28:9508-9514 (1989)).
  • Such methods have been used to deliver nucleic acid molecules to the nucleus and cytoplasm of cells of the MOLT-3 leukemia cell line (Thierry and Dritschilo, Nucl. Acids Res. , 20:5691-5698 (1992)).
  • the disclosed compositions can be incorporated within microparticles, or bound to the outside of the microparticles, either ionically or covalently.
  • Cationic liposomes or microcapsules are microparticles that are particularly useful for delivering negatively charged compounds such as the disclosed compounds, which can bind ionically to the positively charged outer surface of these liposomes.
  • Various cationic liposomes have previously been shown to be very effective at delivering nucleic acids or nucleic acid-protein complexes to cells both in vitro and in vivo, as reported by Feigner et al. , Proc. Natl Acad. Sci. USA, 84:7413-7417 (1987); Feigner, Advanced Drug Delivery Reviews, 5: 163-187 (1990); Clarenc et al , Anti-Cancer Drug Design, 8:81-94 (1993).
  • Cationic liposomes or microcapsules can be prepared using mixtures including one or more lipids containing a cationic side group in a sufficient quantity such that the liposomes or microcapsules formed from the mixture possess a net positive charge which will ionically bind negatively charged compounds.
  • positively charged lipids examples include the aminolipid dioleoyl phosphatidyl ethanolamine (PE), which possesses a positively charged primary amino head group; phosphatidylcholine (PC), which possess positively charged head groups that are not primary amines; and N[l-(2,3- dioleyloxy)propyl]-N,N,N-triethylammonium ("DOTMA, " see Feigner et al, Proc. Natl Acad. Sci USA, 84:7413-7417 (1987); Feigner et al , Nature, 337:387-388 (1989); Feigner, Advanced Drug Delivery Reviews, 5: 163-187 (1990)).
  • PE aminolipid dioleoyl phosphatidyl ethanolamine
  • PC phosphatidylcholine
  • DOTMA N[l-(2,3- dioleyloxy)propyl]-N,N,N-triethylammonium
  • a preferred form of microparticle for delivery of the disclosed compositions are heme-bearing microparticles.
  • heme is intercalated into or covalently conjugated to the outer surface of the microparticles.
  • Heme-bearing microparticles offer an advantage in that since they are preferentially bound and taken up by cells that express the heme receptor, such as hepatocytes, the amount of drug required for an effective dose is significantly reduced.
  • Such targeted delivery may also reduce systemic side effects that can arise from using relatively high drug concentrations in non-targeted delivery methods.
  • Preferred lipids for forming heme-bearing microparticles are l,2-dioleoyloxy-3-(trimethylammonium) propane (DOTAP) and dioleoyl phosphatidyl ethanolamine (DOPE).
  • DOTAP l,2-dioleoyloxy-3-(trimethylammonium) propane
  • DOPE dioleoyl phosphatidyl ethanolamine
  • compositions can also be encapsulated by or coated on cationic liposomes which can be injected intravenously into a mammal.
  • This system has been used to introduce DNA into the cells of multiple tissues of adult mice, including endothelium and bone marrow, where hematopoietic cells reside (see, for example, Zhu et al, Science, 261 :209-211 (1993)).
  • Liposomes containing the disclosed compositions can be administered systemically, for example, by intravenous or intraperitoneal administration, in an amount effective for delivery of the disclosed compositions to targeted cells.
  • Other possible routes include trans-dermal or oral, when used in conjunction with appropriate microparticles.
  • the total amount of the liposome-associated oligomer administered to an individual will be less than the amount of the unassociated oligomer that must be administered for the same desired or intended effect.
  • Compositions including various polymers such as the polylactic acid and polyglycolic acid copolymers, polyethylene, and polyorthoesters and the disclosed compositions can be delivered locally to the appropriate cells by using a catheter or syringe.
  • compositions locally to cells include using infusion pumps (for example, from Alza Corporation, Palo Alto, California) or incorporating the compositions into polymeric implants (see, for example, Johnson and Lloyd- Jones, eds. , Drug Delivery Systems (Chichester, England: Ellis Horwood Ltd., 1987), which can effect a sustained release of the therapeutic compositions to the immediate area of the implant.
  • the active substance is preferably administered at a concentration of 0.01 to 10,000 ⁇ g/kg body weight, more preferably of 0.1 to 1000 ⁇ g/kg body weight.
  • the administration can, for example, be carried out by injection, inhalation (for example as an aerosol), as a spray, orally (for example as tablets, capsules, coated tablets etc.), topically or rectally (for example as suppositories).
  • compositions can be used in a method for the specific inactivation of the expression of genes in which an active concentration of the composition is taken up into a cell so that the composition specifically cleaves a predetermined RNA molecule which is present in the cell, the cleavage preferably occurring catalytically.
  • Similar compositions which are described in U.S. Patent No. 5,334,711, have been used successfully in mice to inactivate a gene (Lyngstadaas et al , EMBO J. 14:5224-5229 (1995)). This process can be carried out in vitro on cell cultures as well as in vivo on living organisms (prokaryotes or eukaryotes such as humans, animals or plants).
  • the disclosed compositions can also be used as RNA restriction enzymes to cleave RNA molecules (in, for example, cell free in vitro reactions).
  • the disclosed compositions can also be used in a reagent kit for the restriction cleavage of RNA molecules which contains, for example, an oligomer and suitable buffer substances.
  • the oligomer and the buffer substances can be present in the form of solutions, suspensions or solids such as powders or lyophilisates.
  • the reagents can be present together, separated from one another or optionally also on a suitable carrier.
  • the disclosed compositions can also be used as a diagnostic agent or to identify the function of unknown genes.
  • Example 1 Cleavage reactions which indicate that an inosine substitution at position 15.1 can effectively cleave
  • a set of 12 substrates was synthesized which covered each permutation of the N 162 C 16 'H 17 motif where H 17 is not guanosine.
  • the oligomers and the corresponding substrates used in the cleavage assays are shown in Table 1. Each of the substrates was labeled with fluorescein at the 5' end and an inverted thymidine cap was used on the 3 '-end.
  • a set of four catalytic oligomers was synthesized, providing an appropriately matched catalytic oligomer for each of the substrates. Each of these catalytic oligomers had an inosine at position 15.1.
  • a control substrate and catalytic oligomer were also synthesized in which there was a U at position 16.1 of the substrate and an A at position 15.1 of the catalytic oligomer.
  • GCC F1-GAAUGCCGGUCGC*T (SEQ ID NO:7)
  • GCA F1-GAAUGCAGGUCGC*T (SEQ ID NO: 8)
  • GCU F1-GAAUGCUGGUCGC*T (SEQ ID NO: 9)
  • the above substrates and catalytic oligomers were used in cleavage reactions to determine the ability of an inosine at position 15.1 to overcome the requirement of a U at position 16.1 for cleavage. All of the reactions were performed using the following protocol. The reactions were typically done in 100 ⁇ l and they contained distilled, autoclaved H 2 0, 10 mM MgCl 2 , 10 mM Tris-HCl pH 7.4, 5 ⁇ M ribozyme, and 0.25 ⁇ M substrate. The catalytic oligomer, substrate, and buffer were added together and heated to 95 °C for 5 minutes. After cooling to room temperamre over 5 minutes the . reactions were brought to 10 mM MgCl 2 , mixed, and placed at 37 °C.
  • the final concentrations of the reaction components were 250 nM substrate, 2.5 ⁇ mol ribozyme, and 10 mM MgCl 2 .
  • Ten microliter samples were removed at various times and mixed with 10 ⁇ l of a 100 mM EDTA, bromphenol blue solution to stop the reaction.
  • Cleavage products were separated from unreacted substrate by PAGE and were quantitated on a Molecular Dynamics Fluorescence Imager.
  • the calculated values of k 2 for the various ribozymes are shown in Table 3. Table 3
  • ACU 0.026 F1-GAAUACUGGUCGC*T (SEQ ID NO:6) gcgacccuGAuGaggccgugaggccGaaIcauuc*T (SEQ ID NO: 18) k 2 (min 1 ) Substrate sequence
  • GCU 0.05 F1-GAAUGCUGGUCGC*T (SEQ ID NO:9) gcgacccuGAuGaggccgugaggccGaaIgauuc*T (SEQ ID NO: 19) kk 22 ((mmiinn '')) Substrate sequence
  • Example 2 Rate of cleavage at GCH and ACH triplets by catalytic oligomers containing only ribonucleotides Cleavage of substrate RNA by all-ribonucleotide versions of oligomers (no modifications) designed to cleave GCH and ACH triplets was assessed.
  • the oligomers used were SEQ ID NO: 17 (cleaves after ACH triplets) (Table 1) and SEQ ID NO: 18 (cleaves after GCH triplets) (Table 1).
  • the corresponding short fluorescent labelled substrates SEQ ID NOS:4, 5, and 6 (containing ACH triplets) (Table 1) and SEQ ID NOS:7, 8, and 9 (containing GCH triplets) (Table 1) were used with catalytic oligomers SEQ ID NO: 17 and SEQ ID NO: 18 respectively.
  • the reactions were performed under single-turnover kinetic conditions, using 2.5 ⁇ M catalytic oligomer and 250 nM substrate, both at pH 6.0 in the presence of 10 mM Mg 2+ and also at pH 7.4 in the presence of 1 mM Mg 2+ . All other reaction conditions were as in Example 1.
  • the all ribonucleotide oligomers targeting GCA, GCC, ACA, and ACC sites have a higher rate of cleavage than the all ribonucleotide oligomers targeting GCU or ACU sites.
  • Table 4 indicates the cleavage activity is very high in the presence of 1 mM Mg 2+ . This level of Mg 2+ is similar to the concentration of Mg 2+ in vivo.
  • Example 3 Rate of cleavage at GCH and ACH triplets by catalytic oligomers containing only 6 ribonucleotides Cleavage of substrate RNA by 6-ribonucleotide versions of oligomers designed to cleave GCH and ACH triplets was assessed.
  • ribonucleotides were present at positions U 4 , G 5 , A 6 , G 8 , G 12 and I 15 - 1 and all other positions were 2'-0-allyl-ribonucleotides (see Figure 2 for numbering).
  • the oligomers used were SEQ ID NO: 17 (cleaves after ACH triplets) (Table 1) and SEQ ID NO: 18 (cleaves after GCH triplets) (Table 1).
  • the corresponding short fluorescent labelled substrates, SEQ ID NOS:4, 5, and 6 (containing ACH triplets) (Table 1) and SEQ ID NOS: 7, 8, and 9 (containing GCH triplets) (Table 1) were used with catalytic oligomers SEQ ID NO: 17 and SEQ ID NO: 18 respectively.
  • the reactions were performed under single-turnover kinetic conditions, using 2.5 ⁇ M catalytic oligomer and 250 nM substrate, both at pH 6.0 in the presence of 10 mM Mg 2+ and also at pH 7.4 in the presence of 1 mM Mg 2+ . All other reaction conditions were as in Example 1.
  • Example 4 Rate of cleavage at a GCA triplet by versions of a catalytic oligomer differing in the sugar modification at position U 4
  • oligomers that contain nuclease resistant modifications retain activity and that different modifications can be made at a given position of the catalytic oligomer while retaining activity.
  • the catalytic oligomers were based on SEQ ID NO: 18.
  • Variant I was made up of SEQ ID NO: 18 with all but five nucleotides modified with 2'-0-allyl-ribonucleotides (ribonucleotides were present at positions G 5 , A 6 , G 8 , G 12 and I 15 ' and all other positions were 2'-O-allyl-ribonucleotides; see Figure 2 for numbering).
  • Variant II was made up of SEQ ID NO: 18, modified with 2'-O-allyl-ribonucleotides at all but six nucleotides
  • Example 5 Comparison of cleavage activities of 2'-O-methyl- and 2'-O- allyl-modified catalytic oligomers at all 12 possible NCH triplets Cleavage of substrate RNA by oligomers with modifications in the nucleotides at all positions except G 5 , A 6 , G 8 , G 12 , and I 15 - 1 were assayed to show cleavage at all NCH sites.
  • Catalytic oligomers were based on SEQ ID NO: 17 (cleaves after ACH triplets), SEQ ID NO: 18 (cleaves after GCH triplets), SEQ ID NO: 19 (cleaves after CCH triplets) and SEQ ID NO:20 (cleaves after UCH triplets) that either contained 2'-0-allyl-ribonucleotides or 2'-0-methyl-ribonucleotides at all positions accept G 5 , A 6 , G 8 , G 12 , and I 15,1 were synthesized.
  • the respective fluorescent labelled substrates SEQ ID NOS:4, 5 and 6 (containing ACH triplets, cleaved by SEQ ID NO: 17), SEQ ID NOS:7, 8 and 9 (containing GCH triplets, cleaved by SEQ ID NO: 18), SEQ ID NOS: 10, 11 and 12 (containing CCH triplets, cleaved by SEQ ID NO: 19) and SEQ ID NOS: 13, 14 and 15 (containing UCH triplets, cleaved by SEQ ID NO: 20) were also synthesized.
  • the sequences of SEQ ID NOS: 4-20 are shown in Table 1.
  • Example 6 Rate of cleavage at a GCA triplet by versions of a catalytic oligomer differing in the nucleobase at position N 7 Cleavage assays were performed to show that different bases with different modifications could be substituted at position N 7 and still retain activity. All catalytic oligomers contained 2'-0-allyl-ribonucleotides at all positions except G 5 , A 6 , G 8 , G 12 and I 15 - 1 which were ribonucleotides. All catalytic oligomers were designed to cleave after GCH triplets. The sequences of the catalytic oligomers were as follows (the N 7 position is marked in boldface):
  • A, G and I are ribonucleotides a, c, g, u and i are 2 '-allyloxy-2' -deoxyribonucleotides q is l-(2-O-allyl-j3-D-ribofuranosyl)quinazoline-2,4-dione n is 5-nitro-l-(2-O-allyl-/3-D-ribofuranosyl)indole
  • FIG. 4 A and 4B Graphs showing fraction product versus time curves of the N 7 variant oligomers are shown in Figures 4 A and 4B.
  • the data indicate that all variants at N 7 are capable of cleaving very well.
  • the catalytic oligomers tolerate bulky groups such as the uracil analogue, quinazoline-2,4-dione quite well. Information such as this is important because it shows that there is a position in the catalytic oligomers which can be varied to optimize catalytic structure for a given substrate.
  • Example 7 In vitro cleavage of a long substrate derived from hepatitis C virus
  • Plasmid pN( 1-4728) contains the first 1358 bases of the hepatitis C virus genome (HCV). The sequence is oriented so as to allow a runoff transcript of the Bam Hi-linearized plasmid that produces a 1358 base transcript.
  • a runoff transcription (3-5 ⁇ g) was performed in a 100 ⁇ l reaction volume contaimng 40 mM Tris-HCl (pH 7.5), 18 mM MgCl 2 , 1 mM spermidine, 5 mM DTT, 2000 U/ml placental RNase inhibitor (Promega), 3 mM of each of ATP, UTP, CTP and GTP, 50 ⁇ Ci of [ ⁇ 32 P]GTP (DuPont NEN) and 3000 U/ml T7 RNA polymerase (New England Biolabs).
  • RNA gel-loading buffer (98% formamide, 10 mM EDTA, 0.025 % xylene cyanol FF and 0.025% bromophenol blue).
  • the mixture was then heated at 90°C for three minutes, snap-cooled on ice and subjected to electrophoresis on a 4% polyacrylamide/7 M urea gel.
  • the 1358 nucleotide long transcript was visualized by UV shadowing, the band was excised and the RNA extracted by electroelution for one hour.
  • the RNA was then recovered by overnight ethanol precipitation. After centrifugation and washing with 70% ethanol the purified transcript was resuspended in 20 ⁇ l of DEPC sterilized water and the concentration was determined by UV measurement.
  • the following oligomers were designed to target the runoff transcript of the HCV.
  • A, G, U and I are ribonucleotides a, c, g and u are 2 '-allyloxy-2' -deoxyribonucleotides These sequences are targeted to the GCA-345 site of the HCV genome which is present in the transcript.
  • Cleavage reactions were carried out in a 10 ⁇ l volume containing 50 mM Tris-HCl (pH 7.5), 10 mM MgCl 2 , 30 nM radiolabeled transcript and 300 nM catalytic oligomer (either SEQ ID NOS:28-31). Incubation was performed at 37 °C for 10 minutes and 60 minutes for each oligomer tested, and the reactions were quenched by addition of 10 ⁇ l of gel-loading buffer containing 20 mM EDTA, heated at 90 °C for 5 minutes and then cooled on ice. Unc leaved transcript and cleavage products were then separated by electrophoresis on a 4% polyacrylamide/7 M urea gel. After electrophoresis the gel was transferred onto Whatman 3MM filter paper and dried for two hours at 80 °C. Bands were quantitated by exposure to a Phosphorlmager screen.
  • Example 8 Comparison of in vitro cleavage of a long substrate derived from hepatitis C virus using catalytic oligomers targeting GCA and GUA triplets Cleavage assays were performed to show that catalytic oligomers designed to cleave the 1358 base HCV substrate function at concentrations as low as 30 nM.
  • the preparation of the runoff transcript was as in Example 7.
  • the oligomers used in these assays were as follows:
  • A, G, U and I are ribonucleotides a, c, g and u are 2 '-allyloxy-2' -deoxyribonucleotides
  • These catalytic oligomers target the GCA 345 triplet (oligomer of SEQ ID NO:28) and the GUA 378 triplet (oligomer of SEQ ID NO:32).
  • the fragments obtained when analyzing cleavage reactions of the 1358 runoff transcript of the HCV are 347 and 1011 nucleotides long for cleavage at the GCA 345 site and 380 and 978 nucleotides long for cleavage at the GUA 378 site.
  • the catalytic oligomers were compared at 1 and 3 ⁇ M with a reaction time of one hour and at concentrations of 30 nM, 100 nM, 300 nM, 1 ⁇ M and 3 ⁇ M with a reaction time of three hours. All other reaction and conditions were as in Example 7. An analysis of the data indicated that the oligomers cleaved the HCV transcript after three hours at all concentrations of catalytic oligomer tested. This indicates that concentrations of catalytic oligomer of 30 nM are capable of cleaving a 1358 base RNA fragment of the HCV genome.
  • Example 9 Cleavage of human IL-2 mRNA in Jurkat cell lysates Cleavage assays were performed to show that catalytic oligomers targeted to IL-2 mRNA were capable of cleaving the native mRNA in a cell lysate solution. These assays were performed with the catalytic oligomer of sequence: L-gacuuagcuGAuGaggccgugaggccGaaIcaaugca*T (SEQ ID NO:33)
  • G, U and I are ribonucleotides a, c, g and u are 2 '-allyloxy-2' -deoxyribonucleotides.
  • RPA ribonuclease protection assay
  • Biotin labelled antisense RNA probes for IL-2 and /3-actin RNA were prepared using an SP6 transcription kit.
  • the template for the 3-actin probe was purchased from Ambion and produced an RNA probe of 334 nucleotides and a protected fragment of 245 nucleotides in length.
  • An IL-2 probe template was made by using RT-PCR to amplify a fragment of the IL-2 sequence from Jurkat cell RNA.
  • One primer was designed to also include the SP6 transcription promoter site so that the resultant DNA probe could be transcribed directly from the PCR reaction.
  • the probe was designed to be 487 nucleotides in length, leading to a protected fragment also of 487 nucleotides after RPA analysis of IL-2 RNA. RPA analysis after cleavage with the catalytic oligomer should identify protected fragments of 428 and 59 nucleotides in addition to the full length RNA.
  • RNA fragments were separated by polyacrylamide gel electrophoresis (5 %), blotted onto nylon membrane and visualized by chemiluminescent detection using the BrightStar Biodetect kit from Ambion. Biotinylated RNA markers of lengths 500, 400, 300 and 200 nucleotides were used.
  • the cell lysate prepared as described above contains, the IL-2 mRNA produced through intracellular transcription. This cell lysate, contains the targeted substrate.
  • the product of the reaction between the substrate and the catalytic oligomer produces a 428 base and 59 base fragment of the IL-2 mRNA. By using a labeled probe for this sequence, the cleavage products can be detected.
  • the IL-2 mRNA was cleaved by the catalytic oligomer, SEQ ID NO:33, in the presence of the cell lysate. This indicates that the catalytic oligomers are capable of cleaving a long, native, mRNA in the presence of the cellular material associated with the mRNA in vivo.
  • Example 10 Cleavage of rat dopamine D2 receptor RNA in CHO cell lysates Cleavage assays were performed to show that catalytic oligomers targeted to rat dopamine D2 receptor mRNA were capable of cleaving the native mRNA in a CHO cell lysate solution. The assays were performed with the catalytic oligomer of sequence:
  • G, U and I are ribonucleotides a, c, g and u are 2 '-allyloxy -2' -deoxyribonucleotides. This sequence was designed to cleave after the GCA, where the A is at position 811, in the rat dopamine D2 receptor RNA (sequence name RND2DOPR in the EMBL Nucleotide Sequence Database 43 rd Edition).
  • Crude cell lysates were made from CHO cells stably transfected with the rat dopamine D2 receptor gene by the freeze-thawing procedure as described in Example 9 above. Each cleavage reaction was carried out at 37°C in a 100 ⁇ l reaction volume including 62.5 ⁇ l of cell lysate, 50 mM Tris pH 7.5, 10 mM MgCl 2 and 0.5 ⁇ M catalytic oligomer for the reaction times: 10, 30, 60, and 120 minutes
  • the following controls were performed: dopamine D2 receptor RNA and /3-actin digested with RNase, dopamine D2 receptor RNA and /3-actin control, rat dopamine D2 receptor RNA probe and /3-actin control, control after 10 minutes with no oligomer, control after 30 minutes with no oligomer, and control after 60 minutes with no oligomer.
  • RNA was purified from the reactions and analyzed by ribonuclease protection assay, using the RPA II kit from Ambion and following the manufacturer's protocol.
  • Biotin labelled antisense RNA probes for rat dopamine D2 receptor and mouse /3-actin RNA (internal standard) were prepared using an SP6 transcription kit.
  • the template for the /3-actin probe was purchased from Ambion and produced an RNA probe of 334 nucleotides and a protected fragment of 245 nucleotides in length.
  • a dopamine D2 receptor probe template was made by using RT-PCR to amplify a fragment of the dopamine D2 receptor sequence from CHO cell RNA.
  • One primer was designed to also include the SP6 transcription promoter site so that the resultant DNA probe could be transcribed directly from the PCR reaction.
  • the probe was designed to be 663 nucleotides after RPA analysis of dopamine D2 receptor RNA. RPA analysis after cleavage with the catalytic oligomer should identify protected fragments of 394 and 269 nucleotides in addition to the full length RNA. Protected RNA fragments were separated by polyacrylamide gel electrophoresis (5%), blotted onto nylon membrane and visualized by chemiluminescent detection using the BrightStar Biodetect kit from Ambion.
  • Example 11 Cleavage of human ICAM-1 mRNA in A549 cell lysates Cleavage assays were performed to show that catalytic oligomers targeted to ICAM-1 mRNA were capable of cleaving the native mRNA in an A549 cell lysate solution. The assays were performed with the catalytic oligomers of sequences:
  • A, G, U and I are ribonucleotides a, c, g and u are 2 '-allyloxy-2' -deoxyribonucleotides.
  • sequences were designed to cleave after the ACA sites where the first A is positioned at base 1205 (SEQ ID NO:35) and position 1592 (SEQ ID NO: 36), in the human intercellular adhesion molecule- 1 mRNA (ICAM-1) (sequence name HSICAM01 in the EMBL Nucleotide Sequence Database 43 rd Edition).
  • IAM-1 human intercellular adhesion molecule- 1 mRNA
  • Crude cell lysates were made from A549 cells, after a five hour stimulation with 10 ng/ml of hTNF ⁇ . to induce expression of ICAM-1 , by the freeze-thawing procedure as described in Example 9 above. Each cleavage reaction was carried out for two hours at 37°C in a 100 ⁇ l reaction volume including 62.5 ⁇ l of cell lysate, 50 mM Tris pH 7.5, 70 mM MgCl 2 and catalytic oligomer to a final concentration of either 500 nM oligomer, 200 nM oligomer, 100 nM oligomer, 50 nM oligomer, control without catalytic oligomer.
  • RNA was purified from the reactions and analyzed by ribonuclease protection assay, using the RPA II kit from Ambion, following the manufacturer's protocol.
  • Biotin labelled antisense RNA probes for human ICAM-1 and GAPDH RNA were prepared using an SP6 transcription kit.
  • the template for the GAPDH probe was purchased from Ambion and produced a protected fragment of 316 nucleotides in length.
  • An ICAM-1 probe template was made by using RT-PCR to amplify a fragment of the ICAM-1 sequence from A549 cell RNA.
  • One primer was designed to also include the SP6 transcription promoter site so that the resultant DNA probe could be transcribed directly from the PCR reaction.
  • the probe was designed to be 598 nucleotides in length, leading to a protected fragment also of 598 nucleotides after RPA analysis of ICAM-1 RNA.
  • RPA analysis after cleavage with the catalytic oligomers should identify protected fragments of 552 and 46 nucleotides (1205 ACA site) and 433 and 165 nucleotides (1592 ACA site) respectively in addition to the full length RNA.
  • RNA fragments were separated by 5% polyacrylamide gel electrophoresis, blotted onto nylon membrane and visualized by chemiluminescent detection using the BrightStar Biodetect kit from Ambion. Biotinylated RNA markers of length 500, 400, 300 and 200 nucleotides were used. Cleavage products were produced at all concentrations of oligomer tested. Cleavage at the 1592 ACA site was particularly effective even using only 50 nM catalytic oligomer.
  • NAME Pabst, Patrea L.

Abstract

On décrit des compositions présentant une activité de clivage de l'ARN ainsi que leur utilisation pour couper in vitro et in vivo des substrats d'ARN. Les compositions contiennent un centre actif dont les sous-unités sont sélectionnées parmi des nucléotides et/ou des analogues de nucléotides, ainsi que des régions flanquantes contribuant à la formation d'une hybridation spécifique avec un substrat d'ARN. Les compositions préférées forment, en combinaison avec un substrat d'ARN, une structure qui ressemble à une structure en tête de marteau. Le centre actif des compositions de cette invention se caractérise par la présence de I15.1 qui permet de couper des substrats d'ARN ayant un C16.1.
EP98930352A 1997-06-19 1998-06-17 Ribozymes en tete de marteau a fonction de clivage etendue Withdrawn EP1019497A1 (fr)

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