EP0886641A2 - Synthese de methoxy nucleosides et de molecules d'acide nucleique enzymatique - Google Patents

Synthese de methoxy nucleosides et de molecules d'acide nucleique enzymatique

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Publication number
EP0886641A2
EP0886641A2 EP96944523A EP96944523A EP0886641A2 EP 0886641 A2 EP0886641 A2 EP 0886641A2 EP 96944523 A EP96944523 A EP 96944523A EP 96944523 A EP96944523 A EP 96944523A EP 0886641 A2 EP0886641 A2 EP 0886641A2
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EP
European Patent Office
Prior art keywords
methyl
nucleic acid
nucleoside
nucleotide
enzymatic nucleic
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP96944523A
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German (de)
English (en)
Inventor
Francine Wincott
Nassim Usman
Leonid Beigelman
Peter Haeberli
Jasenka Matulic-Adamic
Alexander Karpeisky
David Sweedler
Thale Jarvis
Anthony Direnzo
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Sirna Therapeutics Inc
Original Assignee
Ribozyme Pharmaceuticals Inc
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Filing date
Publication date
Priority claimed from US08/585,682 external-priority patent/US5728818A/en
Priority claimed from US08/632,882 external-priority patent/US5998203A/en
Application filed by Ribozyme Pharmaceuticals Inc filed Critical Ribozyme Pharmaceuticals Inc
Priority to EP01103093A priority Critical patent/EP1108724B1/fr
Publication of EP0886641A2 publication Critical patent/EP0886641A2/fr
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/12—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes
    • C12N2310/121—Hammerhead

Definitions

  • This invention relates to the chemical synthesis of 2'-0-methyl, 3'-0- methyl and ⁇ '-O-methyl nucleosides, incorporation of novel chemical modifications in enzymatic nucleic acid molecules and improved methods for the synthesis of enzymatic nucleic acid molecules.
  • the invention features chemical synthesis of 2'-0-methyl
  • Robins et al., 1974 J. Org. Chem. 39, 1891 describe the treatment of a methanolic solution of uridine with diazomethane (in glyme) in the presence of stannous chloride dihydrate (in methanol) to synthesize 2'-0-methyluridine (58% yield). This reaction also yielded a significant fraction (28%) of 3'-0- methyluridine which is purified away from the 2'-0-methyl form by chromatography.
  • Nucleic Acids Res. 15, 613 describe a process for the synthesis of 2'-0- methyl ribonucleosides involving alkylation of 3' ,5'- 0 - (tetraisopropyldisiloxane-1 , 3-diyl) (TIPDS)-ribonucleosides with methyl iodide.
  • TIPDS tetraisopropyldisiloxane-1 , 3-diyl
  • This procedure uses a multi-step process involving- "a facile obtention of the 2'-0-methyl sugar synthon using totally selective and efficient methylation cond ⁇ tions;...a stereoselective high-yield condensation with an uracil derivattve, yielding the desired ⁇ -form with a satisfactory anomeric excess.” (page 5361 , fifth paragraph).
  • 3'-0-TBDMS-derivatives of protected ribonucleosides are byproducts obtained during the preparation of 2'-0-TBD S derivatives - key building blocks in oligo ⁇ bonucleotide synthesis.
  • 3'-0-TBD S-isomers could be useful starting compounds in the preparation of 2'-0-methyl-3'-0-phosphoramid ⁇ tes.
  • cytidine derivative 14 Reaction of 3'-0-TBDMS-5'-0- DMT-N 4 - -Bu-cyt ⁇ d ⁇ ne (14) with Ag2 ⁇ -CH3l using a modified method of Ohtsuka et al.
  • DMAP Nucleoside 19 afforded methythiophenyl ether 20 in 65-70% yield, and ⁇ - ⁇ bofuranose 21 was transformed into ⁇ -furanose 22 in 60% yield.
  • Different attempts to radically (Bu3SnH, BZ2O2) reduce the thiophenyl group of furanose 22 were not successful, providing only starting material.
  • nucleoside 20 afforded 2'-0-Me derivative 24 in 70% yield.
  • the invention features improved methods for the synthesis of enzymatic nucleic acid molcules.
  • Ribozymes are nucleic acid molecules having an enzymatic activity which is able to repeatedly cleave other separate RNA molecules in a nucleotide base sequence specific manner. Such enzymatic RNA molecules can be targeted to virtually any RNA transcript, and efficient cleavage achieved in vitro. Kim et al., 84 Proc. Natl. Acad. Sci. USA 8788, 1987; Haseloff and Gerlach, 334 Nature 585, 1988; Cech, 260 JAMA 3030, 1988; and Jefferies et al., 17 Nucleic Acids Research 1371 , 1989.
  • Ribozymes act by first binding to a target RNA. Such binding occurs through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA which acts to cleave the target RNA. Thus, the ribozyme 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 a ribozyme 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.
  • complementarity is meant a nucleic acid that can form hydrogen bond(s) with other RNA sequences by either traditional Watson-Crick or other non-traditional types (for example, Hoogsteen type) of base-paired interactions.
  • enzymatic nucleic acids 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.
  • 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.
  • ribozyme The enzymatic nature of a ribozyme is advantageous over other technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its translation) since the effective concentration of ribozyme necessary to effect a therapeutic treatment is lower than that of an antisense oligonucleotide.
  • This advantage reflects the ability of the ribozyme to act enzymatically.
  • a single ribozyme molecule is able to cleave many molecules of target RNA.
  • the ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding, but also on the mechanism by which the molecule inhibits the expression of the RNA to which it binds. That is, the inhibition is caused by cleavage of the RNA target and so specificity is defined as the ratio of the rate of cleavage of the targeted RNA over the rate of cleavage of non-targeted RNA. This cleavage mechanism is dependent upon factors additional to those involved in base pairing. Thus, it is thought that the specificity of action of a ribozyme is greater than that of antisense oligonucleotide binding the same RNA site.
  • Jennings et al. US Patent No. 5, 298, 612 describe the use of non- nucleotides to assemble a hammerhead ribozyme lacking a stem II portion.
  • Draper et al., WO 93/23569 (PCT/US93/04020) describes synthesis of ribozymes in two parts in order to aid in the synthetic process (see, e.g.. p. 40).
  • enzymatic nucleic acid molecules having non-nucleotides within their structure. Such non-nucleotides can be used in place of nucleotides to allow formation of an enzymatic nucleic acid.
  • the invention features enzymatic nucleic acid molecules with chemical modifications at the 5'- and/or 3'-ends.
  • Chemically-modified ribozymes can be synthesized which are stable in human serum for up to 260 hours (Beigelman et al., 1995 supra) and maintain near wild type (chemically unmodified equivalent of modified ribozyme) activity in vitro.
  • a number of laboratories have reported that the enhanced cellular efficacy of phosphorothioate-substituted antisense molecules. The enhanced efficacy appears to result from either i) increased resistance to 5'-exonuclease digestion (De Clercq et al.., 1970 Virology 42, 421-428; Shaw et al.., 1991 Nucleic Acids Res.
  • B(OMe)3] would provide the same effect directly or in the case of methanolysis, complexation of the MeOH with Lewis acids would acidify the related proton leading to potential protonation of the N3 atom of the above-mentioned anhydro derivatives.
  • Applicant investigated methanolysis of 2,2'-, 2,3' or 2,5'-anhydro pyrimidine nucleosides in the presence of a Lewis acid, such as B(OMe)3 and/or BF3.MeOH.
  • Lewis Acid is meant a substance that can accept an electron pair from a base.
  • Lewis acids are, B(OCH 3 ) 3 , BF 3 , AICI 3 , and SO 3 .
  • the invention features a process for the synthesis of a 2'-0 methyl adenosine nucleoside, comprising the step of contacting a solution of N 4 -acetyl-5',3'-di-0-acetyl-2'-0-methyl cytidine with a Lewis acid under conditions suitable for the formation of said nucleoside.
  • the invention features a process for the synthesis of 2'- O-methyl guanosine nucleoside, comprising the steps of: a) methylating 2- amino-6-chloropurine riboside by contacting said 2-amino-6-chloropurine riboside with sodium hydride, dimethylformamide and methyl iodide under conditions suitable for the formation of 2'-0-methyl-2-amino-6-chloropurine riboside; b) contacting said 2'-0-methyl-2-amino-6-chloropurine riboside with 1 ,4-diazabicyclo(2.2.2) octane and water under conditions suitable for the formation of said 2'-0-methyl guanosine nucleoside in a crude form; and c) purifying said 2'-0-methyl guanosine nucleoside from said crude form.
  • the invention features a process for the synthesis of 2'-
  • O-methyl adenosine nucleoside comprising the steps of: a) methylating 2- amino-6-chloropurine riboside by contacting said 2-amino-6-chloropurine riboside with sodium hydride, dimethylformamide and methyl iodide under conditions suitable for the formation of 2'-0-methyl-2-amino-6-chloropurine riboside; b) contacting said 2'-0-methyl-2-amino-6-chloropurine riboside with acetic anhydride, 4-dimethylaminopyridine and triethylamine under conditions suitable for the formation of 3',5'-di-0-acetyl-2'-0-methyl-6-chloro-2- aminopurine riboside; c) deaminating said 3 ⁇ 5'-di-0-acetyl-2'-0-methyl-6- chloro-2-aminopurine riboside with isoamyl nitrite and tetrahydro
  • the invention features a process for the synthesis of 2'-Omethyl guanosine nucleoside, comprising the steps of: a) contacting 2,6- diaminopurine nucleoside with anhydrous pyridine and tetraisopropyl D-silyl chloride under conditions suitable for the formation of 2,6-diamino-9-(3,5-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) purine; b) methylating said 2,6-Diamino-9-(3,5-0-tetraisopropyldisiloxane-( 1 ,3-diyl)- ⁇ - D - ribofuranosyl) purine by contacting said 2,6-Diamino-9-(3,5-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) pur
  • the invention features a process for the synthesis of 2'-0- methyl guanosine nucleoside, comprising the steps of: a) contacting 2,6- diaminopurine nucleoside with anhydrous pyridine and tetraisopropyl D-silyl chloride (TIPSCI) under conditions suitable for the formation of 2,6-Diamino-9- (3',5'-0-tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) purine; b) methylating said 2,6-Diamino-9-(3,5-0-tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D- ribofuranosyl) purine by contacting said 2,6-Diamino-9-(3,5-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-D-
  • the invention features a process for the synthesis of 2-0- methyl guanosine nucleoside, comprising the steps of: a) contacting guanosine with N,N-dimethylformamide dibenzyl acetal under conditions suitable for the formation of N1 -benzyl guanosine; b) methylating said N1 - benzyl guanosine by contacting said N1 -benzyl guanosine with silver acetylacetonate, trimethylsulphonium hydroxide and dimethylformamide under conditions suitable for the formation of N1 -benzyl-2'-0-methyl guanosine in a crude form; c) purifying said N1-benzyl-2'-Omethyl guanosine from said crude form; d) removing the N1 -benzyl protection from said N1 - benzyl-2'-0-methyl guanosine by contacting said N1-benzyl-2'-0-methyl guanosine
  • the invention features a process for the synthesis of 2'-0-methyl adenosine nucleoside, comprising the steps of: a) methylating adenosine by contacting said adenosine with dimethylformamide, silver acetylacetonate and trimethylsulphonium hydroxide under conditions suitable for the formation of 2'-0-methyl adenosine in a crude form; and b) purifying said 2'-0-methyl adenosine from said crude form.
  • the invention also features a process for the synthesis of 2'-0-methyl guanosine nucleoside, comprising the steps of: a) contacting guanosine with N,N-dimethylformamide dibenzyl acetal under conditions suitable for the formation of N1 -benzyl guanosine; b) methylating said N1- benzyl guanosine by contacting said N1 -benzyl guanosine with magnesium acetylacetonate, trimethylsulphonium hydroxide and dimethylformamide under conditions suitable for the formation of N1 -benzyl-2'-0-methyl guanosine in a crude form; c) purifying said N1-benzyl-2'-0-methyl guanosine from said crude form; d) removing the N1 -benzyl protection from said N1 - benzyl-2'-0-methyl guanosine by contacting said N1 -benzyl-2'-0-methyl guanosine by
  • the invention features a process for the synthesis of 2'-0- methyl adenosine nucleoside, comprising the steps of: a) methylating adenosine by contacting said adenosine with dimethylformamide, magnesium acetylacetonate and trimethylsulphonium hydroxide under conditions suitable for the formation of 2'-0-methyl adenosine in a crude form; and b) purifying said 2'-0-methyl adenosine from said crude form.
  • the invention features a process for the synthesis of 2'-0- methyl adenosine nucleoside, comprising the steps of: a) methylating adenosine by contacting said adenosine with dimethylformamide, strontium acetylacetonate and trimethylsulphonium hydroxide under conditions suitable for the formation of 2'-0-methyl adenosine in a crude form; and b) purifying said 2'-0-methyl adenosine from said crude form.
  • the invention features a process for the synthesis of 2'-0- methyl guanosine nucleoside, comprising the steps, of: a) contacting 2,6- diaminopurine nucleoside with anhydrous pyridine and TIPSCI under conditions suitable for the formation of 2,6-diamino-9-(3',5'-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) purine; b) methylating said 2,6-Diamino-9-(3,5- -tetraisopropyldisiloxane-( 1 ,3-diyl)- ⁇ - D - ribofuranosyl) purine by contacting said 2,6-Diamino-9-(3',5'-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl
  • the invention features a process for the synthesis of 2'-0-methyl guanosine nucleoside, comprising the steps of: a) contacting 2,6-diaminopurine nucleoside with anhydrous pyridine and TIPSCI under conditions suitable for the formation of 2,6-Diamino-9-(3,5-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) purine; b) methylating said 2,6-Diamino-9-(3,5-0-tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ - D - ribofuranosyl) purine by contacting said 2,6-Diamino-9-(3,5-0- tetraisopropyldisiloxane-(1 ,3-diyl)- ⁇ -D-ribofuranosyl) purine with anhydrous DMF and methyl
  • This invention features an improved and economical synthetic method for the preparation of 2'-0-methyl nucleosides in high yield.
  • the method is not only cost efficient, but can be scaled up to several hundred gram quantities.
  • the method generally utilizes inexpensive commercially available 2,2'- anhydro-1 ( ⁇ -D-arabinofuranosyl)base, such as 2,2'-anhydro-1 ( ⁇ -D- arabinofuranosyl)uracil or 2,2'-anhydro-1( ⁇ -D-arabinofuranosyl)cytosine, as a starting material which is converted in a one or two step reaction sequence to 2'-0-methyl nucleosides with a yield of about 90-100%.
  • the 2'-0-methyl or 3'-0-methyl nucleosides can be used for chemical synthesis of nucleotides, nucleotide-tri-phosphates and/or phosphoramidites as a building block for selective incorporation into oligonucleotides.
  • These oligonucleotides can be used as an antisense molecule, 2-5A antisense chimera, triplex molecule or as an enzymatic nucleic acid molecule.
  • the oligonucleotides can also be used as probes or primers for synthesis and/or sequencing of RNA or DNA.
  • antisense it is meant a non-enzymatic nucleic acid molecule that binds to target RNA by means of RNA-RNA or RNA-DNA or RNA-PNA (protein nucleic acid; Egholm et al., 1993 Nature 365, 566) interactions and alters the activity of the target RNA (for a review see Stein and Cheng, 1993 Science
  • 2-5A antisense chimera an antisense oligonucleotide containing a 5' phosphorylated 2'-5'-linked adenylate residues. These chimeras bind to target RNA in a sequence-specific manner and activate a cellular 2-5A-dependent ribonuclease which, in turn, cleaves the target RNA
  • triplex DNA it is meant an oligonucleotide that can bind to a double- stranded DNA in a sequence-specific manner to form a triple-strand helix. Formation of such triple helix structure has been shown to inhibit transcription of the targeted gene (Duval-Valentin et al., 1992 Proc. Natl. Acad. Sci. USA 89, 504).
  • zymatic nucleic acid it is meant a nucleic acid molecule capable of catalyzing reactions including, but not limited to, site-specific cleavage and/or ligation of other nucleic acid molecules, cleavage of peptide and amide bonds, and trans-splicing.
  • the invention features a method for chemical synthesis of 2'-0-methyl or 3'-0-methyl nucleosides in which 2,2'-anhydro- 1 ( ⁇ -D-arabinofuranosyl) cytosine, 2,2'-anhydro-1 ( ⁇ -D-arabinofuranosyl) uracil, 2, 3'-anhydro- 1 ( ⁇ -D-arabinofuranosyl) uracil, or 2, 3'-anhydro-1 ( ⁇ - D- arabinofuranosyl) cytidine is used as the starting material, and wherein said starting material is reacted with a Lewis acid.
  • Another preferred embodiment of the invention features a method for chemical synthesis of 5'-0-methyl pyrimidine nucleoside in which 2,5'- anhydro-1 ( ⁇ -D-arabinofuranosyl) pyrimidine is used as the starting material and is reacted with a Lewis acid.
  • the invention features novel processes for the synthesis of 2'-0-methyl purine nucleosides.
  • Another preferred embodiment of the invention features a method for the chemical synthesis of Purines.
  • This invention relates to improved methods for synthesis of enzymatic nucleic acids and, in particular, hammerhead and hairpin motif ribozymes.
  • This invention is advantageous over iterative chemical synthesis of ribozymes since the yield of the final ribozyme can be significantly increased.
  • two partial ribozyme portions e.g.. a 20mer and a 17mer, can be synthesized in significantly higher yield, and the two reacted together to form the desired enzymatic nucleic acid.
  • each n or n' is independently any desired nucleotide or non-nucleotide
  • each filled-in circle represents pairing between bases or other entities
  • the solid line represents a covalent bond.
  • each n and n' may be a ribonucleotide, a 2'-methoxy-substituted nucleotide, or any other type of nucleotide which does not significantly affect the desired enzymatic activity of the final product (see Usman et al., supra).
  • ribonucleotides are provided at rG5, rA6, rG8, rG12, and rA15.1.
  • U4 and U7 may be abasic ( e ⁇ , lacking the uridine moiety) or may be ribonucleotides, 2'- methoxy substituted nucleotides, or other such nucleotides.
  • a9, a13, and a14 are preferably 2'-methoxy or may have other substituents.
  • the synthesis of this hammerhead ribozyme is performed by synthesizing a 3' and a 5' portion as shown in a lower part of Fig. 16.
  • Each 5' and 3' portion has a chemically reactive group X and Y, respectively.
  • Non-limiting examples of such chemically reactive groups are provided in Fig. 17. These groups undergo chemical reactions to provide the bonds shown in Fig. 17.
  • the X and Y can be used, in various combinations, in this invention to form a chemical linkage between two ribozyme portions.
  • the invention features a method for synthesis of an enzymatically active nucleic acid (as defined by Draper, supra) by providing a 3' and a 5' portion of that nucleic acid, each having independently chemically reactive groups at the 5' and 3' positions, respectively.
  • the reaction is performed under conditions in which a covalent bond is formed between the 3' and 5' portions by those chemically reactive groups.
  • the bond formed can be, but is not limited to, either a disulfide, morpholino, amide, ether, thioether, amine, a double bond, a sulfonamide, carbonate, hydrazone or ester bond.
  • the bond is not the natural bond formed between a 5' phosphate group and a 3' hydroxyl group which is made during normal synthesis of an oligonucleotide.
  • more than two portions can be linked together using pairs of X and Y groups which allow proper formation of the ribozyme.
  • chemically reactive group is simply meant a group which can react with another group to form the desired bonds. These bonds may be formed under any conditions which will not significantly affect the structure of the resulting enzymatic nucleic acid. Those in the art will recognize that suitable protecting groups can be provided on the ribozyme portions.
  • the nucleic acid has a hammerhead motif and the 3' and 5' portions each have chemically reactive groups in or immediately adjacent to the stem II region (see Fig. 1 ).
  • the stem II region is evident in Fig. 1 between the bases termed a9 and rG12.
  • the C and G within this stem defines the end of the stem II region.
  • any of the n or n' moieties within the stem II region can be provided with a chemically reactive group.
  • the chemically reactive groups need not be provided in the solid line portion but can be provided at any of the n or n'. In this way the length of each of the 5' and 3' portions can vary by several bases.
  • the chemically reactive group can be, but is not limited to, (CH 2 )nSH; (CH 2 )n NHR; (CH 2 )nX; ribose; COOH; (CH 2 )n PPh 3 ; (CH 2 ) n S0 2 CI; (CH 2 ) n COR; (CH 2 ) n RNH or (CH 2 ) n OH, where, CH 2 can be replaced by another group which forms linking chain containing various atoms including, but not limited to CH 2 , such as methylenes, ether, ethylene glycol, thioethers, double bonds, aromatic groups and others; each n independently is an integer from 0 to 10 inclusive and may be the same or different; each R independently is a proton or an alkyl, alkenyl and other functional groups or conjugates such as peptides, steroids, hoemones, lipids, nucleic acid sequences and others that provides nuclease resistance, improved cell association, improved
  • an "alkyl” group refers to a saturated aliphatic hydrocarbon, including straight-chain, branched-chain, and cyclic alkyl groups.
  • the alkyl group has 1 to 12 carbons. More preferably it is a lower alkyl of from 1 to 7 carbons, more preferably 1 to 4 carbons.
  • alkenyl groups which are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight-chain, branched-chain, and cyclic groups.
  • the alkenyl group has 1 to 12 carbons. More preferably it is a lower alkenyl of from 1 to 7 carbons, more preferably 1 to 4 carbons.
  • alkyl also includes alkynyl groups which have an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, including straight-chain, branched-chain, and cyclic groups.
  • the alkynyl group has 1 to 12 carbons. More preferably it is a lower alkynyl of from 1 to 7 carbons, more preferably 1 to 4 carbons.
  • alkyl groups may also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups.
  • An "aryl” group refers to an aromatic group which has at least one ring having a conjugated ⁇ electron system and includes carbocyclic aryl, heterocyclic aryl and biaryl groups, all of which may be optionally substituted.
  • the preferred substituent(s) of aryl groups are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups.
  • alkylaryl refers to an alkyl group (as described above) covalently joined to an aryl group (as described above.
  • Carbocyclic aryl groups are groups wherein the ring atoms on the aromatic ring are all carbon atoms. The carbon atoms are optionally substituted.
  • Heterocyclic aryl groups are groups having from 1 to 3 heteroatoms as ring atoms in the aromatic ring and the remainder of the ring atoms are carbon atoms.
  • Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl and the like, all optionally substituted.
  • An "amide” refers to an -C(0)-NH-R, where R is either alkyl, aryl, alkylaryl or hydrogen.
  • An “ester” refers to an -C(0)-OR', where R is either alkyl, aryl, alkylaryl or hydrogen.
  • the conditions include provision of Nal ⁇ 4 in contact with the ribose, and subsequent provision of a reducing group such as NaBH4 or NaCNBH ⁇ -, or the conditions include provision of a coupling reagent.
  • the invention features a mixture of the 5' and 3' portions of the enzymatically active nucleic acids having the 3" and 5' chemically reactive groups noted above.
  • the hairpin ribozyme may be synthesized by inclusion of chemically reactive groups in helix IV and in other helices which are not critical to the enzymatic activity of the nucleic acid.
  • Enzvmatic nucleic acid molecules containing 5'- and/or 3'-cap structures This invention relates to the incorporation of chemical modifications at the 5' and/or 3' ends of nucleic acids, which are particularly useful for enzymatic cleavage of RNA or single-stranded DNA. These terminal modifications are termed as either a 5'-cap or a 3'-cap depending on the terminus that is modified. Certain of these modifications protect the enzymatic nucleic acids from exonuclease degradation. Resistance to exonuclease degradation can increase the half-life of these nucleic acids inside a cell and improve the overall effectiveness of the enzymatic nucleic acids.
  • terminal modifications can also be used to facilitate efficient uptake of enzymatic nucleic acids by cells, transport and localization of enzymatic nucleic acids within a cell, and help achieve an overall improvement in the efficacy of ribozymes in vitro and in vivo.
  • chemical modification refers to any base, sugar and/or phosphate modification that will protect the enzymatic nucleic acids from degradation by nucleases.
  • Non-limiting examples of some of the chemical modifications and methods for their synthesis and incorporation in nucleic acids are described in Figures 28, 29, 32-37 and infra.
  • chemical modifications of enzymatic nucleic acids are featured that provide resistance to cellular 5'-exonuclease and/or 3'- exonuclease digestion without reducing the catalytic activity or cellular efficacy of these nucleic acids .
  • the invention features enzymatic nucleic acids with 5'-end modifications (5'-cap) having the formula:
  • Another preferred embodiment of the invention features enzymatic nucleic acid molecules having a 5'-cap, wherein said cap is selected from but not limited to, a group comprising, 4',5'-methylene nucleotide; 1 -( ⁇ -D- erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 5'- amino-alkyl phosphate; 1 ,3-diamino-2-propyl phosphate, 3-aminopropyl phosphate; 6-aminohexyl phosphate; 12-aminododecyl phosphate; hydroxypropyl phosphate; 1 ,5-anhydrohexitol nucleotide; L-nucleotide; ⁇ - nucleotide; modified base nucleotide; phosphorodithioate; threo- pentofuranosyl nucleotide; acyclic 3'
  • the invention features enzymatic nucleic acids with 3'- end modifications (3'-cap) having the formula:
  • X represents 4'-thio nucleotide, carbocyclic nucleotide; 1 ,5- anhydrohexitol nucleotide; L-nucleotides; ⁇ -nucleotides; modified base nucleotide; phosphorodithioate linkage; fhreo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5- dihydroxypentyl nucleotide, 3'-3'-inverted nucleotide moeity; 3'-3'-inverted abasic moeity; 3'-2'-inverted nucleotide moeity; 3'-2'-inverted abasic moeity; 1 ,4-butanediol; 3'-phosphoramidate; hexylphosphate; aminohexyl phosphate;
  • the invention features enzymatic nucleic acid molecules having a 3'-cap, wherein said cap is selected from but not limited to, a group comprising, 4'-thio nucleotide, carbocyclic nucleotide;
  • the invention features enzymatic nucleic acids with both 5'-cap and a 3'-cap which may be same or different.
  • nucleotide is used as recognized in the art to include natural bases, and modified bases well known in the art. Such bases are generally located at the 1 ' position of a sugar moiety. Nucleotide generally comprise a base, sugar and a phosphate group. The nucleotide can be unmodified or modified at the sugar, phosphate and/or base moeity.
  • abasic or “abasic nucleotide” as used herein encompasses sugar moieties lacking a base or having other chemical groups in place of base at the 1 1 position.
  • zymatic nucleic acid a catalytic modified- nucleotide-containing nucleic acid molecule that has complementarity in a substrate binding region to a specified gene target, and also has an enzymatic activity that specifically cleaves RNA or DNA in that target. That is, the enzymatic nucleic acid 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 phosphate groups.
  • enzymatic nucleic acid is used interchangeably with phrases such as ribozymes, catalytic RNA, enzymatic RNA, catalytic DNA, nucleozyme, DNAzyme, RNA enzyme, endoribonuclease, minizyme, leadzyme or DNA enzyme. All of these terminologies describe nucleic acid molecules with enzymatic activity.
  • modified bases As it relates to nucleic acids, is well known in the art and has recently been summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183.
  • Some of the non-limiting examples of base modifications that can be introduced into enzymatic nucleic acids without significantly effecting their catalytic activity include, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2, 4, 6-trimethoxy benzene, 3- methyluracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), 5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6- methyluridine); Guanosine or adenosine residues may be replaced by diaminopurine
  • the 5'-cap and/or 3'-cap derivatives of this invention provide enhanced activity and stability to the enzymatic nucleic acids containing them.
  • complementarity is meant a nucleic acid that can form hydrogen bond(s) with other RNA sequence by either traditional Watson-Crick or other non-traditional types (for example, Hoogsteen type) of base-paired interactions.
  • bridging and “nonbridging” are meant to indicate the relative positions of oxygen atom involved in the formation of standard phosphodiester linkage in a nucleic acid. These backbone oxygen atoms can be readily modified to impart resistance against nuclease digestion. The terms are further defined as follows:
  • the enzymatic nucleic acid molecule is formed in a hammerhead or hairpin motif, but may also be formed in the motif of a hepatitis delta virus (HDV), group I intron, RNaseP RNA (in association with an RNA guide sequence) or Neurospora VS RNA.
  • HDV hepatitis delta virus
  • group I intron group I intron
  • RNaseP RNA in association with an RNA guide sequence
  • Neurospora VS RNA Neurospora VS RNA.
  • Examples of such hammerhead motifs are described by Rossi et al., 1992, Aids Research and Human Retroviruses 8, 183, of hairpin motifs by Hampel et al., EP0360257, Hampel and Tritz, 1989 Biochemistry 28, 4929, and Hampel et al., 1990 Nucleic Acids Res.
  • the invention provides a method for producing a class of enzymatic cleaving agents which exhibit a high degree of specificity for the RNA of a desired target.
  • the enzymatic nucleic acid molecule is preferably targeted to a highly conserved sequence region of a target such that specific treatment of a disease or condition can be provided with a single enzymatic nucleic acid.
  • Such enzymatic nucleic acid molecules can be delivered exogenously to specific cells as required.
  • the small size (less than 60 nucleotides, preferably between 30-40 nucleotides in length) of the molecule allows the cost of treatment to be reduced compared to other ribozyme motifs.
  • nucleic acids greater than 100 nucleotides in length is difficult using automated methods, and the therapeutic cost of such molecules is prohibitive.
  • small enzymatic nucleic acid motifs e.g., of the hammerhead structure
  • the simple structure of these molecules increases the ability of the enzymatic nucleic acid to invade targeted regions of the mRNA structure.
  • the hammerhead structure is included within longer transcripts, there are no non- enzymatic nucleic acid flanking sequences to interfere with correct folding of the enzymatic nucleic acid structure or with complementary regions.
  • Therapeutic ribozymes must remain stable within cells until translation of the target mRNA 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. Clearly, ribozymes must be resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of RNA (Wincott et al., 1995 Nucleic Acids Res. 23, 2677; incorporated by reference herein) have expanded the ability to modify ribozymes to enhance their nuclease stability. The majority of this work has been performed using hammerhead ribozymes (reviewed in Usman and McSwiggen, 1995 supra) and can be readily extended to other ribozyme motifs.
  • Figure 1 is a diagrammatic representation of the hammerhead ribozyme domain known in the art.
  • Stem II can be > 2 base-pair long.
  • Each N is independently any base or non-nucleotide as used herein.
  • Figure 2a is a diagrammatic representation of the hammerhead ribozyme domain known in the art
  • Figure 2b is a diagrammatic representation of the hammerhead ribozyme as divided by Uhlenbeck (1987, Nature, 327, 596- 600) into a substrate and enzyme portion
  • Figure 2c is a similar diagram showing the hammerhead divided by Haseloff and Gerlach (1988, Nature , 334, 585-591 ) into two portions
  • Figure 2d is a similar diagram showing the hammerhead divided by Jeffries and Symons (1989, Nucl. Acids. Res., 17, 1371-1371) into two portions.
  • FIG 3 is a diagrammatic representation of the general structure of a hairpin ribozyme.
  • Helix 2 (H2) is provided with a least 4 base pairs (i.e., n is 1 , 2, 3 or 4) and helix 5 can be optionally provided of length 2 or more bases (preferably 3 - 20 bases, i.e., m is from 1 - 20 or more).
  • Helix 2 and helix 5 may be covalently linked by one or more bases (i.e., r is > 1 base).
  • Helix 1 , 4 or 5 may also be extended by 2 or more base pairs (e.g., 4 - 20 base pairs) to stabilize the ribozyme structure, and preferably is a protein binding site.
  • each N and N' independently is any normal or modified base and each dash represents a potential base-pairing interaction.
  • These nucleotides may be modified at the sugar, base or phosphate. Complete base-pairing is not required in the helices, but is preferred.
  • Helix 1 and 4 can be of any size (i.e., o and p is each independently from 0 to any number, e.g., 20) as long as some base-pairing is maintained.
  • Essential bases are shown as specific bases in the structure, but those in the art will recognize that one or more may be modified chemically (abasic, base, sugar and/or phosphate modifications) or replaced with another base without significant effect.
  • Helix 4 can be formed from two separate molecules, i.e., without a connecting loop.
  • the connecting loop when present may be a ribonucleotide with or without modifications to its base, sugar or phosphate.
  • "q" is > 2 bases.
  • the connecting loop can also be replaced with a non-n
  • H refers to bases A, U, or C.
  • Y refers to pyrimidine bases.
  • " refers to a covalent bond.
  • Figure 4 is a representation of the general structure of the hepatitis delta virus ribozyme domain known in the art.
  • each N and N' independently is any normal or modified base and each dash represents a potential base-pairing interaction.
  • These nucleotides may be modified at the sugar, base or phosphate.
  • Figure 5 is a representation of the general structure of the self-cleaving VS RNA ribozyme domain.
  • Figure 6 is a diagrammatic representation of a scheme involved in the synthesis of 2, 2'-anhydro-1 ( ⁇ -D-arabinofuranosyl) uracil (2).
  • Figure 7 is a diagrammatic representation of a scheme involved in the synthesis of 2'-0-methyl uridine (3) by the method of this invention.
  • Figure 8 is a diagrammatic representation of a scheme involved in the synthesis of 2'-0-methyl cytidine (5) by the method of this invention.
  • Figure 9 is a diagrammatic representation of a scheme involved in the synthesis of 3'-0-methyl pyrimidine nucleosides.
  • Figure 10 is a diagrammatic representation of a scheme involved in the synthesis of 5'-0-methyl pyrimidine nucleosides.
  • Figure 11 shows NMR profile of 2'-0-methyl nucleosides.
  • A) 2'-0-methyl Uridine nucleoside.
  • B) 2'-0-methyl cytidine nucleoside.
  • Figure 12 is a diagrammatic representation of a scheme for the synthesis of 2'-0-methyl adenosine nucleoside.
  • Figure 13 is a diagrammatic representation of a scheme for the synthesis of 2'-0-methyl adenosine and guanosine nucleosides.
  • Figure 14 is a diagrammatic representation of a scheme for the synthesis of 2'-0-methyl guanosine nucleoside.
  • Figure 15 is a diagrammatic representation of a scheme for the synthesis of methoxy nucleosides via N1 -Benzyl guanosine route.
  • Figure 16 shows a strategy used in synthesizing a hammerhead ribozyme from two halves.
  • X and Y represent reactive moieties that can undergo a chemical reaction to form a covalent bond (represented by the solid curved line).
  • FIG 17 shows various non-limiting examples of reactive moieties that can be placed in the nascent loop region to form a covalent bond to provide a full-length ribozyme.
  • CH can be any linking chain as described above including groups such as methylenes, ether, ethylene glycol, thioethers, double bonds, aromatic groups and others; each n independently is an integer from 0 to 10 inclusive and may be the same or different; each R independently is a proton or an alkyl, alkenyl and other functional groups or conjugates such as peptides, steroids, hoemones, lipids, nucleic acid sequences and others that provides nuclease resistance, improved cell association, improved cellular uptake or interacellular localization.
  • Figure 18 shows non-limiting examples of covalent bonds that can be formed to provide the full length ribozyme.
  • the morpholino group arises from reductive reaction of a dialdehyde, which arises from oxidative cleavage of a ribose at the 3'-end of one half ribozyme with an amine at the 5'-end of the half ribozyme.
  • the amide bond is produced when an acid at the 3'-end of one half ribozyme is coupled to an amine at the 5'-end of the other half ribozyme.
  • Figure 19 shows non-limiting examples of three ribozymes that were synthesized from coupling reactions of two halves. All three were targeted to the 575 site of c-myb RNA.
  • Rz 1 was formed from the reaction of two thiols to provide the disulfide linked ribozyme.
  • Rz 2 and Rz 3 were formed using the morpholino reaction.
  • Rz 2 contains a five atom spacer linking the terminal amine to the 5'-end of the half ribozyme.
  • Rz 3 contains a six carbon spacer linking the terminal amine to the 5'-end of the half ribozyme.
  • Figure 20 shows comparative cleavage activity of half ribozymes, containing five and six base pair stem II regions, that are not covalently linked vs a full length ribozyme. Assays were carried out under ribozyme excess conditions.
  • Figure 21 shows comparative cleavage activity of half ribozymes, containing seven and eight base pair stem II regions, that are not covalently linked vs a full length ribozyme. Assays were carried out under ribozyme excess conditions.
  • Figure 22 shows comparative cleavage assay of Rz 1 , 2 and 3 (see Figure 19) formed from crosslinking reactions vs a full length ribozyme control. Assays were carried out under ribozyme excess conditions.
  • Figure 23 is a diagrammatic representation of c-myb site 575 hammerhead half-ribozymes and substrate RNA. The arrow indicates the site of cleavage.
  • Figure 24 A) shows the synthesis of acyclic 2', 3'-dialdehyde-5'-half riboyme (4) and 3'-phosphoryl-5'-half-ribozyme (5) from 3'-uridilyl-5'-half- ribozyme (1).
  • B) shows anion exchange HPLC analysis of reaction of 1 with
  • Figure 25 is a schematic representation of synthesis of morpholino-linked ribozymes.
  • Figure 26 shows an anion-exchange HPLC analysis of the reductive alkylation of compunds 2 and 4.
  • Figure 27 is a diagrammatic representation of a hammerhead ribozyme- substrate complex.
  • the ribozyme is targeted against site 575 within c-myb RNA.
  • Lowercase alphabets indicate 2'-0-methyl substitution; uppercase alphabets indicate ribonucleotides; Arrow incates the site of RNA cleavage; U4 and U7, represent modification with 2'-amino group; and Z, represent 5'- and 3'- caps which may be same or different.
  • Figure 28 A) is a general formula for 5'-end modifications.
  • B) a synthesis scheme for 5'-amino-5'-deoxy-2'-0- methyl uridine and guanosine phosphoramidites;
  • Figure 30 shows ribozyme-mediated inhibition of smooth muscle cell proliferation.
  • Inactive ribozyme (5 - amino Inactive RZ) with G5 to U and A14 to U substitution was synthesized and used as a negative control.
  • Figure 31 shows ribozyme-mediated inhibition of smooth muscle cell proliferation.
  • HH hammerhead
  • Figure 32 A) chemical structures of a few of the 3'-end modifications. B) diagrammatic representation of a few 3'-end mofication linkages.
  • Figure 33 is a synthesis scheme for phosphorodithioate linkages.
  • Figure 34 is a synthesis scheme for 3'-2'-inverted nucleoside or an abasic nucleoside linkages.
  • Compound 2 can be reacted with compound 3 to yield either a 3'-2'-inverted nucleotide linkage as shown in Figure 32B, infra, or a 3'-2'-inverted abasic ribose, deoxyribose or variations thereof (see Figure 32B).
  • Figure 35 is a synthesis scheme for carbocyclic nucleoside phosphoramidite.
  • Figure 36 is a synthesis scheme for alpha nucleoside phosphoramidite.
  • Figure 37 is a synthesis scheme for l-( ⁇ -D-erythrofuranosyl) nucleoside phosphoramidite.
  • Figure 38 is a synthesis scheme for inverted deoxyabasic 5'-0-succinate and ⁇ '-O-phosphoramidite.
  • Figure 39 is a graphical representation of RNA cleavage reaction catalyzed by hammerhead ribozymes containing either one or two 5'-terminal phosphorodithioate modifications.
  • Ribozyme .4654/1 5'-dithio represents a hammerhead ribozyme targeted to c-myb site 575 as shown in Figure 28, and were chemically modified such that the ribozyme consists of ribose residues at five positions; U4 position contains 2'-C-allyl modification, the remaining nucleotide positions contain 2'-0-methyl substitutions.
  • Ribozyme .4657/2 5'-dithio represents a hammerhead ribozyme targeted to c-myb site 575 as shown in Figure 28, and were chemically modified such that the ribozyme consists of ribose residues at five positions; U4 position contains 2'-C-allyl modification, the remaining nucleotide positions contain 2'-0-methyl substitutions.
  • the 5'-end of the ribozyme contains two phosphorodithioate modification and the 3' end of the ribozyme contains a 3'-3' linked inverted abasic deoxyribose (designated as 3'-iH).
  • 2 , 2'-anhydro- 1 ( ⁇ -D-arabinofuranosyl) uracil (2) can either be purchased from Sigma Chemicals or can be synthesized using the scheme described by Verheyden et al., 1971 (J. Org. Chem. 36, 250). Briefly, to an oven baked 1 L 3-neck round bottom flask equipped with mechanical stirrer, reflux condenser, and positive pressure of argon, 200g (0.819 mol) of uridine (1 ) was added. The reaction was carried out in the presence of diphenylcarbonate (191.2 g, 0.9 mol), and DMF (300 ml). The resulting light yellow suspension was heated to 90'C at which time sodium bicarbonate (2.0 g) was added.
  • reaction mixture was then heated to 110 " C for two hours during which time CO 2 evolved. Over this two hour period, the reaction mixture transformed from a slurry to a homogeneous solution and back to a slurry.
  • the reaction mixture was filtered and the filter bed washed with ethanol and cold methanol. The filter bed was then suspended in methanol (500 ml) and heated to reflux for three hours. After cooling to -10 * C, the reaction mixture was filtered. The filter bed was washed with cold methanol and dried to retrieve 2 as an off white solid (140g; 76%).
  • 2'-0-methyl nucleosides of the present invention can be readily converted into phosphoramidites using standard procedures and phosphoramidites can be readily incorporated into oligonucleotides, such as RNA, using standard procedures described in Sproat & Gait, 1984 in Oligonucleotide Synthesis: A Practical Approach, ed. Gait, M. J. (IRL, Oxford), pp 83-115; 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.
  • Applicant describes transglycosilation of suitably protected 2'-o-Me-pyrimidine ribonucleosides obtained through B(OMe)3 mediated opening of 2,2'-anhydronycleosides.
  • Transglycosylation reaction proceeds usually with high ⁇ -selectivity, if the carbohydrate donor contains a 2'-0-acyl group capable of stabilising the postulated C-1 carboxonium ion for exclusive ⁇ - attack by the incoming silylated base.
  • N 2 - isobutyryl intermediate 13 was isolated in 97% yield.
  • the structure of 13 was confirmed by NMR data and by deamination to N 2 -isobutyryl-2'-0- methylguanosine ⁇ - with NaN0 2 /CH 3 COOH followed by desilylation with TEA-3HF.
  • Applicant also observed that during deamination with NaNO 2 /CH 3 COOH, 3',5 * -0-cyclic silyl group opened, presumably at the 5'- position.
  • This intermediate was not isolated but desilylated directly with TEA»3HF. It is worth noting that N -isobutyryl group was completely stable during deamination.
  • the presence of hydrophobic silyl group in the intermediate allowed easy separation by extraction from excess of inorganic salts which made possible the subsequent desilylation without isolation.
  • metal acetylacetonates can direct methylation of ribonucleosides with trimethylsulfonium hydroxide, mostly at the 2' and 3' hydroxyl groups of Uridine, Cytidine and Adenosine (Yamauchi et al., J. Org Chem. 1980, 45, 3865-68).
  • Application of this procedure to the synthesis of Guanosine derivatives resulted in the isolation of 6 compounds with methylation in the base and the ribose moeties.
  • N 1 -methyl- guanosine was subjected to the same methylation conditions 1 ,2' and 1 ,3' di- N-O methyl guanosines were isolated in 82% yield.
  • Applicant investigated procedures for metal-directed methylation of N 1 - protected Guanosine with trimethylsulfonium hydroxide to optimize the ratio of 2' : 3' methylated products with subsequent separation and debloking to obtain 2'-0-Methyl guanosine.
  • N 1 in guanosine was achieved using N 1 benzylation with N,N-dimethylformamide dibenzyl acetal (Philips and Horwitz J.Org. Chem. 1975, 40, 1856). Applicant observed that complete cleavage of 2',3'- orthoamide required more drastic conditions than previously reported (2N NaOH vs MeOH/NH 3 ) ( Figure 15). The target compound was isolated in 80% yield after crystallization.
  • Applicant investigated 12 different acetylacetonates in the direct methylation of Adenosine (Table II). Whereas Fe and Cu acetylacetonates provided 1 :1 and 2:1 ration of 2' and 3' isomers as reported, Applicant discovered that Ag * and Sr 2+ allows equilibrium to shift towards 2'-isomer, providing 4:1 and 8:1 ratio. This allows the isolation of 2'-0-Me adenosine in 75-80% yield.
  • NMR spectra were recorded on a Varian Gemini 400 spectrometer operating at 400.075 MHz for proton and 161.947 MHz for phosphorus. Chemical shifts in ppm refer to TMS and H3PO4, respectively.
  • Analytical thin- layer chromatography (TLC) was performed with Whatman MK6F silica gel 60 A F25 4 plates and column chromatography using Merck 0.040-0.063 mm Silica gel 60.
  • reaction mixture was then heated to 75 * C for 16 hours while stirring under positive pressure argon. Upon cooling, an additional 1.03 ml (5.16 mmol) of TMStriflate was added, and the reaction heated to 75'C for an additional 20 hours. Once cool, the reaction mixture was diluted with two volumes of dichloromethane and washed with sat. NaHC0 3 . The organic layer was then dried over Na 2 S0 and evaporated in vacuo. Flash chromatography employing a gradient of 10 to 80% ethyl acetate/hexanes afforded (1 ) as a white foam; 0.403 g, 50% yield.
  • N 2 -isopropylphenoxyacetyl-2'-Q-methylguanosine (15): A solution of (12) (47.4 g, 88 mmol) in anhydrous pyridine (500 ml) was cooled to -10 * C in an ice/ethanol bath while stirring under argon. Isopropylphenoxyacetyl chloride (96.8 mmol, 20.6 ml) was added dropwise to the stirred -10'C solution over a period of 5 minutes. The reaction mixture was stirred at -10'C for 2 hours followed by 1 hour at rt then quenched with ethanol (20 ml).
  • the reaction mixture was diluted with one volume of n-butanol and evaporated in vacuo to 50% of the original volume.
  • Co-evaporation with n- butanol (3X) was followed by partitioning the crude syrup between ethyl acetate and sat. aqueous NaHC0 3 . After back extracting the aq. layer with ethyl acetate, the combined organics were evaporated to dryness in vacuo .
  • the crude residue was then dissolved in anhydrous dichloromethane (500 ml) and treated with a solution of TEA-3HF (278.4 mmol, 45.4 ml) and TEA (81.7 ml), in dichloromethane (200 ml).
  • Guanosine hydrate (50 grams, 177mmol) was coevaporated twice from dimethylformamide (2 x 250ml) and dissolved in dry dmf (400 mis). N,N- dimethylformamide dibenzyl acetal was added (240 grams, 230 ml, 885 mmol) and the solution was heated with stirring to 80 °C for 18 hrs. The excess acetal was removed by steam distillation on a rotary evaporator. The product was recovered without chromatography by washing with dichloromethane / hexanes (1 :1 v/v) to yield 84 g of the ortho-amide intermediate.
  • the o ortho- amide was cleaved by treatment with aqueous sodium hydroxide (2N, 133 ml) at room temperature for four hours. The product was recrystallized from boiling water to yield 54 g (145 mmol, 82%) of pure (16).
  • a 1 L pear shaped recovery flask with stir bar was charged with a mixture of 16 (50g, 134 mmol) , silver acetylacetonate (41 g 200mmol), TMSH (200 ml of 1 N solution in methanol) and dimethylformamide (400 ml).
  • the flask was heated to 70°C for two hours.
  • the solution was cooled to ambient temperature, neutralized to pH 7 with 1 M HCl, and dried to a solid tar.
  • the tar was dissolved in water (500ml) and filtered through a sintered glass funnel to remove silver salts.
  • the product was evaporated to dryness to remove water and residual solvents and 10 grams (26mmols) was redissolved in 50 ml of water prior to purification on a Waters Delta-Pak ODS 50mm x 300mm HPLC column.
  • the N1-Bz-2'-OMe guanosine isomer eluted first and was recovered using a rotary evaporator.
  • the product (7 g, 18mm, 70%) was identical to an authentic sample by HPLC, UV- , 1 H-NMR-spectroscopy.
  • TMSH Trimethylsulfonium Hydroxide
  • TMSI trimethyl sulfonium iodide
  • methanol and water 9:1 , v/v
  • the clear, colorless solution was allowed to cool to r.t.
  • a glass chromatography column (Ace #50 thread; 75mm x 300mm) containing Duolite 147 anion exchange resin (900 g) in the hydroxide form was previously packed and used for the conversion of TMSI to TMSH.
  • the solution was pumped over the column using a gear pump at 100 ml per minute.
  • the resin was washed with an additional 1 liter of 90% methanol and the total 3.5 liters was reduced in volume to 500 ml using a rotary evaporator with the bath set at 20 °C.
  • the solution was checked for the presence of iodide ion using acidified silver nitrate solution and found to be negative.
  • the solution was not characterized further and was stored in a teflon bottle with a gas vent at 5 °C.
  • a solution of adenosine (50 g, 187mmol) in dimethylformamide (400 ml) was prepared by heating to 50 °C with continuous mixing for 10 minutes in a 1 L pear shaped recovery flask containing a stir bar.
  • Silver acetylacetonate (58 g, 280 mmol) and TMSH (280 ml of a 1 M) solution was added and the mixture was stirred immediately.
  • the reaction mixture was heated to 75 °C with stirring for 45 minutes.
  • a sample of the mixture showed no starting adenosine and two spots of which the predominant one comigrates with an authentic sample of 2'-OMe adenosine.
  • Ribozymes were synthesized in two parts and tested without ligation for catalytic activity. Referring to Fig. 20, the cleavage activity of the half ribozymes containing between 5 and 8 base pairs stem Its at 40 nM under single turnover conditions was comparable to that of the full length oligomer as shown in Figs. 21 and 22. The same half ribozymes were synthesized with suitable modifications at the nascent stem II loop to allow for crosslinking. The halves were purified and chemically ligated, using a variety of crosslinking methods. The resulting full length ribozymes (see Fig. 19) exhibited similar cleavage activity as the linearly synthesized full length oligomer as shown in Fig. 22.
  • oligonucleotide synthesis reagents for the 394 Detritylation solution was 2% TCA in methylene chloride (ABI); capping was performed with 16% ⁇ /-Methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution was 16.9 mM 12, 49 mM pyridine, 9% water in THF (Millipore).
  • B & J Synthesis Grade acetonitrile was used directly from the reagent bottle.
  • S-Ethyl tetrazole solution (0.25 M in acetonitrile) was made up from the solid obtained from American International Chemical, Inc.
  • the polymer-bound oligoribonucleotide, trityl-off, was transferred from the synthesis column to a 4 mL glass screw top vial and suspended in a solution of methylamine (MA) at 65 °C for 10 min. After cooling to -20 °C, the supernatant was removed from the polymer support. The support was washed three times with 1.0 mL of EtOH:MeCN:H 2 0/3:1 :1 , vortexed and the supernatant was then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, were dried to a white powder.
  • MA methylamine
  • the base-deprotected oligoribonucleotide was resuspended in anhydrous TEA»HF/NMP solution (250 ⁇ L of a solution of 1.5 mL N- methylpyrrolidinone, 750 ⁇ L TEA and 1.0 mL TEA » 3HF to provide a 1.4 M HF concentration) and heated to 65 °C for 1.5 h.
  • the resulting, fully deprotected, oligomer was quenched with 50 mM TEAB (9 mL) prior to anion exchange desalting.
  • the TEAB solution was loaded onto a Qiagen 500® anion exchange cartridge (Qiagen Inc.) that was prewashed with 50 mM TEAB (10 mL). After washing the loaded cartridge with 50 mM TEAB (10 mL), the RNA was eluted with 2 M TEAB (10 mL) and dried down to a white powder (Scaringe et al., 1990 Nucleic Acids Res., 18, 5433).
  • the crude material was diluted to 5 mL with RNase free water.
  • the sample was injected onto either a Pharmacia Mono Q® 16/10 mm or Dionex NucleoPac® PA-100 22 x 250 mm column with 100% buffer A (10 mM NaCI0 4 ).
  • NucleoPac® anion-exchange column was used to elute the RNA. Fractions were analyzed by HPLC and those containing full length product -80% by peak area were pooled for desalting. The pooled fractions were applied to a SepPak cartridge (C- j ⁇ ) tnat was prewashed successively with CH 3 CN (10 mL), CH 3 CN/MeOH/H 2 0:1/1/1 (10 mL) and RNase free H 2 0 (20 mL). Following sample application, the cartridge was washed with RNase free H 2 0 (10 mL) to remove the salt. Product was then eluted from the column with CH 3 CN/MeOH/H 2 0:1/1/1 (10 mL) and dried.
  • Ribozymes and 5'- ⁇ 2 P-end-labeled substrate were heated separately in reaction buffer (50 mM Tris-CI, pH 7.5; 10 mM MgCI 2 ) to 95 °C for 2 min, quenched on ice, and equilibrated to 37 °C prior to starting the reactions. Reactions were carried out in enzyme excess, and were started by mixing -1 nM substrate and 40 nM ribozyme to a final volume of 50 ⁇ L. Aliquots of 5 ⁇ L were removed at 1 , 5, 15, 30, 60 and 120 min, quenched in formamide loading buffer, and loaded onto 15% polyacrylamide/8 M urea gels.
  • reaction buffer 50 mM Tris-CI, pH 7.5; 10 mM MgCI 2
  • the fraction of substrate and product present at each time point was determined by quantitation of scanned images from a Molecular Dynamics Phosphorlmager®. Ribozyme cleavage rates were calculated from plots of the fraction of substrate remaining vs time using a double exponential curve fit (Kaleidagraph, Synergy Software).
  • Example 10 Referring to Fig. 18 the 5" half of a hammerhead ribozyme was provided with a ribose group. This was oxidatively cleaved with Nal ⁇ 4 and reacted with the 3' half of the ribozyme having an amino group under reducing conditions. The resulting ribozyme consisted of the two half ribozyme linked by a morpholino group.
  • RPI3631 5" half hammerhead with a 3'OH
  • the limiting oligonucleotide was oxidized first with 3.6 equivalents of sodium periodate for sixty minutes on ice in DEPC water quenched with 7.2 equivalents of ethylene glycol for 30 minutes on ice and the 5 equivalents of the amino oligo added.
  • 50 equivalents of sodium cyanoborohydride was then added and the pH reduced to 6.5 with acetic acid and reaction left for 60 minutes on ice. The resulting full length ribozyme was then purified for further analysis.
  • a 5' half of ribozyme was provided with a carboxyl group at its 2' position and was coupled with an amine containing 3' half ribozyme.
  • the provision of a coupling reagent resulted in a full-length ribozyme having an amide bond.
  • RPI.2972 is a chemically stabilized ribozyme targeted against site 575 of c- myb mRNA that inhibits smooth muscle cell proliferation with an IC50 of approximately 75 nM (Stinchcomb et al., International PCT Publication No. WO 95/31541.
  • IC50 approximately 75 nM
  • the half-ribozymes, 1 and 2 used in this study contained a modified 5 base-paired stem II and the appropriate reactive groups at the termini.
  • Half-ribozymes 1 and 2 were synthesized and purified according standard methods.
  • the 3'-uridilyl-5'-half-ribozyme, 1 (150 ⁇ M) was dissolved in sodium N 2 -acetamido-2-imino-diacetate (ADA) buffer (100 mM, pH 6.0) and subjected to oxidative cleavage with 2 molar equivalents of a 100 mM aqueous solution of sodium periodate (Figure 24A). After 2 h, the acyclic 2',3'- dialdehyde derivative 4 was formed quantitatively, as confirmed by HPLC monitoring ( Figure 24B).
  • ES-MS analysis performed on purified 1 (calc.
  • Example 14 Synthesis of enzymatic nucleic acids containing 5'- and/or 3'-cap structures
  • the method of synthesis follows the procedure for normal RNA synthesis as described in Usman, N.; Ogilvie.K.K.; Jiang, M.-Y.; Cedergren.R.J. J. Am. Chem. Soc. 1987, 109, 7845-7854; Scaringe.S.A.; Franklyn.C; Usman, N. Nucleic Acids Res. 1990, 18, 5433-5441 ; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677 (all of these references are incorporated by reference herein in their entirety) and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end.
  • common nucleic acid protecting and coupling groups such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end.
  • Phosphoramidites of the 5'-cap and/or 3'-cap structures selected from those described and illustrated in Figures 28-29 and 32-38 may be incorporated not only into hammerhead ribozymes, but also into hairpin, hepatitis delta virus, VS RNA, RNase P ribozyme, Group I or Group II intron catalytic nucleic acids. They are, therefore, of general use in any enzymatic nucleic acid structure.
  • Example 15 Incorporation of 5'-Amino- and 5'-Mercapto-5'-Deoxy-2'-Q-Methyl Nucleosides Into Hammerhead Ribozymes
  • Non-chiral phosphoramidate and phosphorothioate linkages (Figure 29) for incorporation at the 5'-end of a hammerhead ribozyme are described infra. These linkages are electronically and sterically similar to their natural congener and introduction of a single 3'-0-P(0)(0-)-NH-5' or 3'-0-P(0)(O" ) -S- 5" link at the 5'-end of the ribozyme has little effect on its hybridization to a substrate and/or ribozyme cleavage activity. Letsinger and Mungall, J. Org. Chem.
  • RNA synthesis and deprotection have been described previously (Wincott et al., supra, incorporated by reference herein in its entirety) Syntheses were conducted on a 394 (ABI) synthesizer using a modified 2.5 ⁇ mol scale protocol with a 5 min coupling step for 2'-O-TB0MSi protected nucleotides and 2.5 min coupling step for 2'-0-methyl nucleotides.
  • a 6.5-fold excess of a 0.1 M solution phosphoramidite and a 24-fold excess of S- ethyl tetrazole relative to polymer-bound 5'-hydroxyl was used in each coupling cycle.
  • MALDI-TOF mass spectra were determined on a PerSeptive Biosystems Voyager spectrometer.
  • the 3',5'-Di-0-p-toluenesulfonyl derivative was also isolated (0.45 g, 15%) from the reaction mixture along with 20% of the unreacted starting material.
  • the mixture was then replaced into the column.
  • the liquid was removed and the support was rinsed with 20 mL of 1 :1 CH 3 CN:H2 ⁇ .
  • the support was then treated with 10 mL 50 mM DTT for 10 min at rt.
  • the support is then washed with 20 mL H 2 0, then 20 mL CH 3 CN.
  • the column was placed on the synthesizer, washed with CH 3 CN for 30 s then reverse flushed for 15 s, this procedure was repeated 4 times.
  • the synthesis was then resumed, with the next phosphoramidite coupling for 400 s and the remaining phosphoramidites coupling for the standard times.
  • the ribozymes were deprotected with 40% aqueous methylamine for 10 min at 65 °C.
  • the silyl groups were removed with TEA/HF solution in 30 min at 65 °C and the oligonucleotides were precipitated from the solution.
  • RPI.4705.5905 yielded 101.5 AU of crude material (half was lost during detritylation of 5'-STr) with 16.5% full length product.
  • Uridine derivative 5 was synthesized in a way similar to that reported by Mag and Engels, supra, for the synthesis of a thymidine analog.
  • 5'-Azido derivative 2 ( Figure 29 B) was synthesized in one step from 2'-0-methyluridine (1) using the procedure of Yamamoto et al., supra. Ammonium hydroxide had to be used instead of water for the hydrolysis of intermediate 5'-phosphinimide during the conversion of 2 to 3 (( Figure 29 B)). It is well documented (Mungall et al., J. Org. Chem. 1975, 40, 1659-1662) that nucleoside phosphinimines are relatively stable in water compared to simple alkyl azides. Protection of the 5'-NH2 group of 3 with 4-methoxytrityl group, followed by standard phosphitylation afforded 3'-0-phosphoramidite 5 in good yield.
  • the oligomer was desilylated with TBAF rather then HF/TEA solution as more full length polymer was produced with the former reagent.
  • a single bridging 5'-phosphorothioate linkage was incorporated into the 5'-end of two ribozymes.
  • the 5'-thiol phosphoramidite 23 was coupled for 300 s and the following phosphoramidite coupled for 400 s.
  • the ribozymes were base deprotected as usual and then treated with TEA/HF at 65 °C for 0.5 h rather than 1.5 h. Using the latter reagent we have not observed substantial cleavage of the P-S bond as observed when TBAF was used (Sund et al., supra).
  • Example 16 Nuclease stability, in vitro activity and cell culture efficacy of 5'- amino-modified ribozymes
  • Ribozymes and substrates were 5'-end-labeled using T4 Polynucleotide Kinase and ⁇ -32p-ATP.
  • ribozymes were synthesized in two halves with the junction 5' to the GAAA sequence in Loop II ( Figure 27). The 3'-half-ribozyme portion was 5'-end-labeled using T4 Polynucleotide Kinase and ⁇ -32p-ATP, and was then ligated to the 5'-half-ribozyme portion using T4 RNA ligase. Labeled ribozymes were isolated from half-ribozymes and unincorporated label by gel electrophoresis.
  • Ribozyme Activity Assay Ribozymes and 5'- 32 P-end-labeled substrate were heated separately in reaction buffer (50 mM Tris-HCI, pH 7.5; 10 mM MgCl2) to 95 °C for 2 min, quenched on ice, and equilibrated to the final reaction temperature (37 °C) prior to starting the reactions. Reactions were carried out in enzyme excess, and were started by mixing -1 nM substrate with the indicated amounts of ribozyme (50 nM-1 - ⁇ M) to a final volume of 50 ⁇ L.
  • reaction buffer 50 mM Tris-HCI, pH 7.5; 10 mM MgCl2
  • Calf Spleen 5'-exonuclease was purchased from Boehringer Mannheim.
  • T4 polynucleotide kinase and Lambda 5'-exonuclease were purchased from GIBCO/BRL. Enzyme reactions were performed according to the manufacturers' suggestions.
  • Rat aortic smooth muscle cells were isolated from aortic tissue explants from 69-84 day-old female Sprague-Dawley rats (Harlan Sprague Dawley, Inc.) and assayed through passage six. SMC were grown in Dulbecco's modified Eagle's Medium (DMEM) supplemented with nonessential amino acids (0.1 mM of each amino acid), 0.1 mM sodium pyruvate, 100 U/mL penicillin, 100 ⁇ g/mL streptomycin, 2 mM L-glutamine, 20 mM HEPES (all from BioWhittaker) and 10% fetal bovine serum (FBS; Hyclone Laboratories, Inc.).
  • DMEM Dulbecco's modified Eagle's Medium
  • nonessential amino acids 0.1 mM of each amino acid
  • 0.1 mM sodium pyruvate 100 U/mL penicillin, 100 ⁇ g/mL streptomycin, 2 mM L-
  • Rat smooth muscle cell nuclear or total cell extracts were prepared by harvesting SMC from 3 confluent T150 flasks. For nuclear lysates, SMC were trypsinized from the flasks, washed twice with PBS, and resuspended in 500 ⁇ L of hypotonic buffer. After 40 strokes with a Dounce B homogenizer, 300 ⁇ L of 34% sucrose was added and nuclei were pelleted by centrifugation at 4 'C and 500 x g for 10 min. The nuclei were washed with a solution containing 500 ⁇ L of hypotonic buffer and 300 ⁇ L of 34% sucrose, then repelleted.
  • the pellet was resuspended in buffer A (10 mM Tris-HCI, pH 7.5; 400 mM NaCI; 1.5 mM MgCI 2 , 0.1 mM EGTA, 5% glycerol, 0.5 mM DTT, and 0.5 mM PMSF) and given 20 strokes in the Dounce B homogenizer.
  • the resultant suspension was gently shaken for 30 min at 4 " C and then dialyzed at 4 * C for 4 h against 100 mL of dialysis buffer (20 mM Tris-HCI, pH 7.5; 0.1 mM EDTA, 75 mM NaCI, 20% glycerol, 0.5 mM DTT and 0.5 mM PMSF).
  • Total cell lysates were prepared by rinsing trypsinized cell preparations 3 x in PBS and pelleting by centrifugation. The pellets were resuspended in 1 mL of DMEM, 0.5 mM PMSF. PMSF was added as a precaution to minimize proteolytic activity during isolation. Cells were freeze-thawed 3 times and disrupted by 40 strokes in a Dounce B homogenizer. Aliquots of whole cell lysates were aliquoted and frozen at -70'C. Separate aliquots were used for each assay.
  • Ribozyme Stability Assay One half pmol of gel-purified, internally labeled ribozyme was added to 20 ⁇ L of reaction buffer (67 mM glycine-KOH [pH 9.4], 2.5 mM MgCI 2 , and 50 ⁇ g/mL BSA; containing either 1 ⁇ L of calf spleen 5'-exonuclease [2U/2 mg/mL] or 10 ⁇ L of smooth muscle cell lysate). Samples were placed at 37 °C and 3 ⁇ L aliquots were withdrawn at 0, 30, 60, 120 and 240 min, and 24 h..
  • Lipid/ribozyme mixtures were vortexed, incubated for 15 minutes, and then added to cells which had been washed twice with PBS containing Ca 2+ /Mg 2+ .
  • Cells were incubated with the ribozyme/lipid complexes at 37 * C for 4 hours before the mixture was aspirated away.
  • Cells were stimulated by the addition of growth medium.
  • Control cells were treated with lipid only and stimulated with growth medium containing either 10% or 0% FBS. All conditions were run in triplicate. At the time of stimulation, 5'-bromo-2'-deoxyuridine (BrdU, Sigma) was added at a final concentration of 10 ⁇ M.
  • ribozymes Internally-labeled ribozymes were prepared by the separate synthesis of 5'-and 3'-half ribozymes, 32p end-labelling of the 3'-half ribozyme at the 5'- terminus and subsequent ligation of appropriate 5'- and 3'-half ribozymes to produce a full-length ribozyme with an internal 32 P label.
  • the 3'-ends of all ribozymes were capped with a 3'-3' linked abasic residue ( Figure 32B; Beigelman et al., 1995 supra).
  • nonessential residues contained 2'-0-Me modifications, while essential residues contained 2'-ribose moieties as illustrated in Figure 27.
  • Modifications to ribozymes at positions 2.1-2.7 and substitutions at positions U4 and U7 are summarized in Table III. While ribozymes containing either ribose (Rz 1 ) or deoxyribose (Rz 2) moieties at positions 2.1 -2.7 were rapidly digested by calf spleen 5'-exonuclease, ribose containing ribozymes appeared to be more resistant to digestion.
  • Ribozymes containing partial P S backbone (positions 2.1-2.7, Rz 4) or
  • ribozymes Internally-labeled ribozymes were prepared for lysate stability assays as described in the previous section and in Materials and Methods. The 3'-ends of all ribozymes contained a 3'-3' linked abasic residue. Ribose and 2'-0-Me substitutions into the ribozyme used standard patterns which were discussed above. Modifications to positions 2.1-2.7 and 5'-end substitution for the ribozymes are summarized in Table III.
  • Catalytic activity of 5'-amino modified ribozymes The relative effect of 5'-amino substitution on ribozyme catalytic activity was investigated under standard assay conditions as described, supra, in Materials and Methods. The catalytic activity of each ribozyme was assayed at two concentrations and the results were plotted to determine the region of the reaction which gave exponential rates at each concentration. Cleavage rates (k ⁇ g values) were calculated from fits of the first exponential. Table IV shows an activity comparison for the five U4/U7-amino containing ribozymes at concentrations of 40 and 500 nM (roughly 4 and 50 fold above K M ). Activity is presented both as the cleavage rate (min '1 ) and as a percentage of the rate for the control, Rz 3.
  • the deoxyribose-substituted Rz 2 is peculiar in that it showed a 6-10 fold reduction in activity when compared with the other 2.1-2.7 position ( Figure 27) substitutions (Rzs 1, 3, 4, and 6).
  • Figure 27 substitutions
  • the similarity in cleavage rates at 40 and 500 nM for this ribozyme suggest that the reduced k obs for Rz 2 was not a result of reduced binding affinity but more likely reflects a 6-10 fold decrease in kc at .
  • Ribozymes After the application of ribozymes, cells were metabolically labeled with BrdU for 24 h and the number of proliferating SMC nuclei were determined by differential staining using an anti-BrdU antibody detection system and hematoxylin. Ribozymes containing ribose (Rz 1 ), deoxyribose (Rz 2) or 2'-0-Me modified (Rz 3) nucleosides at positions 2.1 -2.7 as well as catalytically inactive (Rzs 5, 7, 9, and 1 1 ) were included as controls for non-specific ribozyme inhibition.
  • Rz 1 ribose
  • Rz 2 deoxyribose
  • Rz 3 2'-0-Me modified
  • the relative abilities of each ribozyme to inhibit SMC proliferation are summarized in Table VII and shown graphically in Figures 30 and 31.
  • ribozymes with ribose (Rz 1), deoxyribose (Rz 2) or 2'-0 -Me (Rz 3) moieties at positions 2.1-2.7 exhibited similarly low levels of inhibitory activity in the SMC proliferation assay.
  • the deficiency of inhibitory action by either Rz 1 or Rz 2 reflected the inherent nuclease susceptibility of these molecules in SMC lysates and suggested that even the low levels of nuclease activity which we observed in the lysates may be enough to digest unstablized ribozymes quickly within the cellular enivironment.
  • Rzs 1 and 2 may be showing lower efficiency of inhibition of cellular proliferation because they are not localized near target molecules.
  • Rz 3 The lower efficacy with Rz 3 is consistent with this latter hypothesis. Based upon our data showing the resistance of Rz 3 to digestion using purified preparations of calf spleen 5'-exonuclease, these molecules are expected to be relatively stable within the cells, yet they don't decrease cellular proliferative rates any better than Rzs 1 or 2. We feel that Rz 3 preparations are stable within cells and the decreased inhibitory activity may be because of issues unrelated to their nuclease susceptibility.
  • nuclease-stable, Rz 5 exhibited better inhibitory activity than nuclease- sensitive, catalytically active Rzs 1 and 2 shows that nuclease stabilization is important for efficient ribozyme efficacy in cells when the ribozymes are delivered exogenously.
  • Relative smooth muscle cell proliferation is calculated as follows: (%proliferation with ribozyme - %basal proliferation) + (%proliferation with serum - %basal proliferation) x 100.
  • a ribozyme with scrambled sequence binding arms exhibited an equivalent degree of inhibition to an inactive ribozyme, indicating that this effect was not mediated by ribozyme binding, but was truly a "non-specific" effect on proliferation.
  • ribozymes with varying numbers of phosphorothioates at the 5'-end The degree of efficacy gradually decreased as the number of phosphorothioate linkages was reduced. From these experiments we concluded that a minimum of four to five phosphorothioate linkages at the 5'-end is sufficient to maintain optimal efficacy.
  • the ribozymes used in this study contained either 3'-phosphorothioate linkages, or a 3'-3' "inverted thymidine" modification to protect against 3'- exonuclease activity.
  • C-myb ribozymes containing various protecting groups including a 3'-3' inverted thymidine, a 3'-3' inverted abasic residue, a 3'- butanediol showed equivalent efficacy in inhibiting smooth muscle cell proliferation .
  • 2'-0-TBDMS-5'-0-DMT-N-protected ribonucleosides, 5'-0-DMT-N-protected deoxy- and 2'-0-Me ribonucleosides were from Chem Genes Corporation, Waltham, MA. Commercially available anhydrous solvents were employed without purification. Concentrations of solutions were carried out in vacuo at 40 'C or lower using an aspirator or an oil vacuum pump. Solids were dried at room temperature in a desiccator over phosphorus pentoxide and potassium hydroxide. 31 P NMR spectra were recorded on a Varian Gemini 400 spectrometer operating at 161.947 MHz with 85% phosphoric acid as external standard. Oligonucleotides were synthesized on an Applied Biosystems 381 A synthesizer using Applied Biosystems columns.
  • Ribonucleoside 3'-S-(2-cyanoethyl)N,N-dimethylthiophosphoramidite synthesis Suitably protected 2'-f-butyldimethylsilyl-5-0'-dimethoxytrityl nucleoside (2.0 mmol) ( Figure 33) was dried and was dissolved in dry dichloromethane (CH2CI2) (20 ml) under argon and the solution was cooled to 0 'C (ice-bath).
  • CH2CI2 dry dichloromethane
  • Model syntheses of ribo and 2'-0-methyl dithioate oligonucleotide sequences was performed on an ABI model 394 synthesizer using a modified synthesis cycle for thiolation.
  • a 10 ⁇ mol cycle was created to accomodate manual sulfurization off of the instrument. This was accomplished by placing an interrupt step immediately after the phosphoramidite coupling step following the final acetonitrile wash and argon flush.
  • the synthesizer column containing the oligo bound solid support was subsequently removed from the instrument. One frit was then removed from the end of the column and a 20 ml syringe attached to that end.
  • Tetrazole was used in place of S-ethyl tetrazole to minimize side reactions.
  • the following bottle positions on the ABI 394 synthesizer were assigned to the following solutions:
  • the synthesis cycle was designed to deliver 12 equivalents or less of phosphoramidite with 600 second coupling times for ribo residues and 300 second coupling times for 2'-0-methyl residues.
  • thiolation solution (bottle #10) is delivered in two pulses.
  • the thiolation time was varied between 1 and 60 minutes, with an optimum time of 6 minutes. Care must be taken to avoid precipitation of sulfur in the synthesizer lines; as such, carbon disulfide (bottle #15) washes precede and follow delivery of the thiolation solution.
  • Dichloromethane washes (bottle #19) are used to remove excess carbon disulfide from the column.
  • carbocyclic nucleosides (1 ) are synthesized essentially as described by Agrofoglio et al., 1994, Tetrahedron 50, 10611. Carbocyclic nucleosides (1 ) were 5'-protected for example by 5'-0- dimethoxytritylating 1 according to the standard procedure (see Oligonucleotide Synthesis: A Practical Approach, M.J. Gait Ed.; IRL Press, Oxford, 1984, p 27, and is incorporated by reference herin in its entirety) to yield 2 in high yield in the form of yellowish foams after silica gel column chromatography.
  • Carbocyclic nucleoside phosphoramidites are incorporated into ribozymes using solid phase synthesis as described by Wincott ef al., 1995 supra, incorporated by reference herein in its entirety.
  • the ribozymes are deprotected using the standard protocol described above.
  • alpha nucleosides (1) are synthesized essentially as described by Debart et al., 1992, Nucleic Acid Res. 20, 1193; and Debart et al. 1995, Tetrahedron Lett. 31 , 3537.
  • Alpha nucleosides (1 ) were 5'-protected for example by 5'-0-dimethoxytritylating 1 according to the standard procedure (see Oligonucleotide Synthesis: A Practical Approach, M.J. Gait Ed.; IRL Press, Oxford, 1984, p 27, and is incorporated by reference herin in its entirety) to yield 2 in high yield in the form of yellowish foams after silica gel column chromatography.
  • Alpha nucleoside phosphoramidites are incorporated into ribozymes using solid phase synthesis as described by Wincott et al., 1995 supra, and is incorporated by reference herin in its entirety.
  • the ribozymes are deprotected using the standard protocol described above.
  • Example 21 General procedure for the synthesis of 1 -( ⁇ -D-erythrofuranosyl) nucleoside Phosphoramidites
  • 1 -( ⁇ -D-erythrofuranosyl) nucleosides (1 ) are synthesized essentially as described by Szekeres et al., 1977, J. Carbohydr. Nucleosides Nucleotides. 4, 147. 1 -( ⁇ -D-erythrofuranosyl) nucleosides (1) were treated with AgN03 (2.4 eq). After 10 minutes tert-butyldimethylsilyl chloride (1.5 eq) was added and the reaction mixture was stirred at room temperature for 12 hours. The resulted suspension was filtered into 100 mL of 5% aq NaHC03. The solution was extracted with dichloromethane (2x100 mL).
  • Example 22 General procedure for the synthesis of Inverted deoxyabasic 5'- O-Succinate and 5'-Q-Phosphoramidite
  • 2- deoxyribose is converted to compound 1 in a two step process.
  • 2- deoxyribose is treated with a mixture of acetyl chloride and methanol.
  • the reaction mixture is treated with p-toluoyl chloride/pyridine mixture to yield 1.
  • Compund 1 is incubated with a mixture of triethyl silane and boron trifluoride in ethanol to yield compound 2.
  • Treatment of 4 with sodium methylate in methanol yield compound 3.
  • Reacting 3 with t-butyl-diphenyl- silyl chloride in pyridine yields compound 4.
  • the 3'-end of 4 is tritylated using 4,4'-dimethoxytrityl chloride in pyridine to yield compound 5.
  • the 5'-protecting group in 5 can be removed using a mixture of triethylamine/hydrogen fluoride/DCM to yield 6.
  • a succinate group can be attached to the 5'-end of compound 6 by reacting the compound with a mixture of succinic anhydride and 4- dimethylaminopyridine to yield compound 7.
  • Compound 6 can be converted into a phosphoramidite by standard phosphitylation reaction described supra to yield compound 8. Reaction of 8 with a standard phosphoramidite will yield a 5'-5'-inverted abasic deoxyribose linkage as shown in Figures 28C.
  • Example 23 General procedure for the synthesis of 3'-2'-inverted nucleotide or 3'-2'-inverted abasic linkage
  • a commercially available 5'-dimethoxytrityl-3'-silyl- containing nucleoside (1) is treated with a standard phosphitylation reagent such as 2-cyanoethyl N',N- dnsopropylchlorophosphoramidite to yield compound 2.
  • compound 7 can be reacted with compound 2 in
  • Radio-labeling of Ribozymes and Substrates were 5'-end- labeled using T4 Polynucleotide Kinase and ⁇ - 32 P-ATP.
  • Ribozyme Activity Assay Ribozymes and 5'- 32 P-end-labeled substrate were heated separately in reaction buffer (50 mM Tris-HCI, pH 7.5; 10 mM MgCl2) to 95 °C for 2 m , quenched on ice, and equilibrated to the final reaction temperature (37 °C) prior to starting the reactions.
  • reaction buffer 50 mM Tris-HCI, pH 7.5; 10 mM MgCl2
  • Reactions were carried out in enzyme excess, and were started by mixing -1 nM substrate with the indicated amounts of ribozyme (50 nM-1 ⁇ M) to a final volume of 50 ⁇ L Aliquots of 5 ⁇ L were removed at 1 , 5, 15, 30, 60 and 120 m , quenched in formamide loading buffer, and loaded onto 15% polyacrylam ⁇ de/8 M Urea gels.
  • the fraction of substrate and product present at each time point was determined by quantitation of scanned images from a Molecular Dynamics Phosphorlmager Ribozyme cleavage rates were calculated from plots of the fraction of substrate remaining vs time using a double exponential curve fit (Kaleidagraph, Synergy Software). The fast portion of the curve was generally 60-90% of the total reaction, so that observed cleavage rates (k 0 bs) were taken from fits of the first exponential.
  • ribozymes with either one or two phosphorodithioate substitutions were capable of catalyzing efficient RNA clevage reactions.
  • the results show that modification of ribozymes at the 5'- end do not significantly effect the activity of ribozymes.
  • the 5'- and/or 3'-substituted enzymatic nucleic acids of this invention can be used to form stable molecules with enhanced activity as discussed above for use in enzymatic cleavage of target RNA.
  • Such nucleic acids can be formed enzymatically using triphosphate forms by standard procedure. Administration of such nucleic acids into cells is by standard methods. Their in vitro utility is as known in the art. See Sullivan et al., PCT WO 94/ 02595.
  • Enzymatic nucleic acids of this invention may 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 ribozyme 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 ribozymes described in this invention one may 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 ribozymes may 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 may be defined as important mediators of the disease.
  • ribozymes of this invention 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 ribozyme using standard methodology.
  • ribozymes which can cleave only wild-type or mutant forms of the target RNA are used for the assay.
  • the first ribozyme is used to identify wild-type RNA present in the sample and the second ribozyme will be used to identify mutant RNA in the sample.
  • synthetic substrates of both wild-type and mutant RNA will be cleaved by both ribozymes to demonstrate the relative ribozyme 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.
  • each analysis will require two ribozymes, two substrates and one unknown sample which will be combined into six reactions.
  • the presence of cleavage products will 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.
  • RNA portion of a ⁇ bonucleoprotein enzyme Cleaves tRNA precursors to form mature tRNA.
  • P refers the target sequence GUC immediately 3' of the cleavage site
  • RNAs of the tobacco ⁇ ngspot virus, arabis mosaic virus and chicory yellow mottle virus which uses RNA as the infectious agent ( Figure 3)
  • HDV Hepatitis Delta Virus
  • a [Rz] 500 nM, [3] - 1 nM, 50 nM tris.HCl pH 8.0, 25°C, 40 nM Mg gsusususuc ccU Gau Gag gcc gaa agg ccG aaA uuc ucc iB
  • k o s is derived from two independent assays and is expressed as average ⁇ range. Values in parentheses express the cleavage rate as a percentage of the control cleavage rate using Rz 3 at equivalent concentrations.
  • Values given represent the percentage of proliferating cell nuclei relative to stimulated lipid-treated cell controls. Mean values of at least 9 experimental points were used to obtain the relative proliferative index for each treatment protocol. Numbers in parentheses represent the standard deviation of the mean values. Unstimulated control values were 5 ( ⁇ 2)%. The percentage of proliferating nuclei in the serum stimulated control wells was 72 ( ⁇ 6)%.

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WO1997026270A2 (fr) 1997-07-24
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ATE373672T1 (de) 2007-10-15
EP1108724A3 (fr) 2003-01-08
AU1430097A (en) 1997-08-11
CA2253382A1 (fr) 1997-07-24
EP1108724A2 (fr) 2001-06-20
DE69637256T2 (de) 2008-06-19

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