Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Patent
1992-11-25
1997-07-08
Jones, W. Gary
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
536 243, 536 2431, 536 2432, 536 245, 536 268, C07H 2100, C07H 2102, C07H 2104, C12Q 168
Patent
active
056459858
ABSTRACT:
Novel oligomers are disclosed which have enhanced ability with respect to forming duplexes or triplexes compared with oligomers containing only conventional bases. The oligomers contain the bases 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine or related analogs. The oligomers of the invention are capable of (i) forming triplexes with various target sequences such as virus or oncogene sequences by coupling into the major groove of a target DNA duplex at physiological pH or (ii) forming duplexes by binding to single-stranded DNA or to RNA encoded by target genes. The oligomers of the invention can be constructed to have any desired sequence, provided the sequence normally includes one or more bases that is replaced with the analogs of the invention. Compositions of the invention can be used used for diagnostic purposes in order to detect viruses or disease conditions.
REFERENCES:
patent: 4415732 (1983-11-01), Caruthers et al.
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4725677 (1988-02-01), Koster et al.
patent: 4904582 (1990-02-01), Tullis
patent: 4959463 (1990-09-01), Froehler et al.
patent: 5264423 (1993-11-01), Cohen et al.
patent: 5484908 (1996-01-01), Froehler et al.
Uhlmann et al., "Antisense olignucleotides: a new therapeutic principle" Chem. Reviews (1990) 90(4):543-584.
van der Krol et al., "Modulation of eukaryotic gene expression by complementary RNA or DNAS sequences" Bioechniques (1988) 6(10):958-976.
Maher, III, et al., "Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation" Science (1989) 245:725-730.
Moser et al., "Sequence-specific cleavage of double helix DNA by triple helix formation" Science (1987) 238:645-650.
Beal et al., "Second structural motif for recognition of DNA by oligonucleotide-directed triple helix formation" Science (1990) 251:1360-1363.
Cooney et al., "Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro" Science (1988) 241:456-459.
Griffin et al., "Recognition of thymine-adenine base pairs by guanine in a pyrimidine triple helix motif" Science (1989) 245:967-971.
Lee et al., "Poly(pyrimidine)-poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH" Nucleic Acids Res. (1984) 12;6603-6614.
Krawczyk et al., "Oligonucleotide-mediated triple helix formation using an N.sup.3 -pronated deoxycytidine analog exhibiting pH-independent binding within the physiological range" Proc. Natl. Acad. Sci. USA (1992) 89:3761-3764.
Ono et al, "Triplex formation of an oligonucleotide containing 2'-O-methlpseudoisocytidine with a DNA duplex at neutral pH" J. Org. Chem. (1992) 57:3225-3230.
Froehler et al., "Triple-helix formation formation by oligonucleotides containing the carbocyclic analogs of thymidine and 5-methyl-2'-deoxycytidine" J. Amer. Chem. Soc. (1992) 114:8820-8822.
U.S. Application Serial No. 07/864,873 (filed Apr. 6, 1992).
Vlassov et al., "Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating olignnucleotide derivatives" Nucleic Acids Res. (1986) 14(10):4065-4076.
Knorre et al., "Reactive olignucleotide derivatives and sequence-specific modification of nucleic acids" Biochemie (1985) 67:785-789.
Iverson et al., "Nonenzymatic sequence-specific cleavage of single-stranded DNA to nucleotide resolution. DNA metyl thioether probes" J. Am. Chem. Soc. (1987) 109:1241-1243.
Meyer et al., "Efficient, specific crosslinking and cleavage of DNA by stable, synthetic complementary olignuleotides" J. Am. Chem. Soc. (1989) 111:8517-8519.
Lee et al., "Interaction of psorlen-derivatized oligodeoxyribonucleoside methylphosphonates with single stranded DNA"Biochemistry (1988) 27:3197-3203.
Horne et al., "Recognition of mixed-sequence duplex DNA by alternate-strand triple helix formation" J. Am. Chem. Soc. (1990) 112:2435-2437.
Webb et al., "Sequence-specific cross-linking of deoxyoligonucleotides via hybridization-triggered alkylation" J. Am. Chem. Soc. (1986) 108:2764-2765.
Webb et al., "Hybridization triggered cross-linking of deoxyligonucleotides" Nucleic Acids Res. (1986) 14:7661-7674.
Matteucci et al., "Synthesis and crosslinking of a deoxyolignucleotide containing N.sup.6, N.sup.6 -ethanodeoxyadenosine" Tetrahedron Letters (1987) 28(22):2469-2472.
Shaw et al., "Specific, high-efficiency, triple-helix-mediated cross-linking to duplex DNA" J. Amer. Chem. Soc. (1991) 113:7765-7766.
Praseuth et al., "Sequence-specific binding and photocrosslinking of .alpha. and .beta. olignucleotides to the major groove of DNA via triple-helix formation" Proc. Natl. Acad Sci. (USA) (1988) 86:1349-1353.
Vlassov et al., "Modified oligodeoxyribunleotides" Gene (1988) pp. 313-322.
Fedorova et al., "Complementary addressed modification of double-stranded DNA within a ternary complex" FEBS (1988) 228(2):273-276.
Capobionco et al., "One pot solution sythesis of cyclic oligodeoxyribnucleotides" Nucleic Acids Res. (1990) 18(9):2661-2669.
van de Sande et al., "Parallel stranded DNA" Science (1988) 241:551-557.
Froehler et al., "Triple-helix formation and cooperative binding by oligonucleotides with a 3'-3' internucleotide junction" Biochemistry (1992) 31:1603-1609.
Young et al., "Triple helix formation inhibits transcription elongation in vitro" Proc. Natl. Acad. Sci. USA (1991) 88:10023-10026.
Rahim et al., "5-alkynyl pyrimidine nucleosides as potent selective inhibitors of varicella-zoster virus" Antiviral Chem. & Chemother. (1992) 3(5):293-297.
DeClercq et al., "Nucleic acid related compounds. 40. Synthesis and biological activiteis of 5-Alkynyluracil nucleotides" J. Med. Chem. (1983) 26:661-666.
Goodchild et al., "Structural reguirements of olefinic 5-substituted deoxyuridines for antiherpes activities" J. Med. Chem. (1983) 26:1252-1257.
Froehler et al., "Oligodeoxynucleotides containing C-5 propyne analogs of 2'-deoxyurdine and 2'-deoxycytidine" Tetrahedron Letters (1992) 33(37):5307-5310.
Valko et al., "Correlation of nucleotide incorporation rate and HPLC retention parameters of substituted nucleosides" J. Liquid Chromatog. (1989) 12(11):2103-2116.
Valko et al., "Application of chromatographic retention data in an investigation of a quantitative structure-nucleotide incorporation rate relationship" J. Chromatog. (1990) 506:35-44.
Augustyns et al., "Incorporation of hexose nucleoside analogues into oligonucleotides: synthesis, base-pairing properties and enzymatic stability" Nucl. Acids Res. (1992) 20(18):4711-4716.
Chiang et al., "Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanism" J. Biol. Chem. (1991) 266(27):18162-18171.
Clivio et al., "Sythesis of dinucleotide phosphates containing sulfur substituted nucleobases: 4-thiouracil, 4-thiothymine and 6-mercaptopurine" Tetrahedron Letters (1992) 33(1):69-72.
Connolly et al., "Synthesis and properties of oligonucleotides containing 4-thiothymidine, 5-methyl-2-pyrimidinone-1-.beta.-D(2'-deoxyriboside) and 2-thiothymidine" Nucl. Acids Res. (1989) 17(13):4957-4974.
Egholm et al., "Peptide nucleic acids (PNA): oligonucleotide analogues with an achiral peptide backbone" J. Amer. Chem. Soc. (1992) 114:1895-1897.
Otvos et al., "Substrate specificty of DNA polymerases. I. Enzyme-catalyzed incorporation of 5-(1-alkenyl)-2'-deoxyuridines into DNA" Nucl. Acids Res. (1987) pp. 1763-1777.
Povsic et al., "Triple helix formation by oligonucloetides on DNA extended to the physiological pH range" J. Am. Chem. Soc. (1989) 111:3059-3061.
Reynolds et al., "Synthesis of thymidine dimers containing internucleoside sulfonate and sulfonamide linkages" J. Org. Chem. (1992) 57:2983-2985.
Robins et al., "Nucleic acid related compounds. 38. Smooth and high-yield iodination and chlorination at C-5 of uracil bases and p-toluly-protected nucleosides" Can J. Chem. (1982) 60:554-557.
Vasseur et al., "Olignucleosides: synthesis of a novel methylhydroxylamine-linked nucleoside dimer and its incorporation into antisense sequences" J. Amer. Chem. Soc. (1992) 114:4006-4007.
Wigernick et al., "5-(5-Bromothein-2-yl)-2'-deoxyuridine and 5-(5-chlorothein-2-yl)-2'-d
Froehler Brian
Gutierrez Arnold J.
Jones Robert J.
Matteucci Mark
Pudlo Jeff
Gilead Sciences, Inc.
Jones W. Gary
Muenchau Daryl D.
Tran Paul B.
LandOfFree
Enhanced triple-helix and double-helix formation with oligomers does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Enhanced triple-helix and double-helix formation with oligomers , we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Enhanced triple-helix and double-helix formation with oligomers will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2408187