Enhanced triple-helix and double-helix formation with oligomers containing modified pyrimidines

Patent Citations (39)

Non-Patent Literature (75)

• Albretsen, et al., “Optimal conditions for hybridization with oligonucleotides: A study with myc-oncogene DNA probes,” Anal. Biochem., 1988, 170, 193-202.Applicant
• Augustyns, et al., “Incorporation of hexose nucleoside analogues into oligonucleotides: synthesis, based-pairing properties and enzymatic stability,” Nuc. Acids Res., 1992, 20, 4711-4716.Applicant
• Balzarini, et al., “Incorporation of 5-substituted pyrimidine nucleoside analogs into DNA of a thymidylate synthetase-deficient murine FM3A carcinoma cell line,” Chem. Ab., 1985, 103(3), 16283a.Applicant
• Beal, et al., “Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation,” Science, 1990, 251, 1360-1363.Applicant
• Capobianco, et al., “One pot solution synthesis of cyclic oligodeoxyribonucleotides,” Nuc. Acids Res., 1990, 18, 2661-2669.Applicant
• Casey, et al., “Rates of formation and thermal stabilities of RNA-DNA duplexes at high concentration of formamide,” Nuc. Acids Res., 1997, 4(5), 1539-1552.Applicant
• Chiang, et al., “Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms,” J. Bio. Chem., 1991, 266, 18162-18171.Applicant
• Civio, et al., “Synthesis of dinucleoside phosphates containing sulfur substituted nucleobase: 4-thiouracil, 4-thiothymine and 6-mercaptopurine,” Tet. Letts., 1992, 33, 69-72.Applicant
• Connolly, et al., “Synthesis and properties of oligonucleotides containing 4-thiothymidine, 5-methyl-2-pyrimidinone-1-b-D(2′-deoxyriboside) and 2-thiothymidine,” Nuc. Acids Res., 1989, 17, 4957-4974.Applicant
• Cooney, et al., “Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro,” Science, 1988, 241, 456-459.Applicant
• De Clercq, et al., “Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides,” J. Med. Chem., 1983, 26, 661-666.Applicant
• Egholm, et la., “Peptide nucleic acids (PNA). Oligonucleotide analogues with an achiral peptide backbone,” J. Am. Chem. Soc., 1992, 114, 1895-1897.Applicant
• Fedorovo, et al., “Complementary addressed modification of double-stranded DNA within a ternary complex,” FEBS, 1988, 228, 273-276.Applicant
• Felgner, et al., “Lipofection: a highly efficient, liqid-mediated DNA-transfection procedure,” Proc. Natl. Acad. Sci., 1987, 84, 7413-7417.Applicant
• Froehler, et al., “Oligodeoxynucleotides containing C-5 propyne analogs of 2′-deoxyuridine and 2′-deoxycytidine,” Tet. Letts., 1992, 33, 5307-5310.Applicant
• Froehler, et al., “Triple-helix formation and cooperative binding by oligodeoxynucleotides with a 3′-3′ internucleotide junction,” Biochem., 1992, 31, 1603-1609.Applicant
• Froehler, et al., “Triple-helix formation by oligodeoxynucleotides containing the carbocyclic analogs of thymidine and 5-methyl-2′-deoxycytidine,” J. Am. Chem. Soc., 1992, 114, 8320-8322.Applicant
• Goodchild, et al., “Structural requirements of olefinic 5-substituted deoxyuridines for antiherpes activity,” J. Med. Chem., 1983, 26, 1252-1257.Applicant
• Griffin, et al., “Recognition of thymine-adenine base pairs by guanine in a pyrimidine triple helix motif,” Science, 1989, 245, 967-971.Applicant
• Hamaguchi, et al., “The effect of electrolytes on the stability of the deoxyribonuclate helix,” J. Am. Chem. Soc., 1962, 84, 1329-1338.Applicant
• Home, et al., “Recognition of mixed-sequence duplex DNA by alternate-strand triple-helix formation,” J. Am. Chem. Soc., 1990, 112, 2435-2437.Applicant
• Hutton, James R., “Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea,” Nuc. Acids Res., Oct. 1977, 3537-3555.Applicant
• Iverson, et al., “Nonenzymatic sequence-specific cleavage of single-stranded DNA to nucleotide resolution. DNA methyl thioether probes,” J. Am. Chem. Soc., 1987, 109, 1241-1243.Applicant
• Knorre, et al., “Reactive oligonucleotide derivatives and sequence-specific modification of nucleic acids,” Biochmie, 1985, 67, 785-789.Applicant
• Krawczyk, et al., “Oligonucleotide-mediated triple helix formation using an N[3]-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range,” Proc. Natl. Acad. Sci., 1992, 89, 37610-3764.Applicant
• Lee, et al., “Interaction of psoralen-derivatized oligodexoyribonucleoside methylphosphonates with single-stranded DNA,” Biochem, 1988, 27, 3197-3203.Applicant
• Lee, et al., “Poly(pyrimidine) poly(purine) synthetic DNAs containing ???,” Nuc. Acids Res., 1984, 12, 6603-6614.Applicant
• Maher, et al., “Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation,” Science, 1989, 245, 725-730.Applicant
• Matteucci, et al., “Synthesis and crosslinking properties of a deoxyoligonucleotide containing N[6],N[6]-ethanodeoxyadenosine,” Tet. Letts., 1987, 28, 2469-2472.Applicant
• Matthews, et al., “Analytical strategies for the use of DNA probes,” Anal. Biochem., 1988, 169, 1-25.Applicant
• Meyer, et al., “Efficient specific cross-linking and cleavage of DNA by stable, synthetic complementary oligodeoxynucleotides,” J. Am. Chem. Soc., 1989, 111, 8517-8519.Applicant
• Moser, et al., “Sequence-specific cleavage of double helical DNA by triple helix formation,” Science, 1987, 238, 645-650.Applicant
• Murakami, et al., “Highly sensitive detection of DNA using enzyme-linked DNA-probe. 1. Colorimetric and fluorometric detection,” Nuc. Acids Res., 1989, 17(14), 5587-5595.Applicant
• Nielsen, et al., “Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide,” Science, 1991, 254, 1497-1500.Applicant
• Ono, et al., “Triplex formation of an oligonucleotide containing 2′0-methylpseudoisocytidine with a DNA dupliex at neutral pH,” J. Org. Chem., 1992, 57, 3225-3230.Applicant
• Petrie, et al., “A novel biotinylated adenylate analogue derived from pyrazolo[3,4-d]pyrimidine for labeling DNA probes,” Biocon. J. Chem., 1991, 2, 441-446.Applicant
• Povsic, et al., “Triple helix formation by oligonucleotides on DNA extended to the physiological pH range,” J. Am. Chem. Soc., 1989, 111, 3059-3061.Applicant
• Praseuth, et al., “Sequence-specific binding and photocrosslinking of a and b oligodeoxynucleotides to the major groove of DNA via triple-helix formation,” Proc. Natl. Acad. Sci., 1988, 85, 1349-1353.Applicant
• Quartin, et al., “Effect of lonic strength on the hybridization of oligodeoxynucleotides with reduced charge due to methylphosphonate linkages to unmodified oligodeoxynucleotides containing the complementary sequence,” Biochem., 1989, 28, 1040-1047.Applicant
• Rahim, “Preparation of 5-prop-1-ynyl-1-(5-0-trimethyl . . . ,” Chem. Ab., 1990, 113(25), 231937d.Applicant
• Rahim, et al., “5-alkynl pyrimidine nucleosides as potent selective inhibitors of varicella-zoster virus,” Antiviral Chem. & Chemo., 1992, 3, 293-297.Applicant
• Reynolds, et al., “Synthesis of thymidine dimers containing internucleoside sulfonate and sulfonamide linkages,” J. org. Chem., 1992, 57, 2983-2985.Applicant
• Robins, et al., “Nucleic acid related compounds, 38. Smooth and high-yield iodination and chlorination at C-5 of uracil bases p-totuyl-protected nucleosides,” Can. J. Chem., 1982, 60, 554-557.Applicant
• Shaw, et al., “Specific, high-efficiency, triple-helix-mediated cross-linking to duplex DNA,” J. Am. Chem. Soc., 1991, 113, 7765-7766.Applicant
• Thompson, et al., “Molecular hybridization with RNA probes in concentrated solutions of guanidine thiocyanate,” Anal Biochem., 1987, 163, 281-291.Applicant
• Uhlmann, et al., “Antisense oligonucleotides: a new therapeutic principle,” chem. Rev., 1990, 90, 543-584.Applicant
• Valko, et al., “Application of chromatographic retention data in a quantitative structure-nucleotide incorporation rate relationship,” J. Chromatog, 1990, 506, 35-44.Applicant
• Valko, et al., “Correlation of nucleotide incorporation rate and HPLC retention parameters of substituted nucleosides,” J. Liquid chromatog, 1989, 12, 2103-2116.Applicant
• Van Ness, et al., “The use of oligodeoxynucleotide probes in chaotrope-based hybridization solutions,” Nuc. Acids Res., 1991, 19(19), 5143-5151.Applicant
• Vasseur, et al., “Oligonucleosides: Synthesis of a novel methylhydroxylamine-linked nucleoside dimer and its incorproation into antisense sequences,” J. Am. Chem. Soc., 1992, 114, 4006-4007.Applicant
• Vlassov, et al., “Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating oligonucleotide derivatives,” Nuc. Acids Res., 1986, 14, 4065-4076.Applicant
• Vlassov, et al., “Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives,” Gene, 1988, 72, 313-322.Applicant
• Webb, et al., “Hybridization triggered cross-linking of deoxyoligonucleotides,” Nuc. Acids Res., 1986, 14, 7661-7674.Applicant
• Webb, et al., “Sequence-specific cross-linking of deoxyoligonucleotides via hybridization-triggered alkylation,” J. Am. Chem. Soc., 1986, 108, 2764-2765.Applicant
• Wigerinck, et al., “5-(5-bromothien-2-yl)-2′-deoxyuridine and 5-(5-chlorothien-2-yl)-2′deoxyuridine are equipotent to (E)-5-(2′-bromovinyl)-2-deoxyuridine in the inhibition of herpes simplex virus type 1 replication,” J. Med. Chem., 1991, 34, 2383-2389.Applicant
• Young, et al., “Triple helix formation inhibits transcription elongation in vitro,” Proc. Natl. Acad. Sci., 1991, 88, 10023-10026.Applicant
• van de Sande, “Parallel stranded DNA,” Science, 1988, 241, 551-557.Applicant
• van der Krol, et al., “Modulation of eukaryotic gene expression by complementary RNA or DNA sequences,” Biotechniques, 1988, 6, 958-976.Applicant
• Ötvös, et al., “Substrate specificity of DNA polymerases. I. Enzyme-catlysed incorporation of 5-(1-alkenyl)-2′-deoxyuridines into DNA,” Nuc. Acids Res., 1987, 15, 1763-1777.Applicant
• Ötvös, et al., “Substrate specificity of DNA polymerases. II. 5-(1-alkynyl)-dUTPs as substrates of the kienow DNA polymerase enzyme,” Chem. Ab., 1987, 107(23), 214012g.Applicant
• Alderfer, et al., “Comparative studies on homopolymers of adenylic acid possessing different C-2′ substituents of the furanose. Poly(deoxyriboadenylic acid), poly(riboadenylic acid), poly(2′-0-methyladenylic acid), and poly(2′-0-ethyladenylic acid),” Biochem., 1974, 13(8), 1615-1622.Applicant
• Al-Razzak, et al., “5-quinone derivatives of 2′-deoxyuridine 5′-phosphate: inhibition and inactivation of thymidylate synthase, antitumor cell, and antiviral studies,” J. Med. Chem., 1987, 30, 409-419.Applicant
• DeClercq, et al., “Thymidylate synthetase as target enzyme for the inhibitory activity of 5-substituted 2′-deoxyuridines on mouse leukemia L1210 cell growth,” Molecular Pharmacology, 1980, 19, 321-330.Applicant
• Vincent, et al., “Synthese de nucleosides substitues en C-5 PAR un carbocycle ou un heterocycle par couplages d'organozinciques avec l'iodo-5-O-bis(trimethylsilyl)-3′,5′desoxy-2′ uridine catalyses par des complexes organopalladies,” Tet. Letts., 1984, 25(2), 201-202.Applicant
• Herdewijn, et al., “Synthesis of 2′-5′ connected oligonucleotides. Prodrugs for antiviral and antitumoral nucleosides,” Helv. Chem. Acta., 1989, 72, 1739-1748.Applicant
• Robins, et al., “Nucleic acid related compounds, 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides,” J. Org. Chem., 1983, 48, 1854-1862.Applicant
• Robins, et al., “Nucleic acid related compounds, 31. Smooth and efficient palladium-copper catalyzed coupling of terminal alkynes with 5-iodouracil nucleosides,” Tet. Letts., 1981, 22, 421-424.Applicant
• Vincent, et al., Tet. Letts., 1981, 22, 945-947.Applicant
• Kielanowska, et al., “Preparation and properties of poly 2′-O-ethyleytidylic acid,” Nuc. Acids Res., Mar. 1976, 3 (3), 817-824.Applicant
• Ransford, et al., “2′-O-ethyl pyrimidine nucleosides (1),” J. carbohydrates Nucls. Nuclt., 1974, 1(3), 275-278.Applicant
• Hobbs, et al., “Palladium-catalyzed synthesis of alkynylamino nucleosides. A universal linker for nucleic acids,” J. Org. Chem., 1989, 54, 3420-3422.Applicant
• Kumar, et al., “Synthesis and antiviral activity of novel 5-(1-azido-2-haloethyl) and 5-(1-azido-,amino-,or methoxyethyl) analogs of 2′-deoxyuridine,” J. Med. Chem., 1993, 36, 2470-2474.Applicant
• Leusink, et al., “Studies in group IV organometalic chemistry XXIV. Structure of products obtained in the hydrostannation of ethynes,” J. Organometal Chem., 1967, 9, 285-294.Applicant
• Loke, et al., “Characterization of oligonucleotide transport into living cells,” Proc. Natl. Acad. Sci., 1989, 86, 3474-3478.Applicant
• Robbins, et al., “Solbent, not palladium oxidation state, is the primary determinant for successful coupling of terminal alkynes with iodo-nucleosides,” Tet. Letts., 1990, 31 (26), 3731-3734.Applicant