Method for nucleic acid replication and novel artificial...

Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives

Reexamination Certificate

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C536S023100, C536S027100, C536S027130

Reexamination Certificate

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08030478

ABSTRACT:
The present invention relates to a method for nucleic acid replication and novel artificial base pairs.The method of the present invention for nucleic acid replication is characterized in that a deoxyribonucleoside 5′-triphosphate, in which the hydroxyl group of phosphoric acid at the γ-position is substituted with a group selected from the group consisting of an amino group, a methylamino group, a dimethylamino group, a mercapto group and a fluoro group, is used as a substrate during replication reaction. The novel artificial base pairs of the present invention are characterized in that 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) or an analog thereof forms a base pair with pyrrole-2-carbaldehyde (Pa) or an analog thereof.

REFERENCES:
patent: 1921141 (2008-05-01), None
patent: WO-01/05801 (2001-01-01), None
patent: WO-2004/007713 (2004-01-01), None
patent: WO-2005/026187 (2005-03-01), None
patent: WO-2007/015557 (2007-02-01), None
Doronin et al. FEBS Letters (1987), vol. 216, pp. 221-224.
Benner, S. A., et al., “Did the RNA World Exploit an Expanded Genetic Alphabet?”, Cold Spring Harbor Laboratory Press, pp. 163-181 (1999).
Henry, A. A., et al., “Beyond A, C, G and T: augmenting nature's alphabet,” Curr. Opin. Chem. Biol., vol. 7, pp. 727-733 (2003).
Moser, M. J., et al., “Enzymatic repair of an expanded genetic information system,” Nucleic Acids Res., vol. 31, No. 17, pp. 5048-5053 (2003).
Bergstrom, D. E., “Orthogonal Base Pairs Continue to Evolve,” Chem. Biol., vol. 11, pp. 18-20 (2004).
Benner, S. A., et al., “Synthetic Biology,” Nature Reviews, Genetics, vol. 6, pp. 533-543 (2005).
Piccirilli, J. A., et al., “Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet,” Nature, vol. 343, pp. 33-37 (1990).
Sismour, A. M., et al., “PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1,” Nucleic Acids Research, vol. 32, No. 2, pp. 728-735 (2004).
Switzer, C. Y., “Enzymatic Recognition of the Base Pair between Isocytidine and Isoguanosine,” Biochemistry, vol. 32, pp. 10489-10496 (1993).
Johnson, S. C., “A third base pair for the polymerase chain reaction: inserting isoC and isoG,” Nucleic Acids Research, vol. 32, No. 6, pp. 1937-1941 (2004).
Ahle, J. D., “Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases,” Nucleic Acids Research, vol. 33, No. 10, pp. 3176-3184 (2005).
Morales, J. C., et al., “Efficient replication between non-hydrogen-bonded nucleoside shape analogs,” Nat. Struct. Biol., vol. 5, No. 11, pp. 950-954 (1998).
Kool, E. T., “Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication,” Angew. Chem. Int. Ed., vol. 39, pp. 990-1009 (2000).
McMinn, D. L., et al., “Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base,” J. Am. Chem. Soc., vol. 121, pp. 11585-11586 (1999).
Wu, Y., et al., “Efforts toward Expansion of the Genetic Alphabet: Optimization of Interbase Hydrophobic Interactions,” J. Am. Chem. Soc., vol. 122, No. 32, pp. 7621-7632 (2000).
Ogawa, A. K., et al., “Efforts toward the Expansion of the Genetic Alphabet: Information Storage and Replication with Unnatural Hydrophobic Base Pairs,” J. Am. Chem. Soc., vol. 122, pp. 3274-3287 (2000).
Fujiwara, T., et al., “Synthesis of 6-(2-Thienyl)purine Nucleoside Derivatives That Form Unnatural Base Pairs with Pyridin-2-one Nucleosides,” Bioorg. Med. Chem. Letters, vol. 11, pp. 2221-2223 (2001).
Hirao, I., et al., “An unnatural base pair for incorporating amino acid analogs into proteins,” Nat. Biotechnol., vol. 20, pp. 177-182 (2002).
Mitsui, T., et al., “An Efficient Unnatural Base Pair for a Base-Pair-Expanded Transcription System,” J. Am. Chem. Soc., vol. 127, pp. 8652-8658 (2005).
Kimoto, M., et al., “Site-Specific Incorporation of a Photo-Crosslinking Component into RNA by T7 Transcription Mediated by Unnatural Base Pairs,” Chem. Biol., vol. 11, pp. 47-55 (2004).
Moriyama, K., et al., “Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs,” Nucleic Acids Research, vol. 33, No. 15, e129 (8 pgs).
Kawai, R., et al., “Site-Specific Fluorescent Labeling of RNA Molecules by Specific Transcription Using Unnatural Base Pairs,” J. Am. Chem. Soc., vol. 127, pp. 17286-17295 (2005).
Matray, T. J., et al., “A specific partner for a basic damage in DNA,” Nature, vol. 399, pp. 704-708 (1999).
Doublie, S., et al., “Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution,” Nature, vol. 391, pp. 251-258 (1998).
Kiefer, J. R., et al., “Visualizing DNA replication in a catalytically activeBacillusDNA polymerase crystal,” Nature, vol. 391, pp. 304-307 (1998).
Morales, J. C., et al., “Functional Hydrogen-Bonding Map of the Minor Groove Binding Tracks of Six DNA Polymerases,” Biochem., vol. 39, No. 42, pp. 12979-12988 (2000).
Mitsui, T., et al., “An Unnatural Hydrophobic Base Pair with Shape Complementarity between Pyrrole-2-carbaldehyde and 9-Methylimidazo[(4,5)-b]pyridine,” J. Am. Chem. Soc., vol. 125, No. 18, pp. 5298-5307 (2003).
Morales, J. C., et al., “Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson-Crick Hydrogen Bonds?,” J. Am. Chem. Soc., vol. 121, pp. 2323-2324 (1999).
Hirao, I., et al., “A Two-Unnatural-Base-Pair System toward the Expansion of the Genetic Code,” J. Am. Chem. Soc., vol. 126, No. 41, pp. 13298-13305 (2004).
Tae, E. L., et al., “Efforts toward Expansion of the Genetic Alphabet: Replication of DNA with Three Base Pairs,” J. Am. Chem. Soc., vol. 123, No. 30, pp. 7439-7440 (2001).
Petruska, J., et al., “Comparison between DNA melting thermodynamics and DNA polymerase fidelity,” Proc. Natl. Acad. Sci., vol. 85, pp. 6252-6256 (1988).
Goodman, M.F., et al., “Biochemical Basis of DNA Replication Fidelity,” Critical Reviews in Biochem. and Mol. Biol., vol. 28, No. 2 pp. 83-126 (1993).
Kimoto, M., et al., “A quantitative, non-radioactive single-nucleotide insertion assay for analysis of DNA replication fidelity by using an automated DNA sequencer,” Biotechnol. Letters, vol. 26, pp. 999-1005 (2004).
Ohtsuki, T., et al., “Unnatural bse pairs for specific transcription,” Proc. Natl. Acad. Sci, vol. 98, No. 9, pp. 4922-4925 (2001).
Mitsui, T., et al., “An Unnatural Hydrophobic Base, 4-Propynylpyrrole-2-carbaldehyde, as an Efficient Pairing Partner of 9-Methylimidazo[(4,5)-b]pyridine,” Bioorg. Med. Chem. Letters, vol. 13, pp. 4515-4518 (2003).
Cha, R. S., et al., “Specificity, Efficiency, and Fidelity of PCR,” Intro to PCR, pp. 37-51.
Himeno, H., et al., “Conversion of aminoacylation specificity from tRNATyrto tRNASerin vitro,” Nucleic Acids Res., vol. 18, No. 23, pp. 6815-6819 (1990).
Bedouelle, H., “Recognition of tRNATyr by tyrosyl-tRNA synthetase,” Biochimie, vol. 72, pp. 589-598 (1990).
Mulder, B. A., et al., “Nucleotide modification at the γ-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase,” Nucleic Acids Res., vol. 33, No. 15, pp. 4865-4873 (2005).
De Roos, K. B., et al., “Deazapurine Derivatives. V, A new synthesis of 1- and 3-deaza-adenine and related compounds,” Recueil, vol. 88, pp. 1263-1274 (1963).
Rolland, V., et al., “Convenient Preparation of 2-Deoxy-3,5-di-O-p-Toluoyl-α-D-etythro-Pentofuranosyl Chloride,” Synthetic Comm., vol. 27, No. 20, pp. 3505-3511 (1997).
Ludwig, J., et

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