Requirement of Watson-Crick Hydrogen Bonding for DNA Synthesis by Yeast DNA Polymerase η

REFERENCES

• Aboul-ela, F., D. Koh, I. J. Tinoco, Jr., and F. H. Martin. 1985. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T). Nucleic Acids Res. 13: 4811–4825.
   PubMed Web of Science ®Google Scholar
• Ciarrocchi, G., and A. M. Pedrini. 1982. Determination of pyrimidine dimer unwinding angle by measurement of DNA electrophoretic mobility. J. Mol. Biol. 155: 177–183.
   PubMedGoogle Scholar
• Creighton, S., L. B. Bloom, and M. F. Goodman. 1995. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol. 262: 232–256.
   PubMedGoogle Scholar
• Cuniasse, P., G. V. Fazakerley, W. Guschlbauer, B. E. Kaplan, and L. C. Sowers. 1990. The abasic site as a challenge to DNA polymerase. A nuclear magnetic resonance study of G, C, and T opposite a model abasic site. J. Mol. Biol. 213: 303–314.
   PubMed Web of Science ®Google Scholar
• Cuniasse, P., L. C. Sowers, R. Eritja, B. Kaplan, M. F. Goodman, J. A. H. Cognet, M. LeBret, W. Guschlbauer, and G. V. Fazakerley. 1987. An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Nucleic Acids Res. 15: 8003–8022.
   PubMed Web of Science ®Google Scholar
• Doublie, S., S. Tabor, A. M. Long, C. C. Richardson, and T. Ellenberger. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391: 251–258.
   PubMed Web of Science ®Google Scholar
• Echols, H., and M. F. Goodman. 1991. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60: 477–511.
   PubMed Web of Science ®Google Scholar
• Eom, S. H., J. Wang, and T. A. Steitz. 1996. Structure of Taq polymerase with DNA at the polymerase active site. Nature 382: 278–281.
   PubMed Web of Science ®Google Scholar
• Goodman, M. F. 1997. Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc. Natl. Acad. Sci. USA 94: 10493–10495.
   PubMed Web of Science ®Google Scholar
• Haracska, L., M. T. Washington, S. Prakash, and L. Prakash. 2001. Inefficient bypass of an abasic site by DNA polymerase η. J. Biol. Chem. 276: 6861–6866.
   PubMed Web of Science ®Google Scholar
• Haracska, L., S.-L. Yu, R. E. Johnson, L. Prakash, and S. Prakash. 2000. Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase η. Nat. Genet. 25: 458–461.
   PubMed Web of Science ®Google Scholar
• Husain, I., J. Griffith, and A. Sancar. 1988. Thymine dimers bend DNA. Proc. Natl. Acad. Sci. USA 85: 2558–2562.
   PubMed Web of Science ®Google Scholar
• Johnson, R. E., L. Haracska, S. Prakash, and L. Prakash. 2001. Role of DNA polymerase η in the bypass of a (6-4) TT photoproduct. Mol. Cell. Biol. 21: 3558–3563.
   PubMed Web of Science ®Google Scholar
• Johnson, R. E., C. M. Kondratick, S. Prakash, and L. Prakash. 1999. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285: 263–265.
   PubMed Web of Science ®Google Scholar
• Johnson, R. E., S. Prakash, and L. Prakash. 1999. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Polη. Science 283: 1001–1004.
   PubMed Web of Science ®Google Scholar
• Johnson, R. E., M. T. Washington, S. Prakash, and L. Prakash. 2000. Fidelity of human DNA polymerase η. J. Biol. Chem. 275: 7447–7450.
   PubMed Web of Science ®Google Scholar
• Kalnik, M. W., C.-N. Chang, A. P. Grollman, and D. J. Patel. 1988. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose. Biochemistry 27: 924–931.
   PubMed Web of Science ®Google Scholar
• Kemmink, J., R. Boelens, T. Koning, G. A. van der Marel, J. H. van Boom, and R. Kaptein. 1987. 1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG) · d(CGCAACGC) containing a thymine photodimer. Nucleic Acids Res. 15: 4645–4653.
   PubMed Web of Science ®Google Scholar
• Kiefer, J. R., C. Mao, J. C. Braman, and L. S. Beese. 1998. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391: 304–307.
   PubMed Web of Science ®Google Scholar
• Kim, J.-K., D. Patel, and B.-S. Choi. 1995. Contrasting structural impacts induced by cis-syn cyclobutane dimer and (6-4) adduct in DNA duplex decamers: implication in mutagenesis and repair activity. Photochem. Photobiol. 62: 44–50.
   PubMed Web of Science ®Google Scholar
• Kool, E. T. 2002. Active site tightness and substrate fit in DNA replication. Annu. Rev. Biochem. 71: 191–219.
   PubMed Web of Science ®Google Scholar
• Kool, E. T. 1998. Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching. Biopolymers 48: 3–17.
   PubMedGoogle Scholar
• Kouchakdjian, M., V. Bodepudi, S. Shibutani, M. Eisenberg, F. Johnson, A. P. Grollman, and D. J. Patel. 1991. NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (-8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn) · dA(anti) alignment at lesion site. Biochemistry 30: 1403–1412.
   PubMed Web of Science ®Google Scholar
• Law, S. M., R. Eritja, M. F. Goodman, and K. J. Breslauer. 1996. Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry 35: 12329–12337.
   PubMed Web of Science ®Google Scholar
• Ling, H., F. Boudsocq, R. Woodgate, and W. Yang. 2001. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107: 91–102.
   PubMed Web of Science ®Google Scholar
• Lipscomb, L. A., M. E. Peek, M. L. Morningstar, S. M. Verghis, E. M. Miller, A. Rich, J. M. Essignman, and L. D. Williams. 1995. X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. Proc. Natl. Acad. Sci. USA 92: 719–723.
   PubMed Web of Science ®Google Scholar
• Masutani, C., R. Kusumoto, A. Yamada, N. Dohmae, M. Yokoi, M. Yuasa, M. Araki, S. Iwai, K. Takio, and F. Hanaoka. 1999. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399: 700–704.
   PubMed Web of Science ®Google Scholar
• Matsuda, T., K. Bebenek, C. Masutani, F. Hanaoka, and T. A. Kunkel. 2000. Low fidelity DNA synthesis by human DNA polymerase η. Nature 404: 1011–1013.
   PubMedGoogle Scholar
• McAuley-Hecht, K. E., G. A. Leonard, N. J. Gibson, J. B. Thomson, W. P. Watson, W. N. Hunter, and T. Brown. 1994. Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. Biochemistry 33: 10266–10270.
   PubMed Web of Science ®Google Scholar
• Morales, J. C., and E. T. Kool. 1998. Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat. Struct. Biol. 5: 950–954.
   PubMedGoogle Scholar
• Morales, J. C., and E. T. Kool. 2000. A functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry 39: 12979–12988.
   PubMed Web of Science ®Google Scholar
• Morales, J. C., and E. T. Kool. 2000. Varied molecular interactions at the active sites of several DNA polymerases: nonpolar nucleotide isosteres as probes. J. Am. Chem. Soc. 122: 1001–1007.
   PubMedGoogle Scholar
• Moran, S., R. X.-F. Ren, and E. T. Kool. 1997. A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity. Proc. Natl. Acad. Sci. USA 94: 10506–10511.
   PubMed Web of Science ®Google Scholar
• Oda, Y., S. Uesugi, M. Ikehara, S. Nishimura, Y. Kawase, H. Ishikawa, H. Inoue, and E. Ohtsuka. 1991. NMR studies of a DNA containing 8-hydroxydeoxyguanosine. Nucleic Acids Res. 19: 1407–1412.
   PubMed Web of Science ®Google Scholar
• Park, H., K. Zhang, Y. Ren, S. Nadji, N. Sinha, J.-S. Taylor, and C. Kang. 2002. Crystal structure of a DNA decamer containing a cis-syn thymine dimer. Proc. Natl. Acad. Sci. USA 99: 15965–15970.
   PubMed Web of Science ®Google Scholar
• Petruska, J., M. F. Goodman, M. S. Boosalis, L. C. Sowers, C. Cheong, and I. Tinoco. 1988. Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc. Natl. Acad. Sci. USA 85: 6252–6256.
   PubMed Web of Science ®Google Scholar
• Schweitzer, B. A., and E. T. Kool. 1994. Aromatic nonpolar nucleosides as hydrophobic isosteres of pyrimidine and purine nucleosides. J. Org. Chem. 59: 7238–7242.
   PubMed Web of Science ®Google Scholar
• Schweitzer, B. A., and E. T. Kool. 1995. Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA. J. Am. Chem. Soc. 117: 1863–1872.
   PubMed Web of Science ®Google Scholar
• Shibutani, S., M. Takeshita, and A. P. Grollman. 1991. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature 349: 431–434.
   PubMed Web of Science ®Google Scholar
• Silvian, L. F., E. A. Toth, P. Pham, M. F. Goodman, and T. Ellenberger. 2001. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat. Struct. Biol. 8: 984–989.
   PubMedGoogle Scholar
• Spratt, T. E. 2001. Identification of hydrogen bonds betweeen Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA. Biochemistry 40: 2647–2652.
   PubMedGoogle Scholar
• Trincao, J., R. E. Johnson, C. R. Escalante, S. Prakash, L. Prakash, and A. K. Aggarwal. 2001. Structure of the catalytic core of S. cerevisiae DNA polymerase η: implications for translesion DNA synthesis. Mol. Cell 8: 417–426.
   PubMed Web of Science ®Google Scholar
• Wang, Y.-C., V. M. Maher, D. L. Mitchell, and J. J. McCormick. 1993. Evidence from mutation spectra that the UV hypermutability of xeroderma pigmentosum variant cells reflects abnormal, error-prone replication on a template containing photoproducts. Mol. Cell. Biol. 13: 4276–4283.
   PubMedGoogle Scholar
• Washington, M. T., R. E. Johnson, S. Prakash, and L. Prakash. 2000. Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase η. Proc. Natl. Acad. Sci. USA 97: 3094–3099.
   PubMed Web of Science ®Google Scholar
• Washington, M. T., R. E. Johnson, S. Prakash, and L. Prakash. 1999. Fidelity and processivity of Saccharomyces cerevisiae DNA polymerase η. J. Biol. Chem. 274: 36835–36838.
   PubMedGoogle Scholar
• Washington, M. T., L. Prakash, and S. Prakash. 2001. Yeast DNA polymerase η utilizes an induced fit mechanism of nucleotide incorporation. Cell 107: 917–927.
   PubMed Web of Science ®Google Scholar
• Washington, M. T., W. T. Wolfle, T. E. Spratt, L. Prakash, and S. Prakash. 2003. Yeast DNA polymerase η makes functional contacts with the DNA minor groove only at the incoming nucleoside triphosphate. Proc. Natl. Acad. Sci. USA 100: 5113–5118.
   PubMedGoogle Scholar
• Yu, S.-L., R. E. Johnson, S. Prakash, and L. Prakash. 2001. Requirement of DNA polymerase η for error-free bypass of UV-induced CC and TC photoproducts. Mol. Cell. Biol. 21: 185–188.
   PubMedGoogle Scholar
• Zhou, B.-L., J. D. Pata, and T. A. Steitz. 2001. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell 8: 427–437.
   PubMedGoogle Scholar