Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 8095-8104

  Petrie, Katherine L ^a   Joyce, Gerald F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

8 OXO DEOXYGUANOSINE TRIPHOSPHATE; DEOXYPYRIMIDINE TRIPHOSPHATASE; DNA POLYMERASE; MUTAGENIC AGENT; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE MUTATION; MUTAGENESIS; MUTATION RATE; MUTATIONAL ANALYSIS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN POLYMERIZATION; REVERSE TRANSCRIPTION; RNA SYNTHESIS; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

DEOXYGUANINE NUCLEOTIDES; DNA MUTATIONAL ANALYSIS; MUTAGENESIS; MUTAGENS; MUTATION; REVERSE TRANSCRIPTION;

EID: 78650499829     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq685     Document Type: Article

References (28)

1. Pavlov, Y.I., Minnik, D.T., Izuta, S. and Kunkel, T.A. (1994) DNA replication fidelity with 8-oxodeoxyguanosine triphosphate. Biochemistry, 33, 4695-4701.
2. 2-dGTP by reverse transcriptases and mammalian DNA polymerases. J. Biol. Chem., 272, 5892-5898.
3. Bebenek, K., Boyer, J.C. and Kunkel, T.A. (1999) The base substitution fidelity of HIV-1 reverse transcriptase on DNA and RNA templates probed with 8-oxo-deoxyguanosine triphosphate. Mutation Res., 429, 149-158.
4. Kong Thoo Lin, P. and Brown, D.M. (1989) Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues. Nucleic Acids Res., 17, 10373-10383.
5. Hill, F., Loakes, D. and Brown, D.M. (1998) Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl Acad. Sci. USA, 95, 4258-4263.
6. Zaccolo, M., Williams, D.M., Brown, D.M. and Gherardi, E. (1996) An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol., 255, 589-603.
7. Altshuler, D., Pollara, V., Cowles, C., Van Etten, W., Baldwin, J., Linton, L. and Lander, E. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407, 513-516.
8. Brockman, W., Alvarez, P., Young, S., Garber, M., Giannoukos, G., Lee, W.L., Russ, C., Lander, E.S., Nusbaum, C. and Jaffe, D.B. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res., 18, 763-770.
9. Ikawa, Y., Tsuda, K., Matsumura, S. and Inoue, T. (2004) De novo synthesis and development of an RNA enzyme. Proc. Natl Acad. Sci. USA, 101, 13750-13755.
10. Wright, M.C. and Joyce, G.F. (1997) Continuous in vitro evolution of catalytic function. Science, 276, 614-617.
11. Kouchakdjian, M., Bodepudi, V., Shibutani, S., Eisenberg, M., Johnson, F., Grollman, A.P. and Patel, D.J. (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.
12. Brown, D.M., Hewlins, M.J.E. and Schell, P. (1968) The tautomeric state of N(4)-hydroxy- and of N(4)-amino-cytosine derivatives. J. Chem. Soc. C, 1925-1929.
13. Moore, M.H., Van Meervelt, L., Salisbury, S.A., Kong Thoo Lin, P. and Brown, D.M. (1995) Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis. J. Mol. Biol., 251, 665-673.
14. Suo, Z. and Johnson, K.A. (1997) Effect of RNA secondary structure on the kinetics of DNA synthesis catalyzed by HIV-1 reverse transcriptase. Biochemistry, 36, 12459-12467. (Pubitemid 27446669)
15. Kim, S., Schroeder, C.M. and Xie, X.S. (2010) Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates. J. Mol. Biol., 395, 995-1006.
16. Voytek, S.B. and Joyce, G.F. (2007) Emergence of a continuously evolving ligase ribozyme. Proc. Natl Acad. Sci. USA, 104, 15288-15293.
17. Fujita, Y., Furuta, H. and Ikawa, Y. (2010) Evolutionary optimization of a modular ligase ribozyme: a small catalytic unit and a hairpin motif masking an element that could form an inactive structure. Nucleic Acids Res., 38, 3328-3339.
18. Hanes, J.W., Thal, D.M. and Johnson, KA. (2006) Incorporation and replication of 8-oxo-deoxyguanosine by the human mitochondrial DNA polymerase. J. Biol. Chem., 281, 36241-36248.
19. 0-dGTP in the confines of a DNA polymerase active site. Nature Struct. Mol. Biol., 17, 889-890.
20. Rasila, T.S., Pajunen, M.I. and Savilahti, H. (2009) Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. Anal. Biochem., 388, 71-80.
21. Abbondanzieri, E.A., Greenleaf, W.J., Shaevitz, J.W., Landick, R. and Block, S.M. (2005) Direct observation of base-pair stepping by RNA polymerase. Nature, 438, 460-465.
22. Christian, T.D., Romano, L.J. and Rueda, D. (2009) Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution. Proc. Natl Acad. Sci. USA, 106, 21109-21114.
23. Leung, D.W., Chen, E. and Goeddel, D.V. (1989) A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique, 1, 11-15.
24. Cadwell, R.C. and Joyce, G.F. (1992) Randomization of genes by PCR mutagenesis. PCR Methods Applic., 2, 28-33.
25. Vartanian, J.-P., Henry, M. and Wain-Hobson, S. (1996) Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res., 24, 2627-2631.
26. Biles, B.D. and Connolly, B.A. (2004) Low fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR. Nucleic Acids Res., 32, e176.
27. Eigen, M. (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwiss., 58, 465-523.
28. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.