Enzymatic repair of an expanded genetic information system

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5048-5053

  Moser, Michael J ^a   Prudent, James R ^a  

^a EraGen Biosciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CELL DIVISION; COVALENT BOND; EXCISION REPAIR; GENETIC CODE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; THERMOPHILIC BACTERIUM; THERMUS AQUATICUS;

BASE PAIR MISMATCH; DEOXYRIBONUCLEASES; DNA; DNA LIGASES; DNA REPAIR; DNA-DIRECTED DNA POLYMERASE; ENZYMES; MODELS, GENETIC;

BACTERIA (MICROORGANISMS); THERMUS; THERMUS AQUATICUS;

EID: 0345306572     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg709     Document Type: Article

References (34)

1. McMinn, D.L., Ogawa, A.K., Wu, Y., Liu, J. and Romesberg, F.E. (1999) Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base. J. Am. Chem. Soc., 121, 11585-11586.
2. Switzer, C.Y., Moroney, S.E. and Benner, S.A. (1989) Enzymatic incorporation of a new base pair into DNA and RNA. J. Am. Chem. Soc., 111, 8322-8323.
3. Tae, E.L., Wu, Y., Xia, G., Schultz, P.G. and Romesberg, F.E. (2001) Efforts toward expansion of the genetic alphabet: replication of DNA with three base pairs. J. Am. Chem. Soc., 123, 7439-7440.
4. Wu, Y., Ogawa, A.K., Berger, M., McMinn, D.L., Schultz, P.G. and Romesberg, F.E. (2000) Efforts toward expansion of the genetic alphabet: optimization of interbase hydrophobic interactions. J. Am. Chem. Soc., 122, 7621-7632.
5. Ohtsuki, T., Kimoto, M., Ishikawa, M., Mitsui, T., Hirao, I. and Yokoyama, S. (2001) Unnatural base pairs for specific transcription. Proc. Natl Acad. Sci. USA, 98, 4922-4925.
6. Mitsui, T., Kitamura, A., Kimoto, M., To, T., Sato, A., Hirao, I. and Yokoyama, S. (2003) An unnatural hydrophobic base pair with shape complementarity between pyrrole-2-carbaldehyde and 9-methylimidazo[(4,5)-b]pyridine. J. Am. Chem. Soc., 125, 5298-5307.
7. Yu, C., Henry, A.A., Romesberg, F.E. and Schultz, P.G. (2002) Polymerase recognition of unnatural base pairs. Angew. Chem. Int. Ed., 41, 3841-3844.
8. Wu, Y., Fa, M., Tae, E.L., Schultz, P.G. and Romesberg, F.E. (2002) Enzymatic phosphorylation of unnatural nucleosides. J. Am. Chem. Soc., 124, 11430-14626.
9. Berger, M., Luzzi, S.D., Henry, A.A. and Romesberg, F.E. (2002) Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues. J. Am. Chem. Soc., 124, 1222-1226.
10. Matsuda, S., Henry, A.A., Schultz, P.G. and Romesberg, F.E. (2003) The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs. J. Am. Chem. Soc., 125, 6134-6139.
11. Lutz, M.J., Horlacher, J. and Benner, S.A. (1998) Recognition of a non-standard base pair by thermostable DNA polymerases. Bioorg. Med. Chem. Lett., 8, 1149-1152.
12. Lutz, M.J., Horlacher, J. and Benner, S.A. (1998) Recognition of 2′-deoxyisoguanosine triphosphate by HIV-1 reverse transcriptase and mammalian cellular DNA polymerases. Bioorg. Med. Chem. Lett., 8, 499-504.
13. Lutz, M.J., Held, H.A., Hottiger, M., Hubscher, U. and Benner, S.A. (1996) Differential discrimination of DNA polymerase for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet. Nucleic Acids Res., 24, 1308-1313.
14. Horlacher, J., Hottiger, M., Podust, V.N., Hubscher, U. and Benner, S.A. (1995) Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc. Natl Acad. Sci. USA, 92, 6329-6333.
15. Switzer, C.Y., Moroney, S.E. and Benner, S.A. (1993) Enzymatic recognition of the base pair between isocytidine and isoguanosine. Biochemistry, 32, 10489-10496.
16. Bain, J.D., Switzer, C., Chamberlin, A.R. and Benner, S.A. (1992) Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code. Nature, 356, 537-539.
17. Piccirilli, J.A., Krauch, T., Moroney, S.E. and Benner, S.A. (1990) Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature, 343, 33-37.
18. Hirao, I., Ohtsuki, T., Fujiwara, T., Mitsui, T., Yokogawa, T., Okuni, T., Nakayama, H., Takio, K., Yabuki, T., Kigawa, T. et al. (2002) An unnatural base pair for incorporating amino acid analogs into proteins. Nat. Biotechnol., 20, 177-182.
19. Lindahl, T. and Wood, R.D. (1999) Quality control by DNA repair. Science, 286, 1897-1905.
20. Harrington, J.J. and Lieber, M.R. (1994) The characterization of a mammalian DNA structure-specific endonuclease. EMBO J., 13, 1235-1246.
21. Lieber, M.R. (1997) The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. Bioessays, 19, 233-240.
22. Wu, X., Wilson, T.E. and Lieber, M.R. (1999) A role for FEN-1 in nonhomologous DNA end joining: the order of strand annealing and nucleolytic processing events. Proc. Natl Acad. Sci. USA, 96, 1303-1308.
23. Barnes, W.M. (1992) The fidelity of Taq polymerase catalyzing PCR is improved by an N-terminal deletion. Gene, 112, 29-35.
24. Kaiser, M.W., Lyamicheva, N., Ma, W., Miller, C., Neri, B., Fors, L. and Lyamichev, V.I. (1999) A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. J. Biol. Chem., 274, 21387-21394.
25. Hosfield, D.J., Mol, C.D., Shen, B. and Tainer, T.A. (1998) Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell, 95, 115-146.
26. Karanjawala, Z.E., Shi, X., Hsieh, C.L. and Lieber, M.R. (2000) The mammalian FEN-1 locus: structure and conserved sequence features. Microb. Comp. Genomics, 5, 173-177.
27. Murante, R.S., Rust, L. and Bambara, R.A. (1995) Calf 5′ to 3′ exo/endonuclease must slide from a 5′ end of the substrate to perform structure-specific cleavage. J. Biol. Chem., 270, 30377-30383.
28. Harrington, J.J. and Lieber, M.R. (1995) DNA structural elements required for FEN-1 binding. J. Biol. Chem., 270, 4503-4508.
29. Roberts, C., Bandaru, R. and Switzer, C. (1997) Theoretical and experimental study of isoguanine and isocytosine: base pairing in an expanded genetic system. J. Am. Chem. Soc., 119, 4640-4649.
30. Timson, D.J., Singleton, M.R. and Wigley, D.B. (2000) DNA ligases in the repair and replication of DNA. Mutat. Res., 460, 301-318.
31. Lehman, I.R. (1974) DNA ligase: structure, mechanism and function. Science, 186, 790-797.
32. Housby, J.N., Thorbjarnardottir, S.H., Jonsson, Z.O. and Southern, E.M. (2000) Optimised ligation of oligonucleotides by thermal ligases: comparison of Thermus scotoductus and Rhodothermus marinus DNA ligases to other thermophilic ligases. Nucleic Acids Res., 28, e10.
33. Friedberg, E.C. (2003) DNA damage and repair. Nature, 421, 436-440.
34. Moser, M.J., Marshall, D.J., Grenier, J.K., Kieffer, C.D., Killeen, A.A., Ptacin, J.L., Richmond, C.S., Roesch, E.B., Scherrer, C.W., Sherrill, C.B. et al. (2003) Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system. Clin. Chem., 49, 407-414.