Beyond A, C, G and T: Augmenting nature's alphabet

Current Opinion in Chemical Biology

Volumn 7, Issue 6, 2003, Pages 727-733

  Henry, Allison A ^a   Romesberg, Floyd E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA POLYMERASE; DOUBLE STRANDED DNA; GUANINE; HYDROGEN; OLIGONUCLEOTIDE; THYMINE;

BASE MISPAIRING; BASE PAIRING; DNA REPLICATION; GENETIC CODE; HUMAN; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR MODEL; PRODUCTIVITY; REVIEW;

EID: 0344851941     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2003.10.011     Document Type: Review

References (49)

1. Benner S.A., Allemann R.K., Ellington A.D., Ge L., Glasfeld A., Leanz G.F., Krauch T., MacPherson L.J., Moroney S., Piccirilli J.A., et al. Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. Cold Spring Harb. Symp. Quant. Biol. 52:1987;53-63.
2. Moran S., Ren R.X.-F., Rumney S. IV, Kool E.T. Difluorotoluene, a nonpolar isostere for thymine codes specifically and efficiently for adenine in DNA replication. J. Am. Chem. Soc. 119:1997;2056-2057.
3. Moran S., Ren R.X.-F., Kool E.T. A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with sequence selectivity. Proc. Natl. Acad. Sci. U.S.A. 94:1997;10506-10511.
4. Roberts C., Bandaru R., Switzer C. Synthesis of oligonucleotides bearing the non-standard bases iso-C and iso-G. Comparison of iso-C-iso-G, C-G and U-A base-pair stabilities in RNA/DNA duplexes. Tetrahedron Lett. 36:1995;3601-3604.
5. Piccirilli J.A., Krauch T., Moroney S.E., Benner S.A. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature. 343:1990;33-37.
6. Switzer C., Moroney S.E., Benner S.A. Enzymatic incorporation of a new base pair into DNA and RNA. J. Am. Chem. Soc. 111:1989;8322-8323.
7. Switzer C.Y., Moroney S.E., Benner S.A. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Biochemistry. 32:1993;10489-10496.
8. Horlacher J., Hottiger M., Podust V.N., Hübscher U., Benner S.A. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc. Natl. Acad. Sci. U.S.A. 92:1995;6329-6333.
9. Rappaport H.P. The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucleic Acids Res. 16:1988;7253-7267.
10. Rappaport H.P. Replication of the base pair 6-thioguanine/5-methyl-2- pyrimidinone with the large Klenow fragment of Escherichia coli DNA polymerase I. Biochemistry. 32:1993;3047-3057.
11. Ishikawa M., Hirao I., Yokoyama S. Synthesis of 3-(2-deoxy-β-D- ribofuranosyl)pyridin-2-one and 2-amino-6-(N,N-dimethylamino)-9-(2-deoxy-β- D-ribofuranosyl)purine derivatives for an unnatural base pair. Tetrahedron Lett. 41:2000;3931-3934.
12. Ishikawa M., Hirao I., Yokoyama S. Chemical synthesis of novel base pairs and their enzymatic incorporation into DNA. Nucleic Acids Symp. Ser. 42:1999;125-126.
13. Fujiwara T., Kimoto M., Sugiyama H., Hirao I., Yokoyama S. Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides. Bioorg. Med. Chem. Lett. 11:2001;2221-2223.
14. Hirao I., Fujiwara T., Kimoto M., Mitsui T., Okuni T., Ohtsuki T., Yokoyama S. Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases. Nucleic Acids Symp. Ser. 44:2000;261-262.
15. Fujiwara T., Sugiyama H., Hirao I., Yokoyama S. Synthesis of 6-(2-thienyl)purine nucleoside derivatives toward the expansion of the genetic code. Nucleic Acids Symp. Ser. 44:2000;43-44.
16. Hirao I., Mitsui T., Fujiwara T., Kimoto M., To T., Okuni T., Sato A., Harada Y., Yokoyama S. Efforts towards creating unnatural base pairs for an expanded genetic code. Nucleic Acids Res. Suppl. 1:2001;17-18.
17. Hirao I., Kimoto M., Mitsuik T., Harada Y., Fujiwara T., Sato A., Yokoyama S. An unnatural base pair between imidazolin-2-one and 2-amino-6(2-thienyl)purine in replication and transcription. Nucleic Acids Res. Suppl. 2:2002;37-38.
18. Wang H., Zhang H., Abou-Zied O.K., Yu C., Romesberg F.E., Glasbeek M. Femtosecond fluorescence upconversion studies of excited-state proton-transfer dynamics in 2-(2′hydroxyphenyl)benzoxazole (HBO) in liquid solution and DNA. Chem. Phys. Lett. 367:2003;599-608.
19. Abou-Zied O.K., Jimenez R., Thompson E.H.Z., Millar D.P., Romesberg F.E. Solvent-dependent photoinduced tautomerization of 2-(2′-hydroxyphenyl) benzoxazole. J. Phys. Chem. A. 106:2002;3665-3672.
20. Abou-Zied O.K., Jimenez R., Romesberg F.E. Tautomerization dynamics of a model base pair in DNA. J. Am. Chem. Soc. 123:2001;4613-4614.
21. Ogawa A.K., Abou-Zied O.K., Tsui V., Jimenez R., Case D.A., Romesberg F.E. A phototautomerizable model DNA base pair. J. Am. Chem. Soc. 122:2000;9917-9920.
22. Morales J.C., Kool E.T. Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat. Struct. Biol. 5:1998;950-954.
23. Morales J.C., Kool E.T. Minor groove interactions between polymerase and DNA: more essential to replication than Watson-Crick hydrogen bonds? J. Am. Chem. Soc. 121:1999;2323-2324.
24. Delaney J.C., Henderson P.T., Helquist S.A., Morales J.C., Essigmann J.M., Kool E.T. High-fidelity in vivo replication of DNA base shape mimics without Watson-Crick hydrogen bonds. Proc. Natl. Acad. Sci. U.S.A. 100:2003;4469-4473.
25. Washington M.T., Helquist S.A., Kool E.T., Prakash L., Prakash S. Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase η Mol. Cell Biol. 23:2003;5107-5112.
26. Matray T.J., Kool E.T. A specific partner for abasic damage in DNA. Nature. 399:1999;704-708.
27. Matray T.J., Kool E.T. Selective and stable DNA base pairing without hydrogen bonds. J. Am. Chem. Soc. 120:1998;6191-6192.
28. Ren R.X.-F., Chaudhuri N.C., Paris P.L., Rumney S. IV, Kool E.T. Naphthalene, phenanthrene, and pyrene as DNA base analogues: synthesis, structure, and fluorescence in DNA. J. Am. Chem. Soc. 118:1996;7671-7678.
29. Smirnov S., Matray T.J., Kool E.T., de los Santos C. Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Res. 30:2002;5561-5569.
30. Schweitzer B.A., Kool E.T. Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA. J. Am. Chem. Soc. 117:1995;1863-1872.
31. Mitsui T., Kitamure A., Kimoto M., To T., Sato A., Hirao I., Yokoyama S. An unnatural hydrophobic base pair with shape complementarity between pyrrole-2-carbaldehyde and 9-methylimidazo[(4,5)-b]pyridine. J. Am. Chem. Soc. 125:2003;5298-5307 Full characterization of dPa:dQ replication with KF, NMR solution structure of the base pair in duplex DNA, and full length studies with AMV reverse transcriptase.
32. Mitsui T., Kimoto M., Harada Y., Sata A., Kitamura A., To T., Hirao I., Yokoyama S. Enzymatic incorporation of an unnatural base pair between 4-propynyl-pyrrole-2-carbaldehyde and 9-methyl-imidazo [(4,5)-b]pyridine into nucleic acids. Nucleic Acids Res. Suppl. 2:2002;219-220.
33. McMinn D.L., Ogawa A.K., Wu Y., Liu J., Schultz P.G., Romesberg F.E. Efforts toward expansion of the genetic alphabet: recognition of a highly stable, self-pairing hydrophobic base. J. Am. Chem. Soc. 121:1999;11585-11586.
34. Ogawa A.K., Wu Y., McMinn D.L., Liu J., Schultz P.G., Romesberg F.E. Efforts toward the expansion of the genetic alphabet: information storage and replication with unnatural hydrophobic base pairs. J. Am. Chem. Soc. 122:2000;3274-3287.
35. Berger M., Ogawa A.K., McMinn D.L., Wu Y., Schultz P.G., Romesberg F.E. Stable and selective hybridizaion of oligonucleotides using unnatural hydrophobic bases. Angew. Chem. Int. Ed. Engl. 39:2000;2940-2942.
36. Wu Y., Ogawa A.K., Berger M., McMinn D.L., Schultz P.G., Romesberg F.E. Efforts toward expansion of the genetic alphabet: optimization of interbase hydrophobic interactions. J. Am. Chem. Soc. 122:2000;7621-7632.
37. Ogawa A.K., Wu Y., Berger M., Schultz P.G., Romesberg F.E. Rational design of an unnatural base pair with increased kinetic selectivity. J. Am. Chem. Soc. 122:2000;8803-8804.
38. Tae E.L., Wu Y.Q., Xia G., Schultz P.G., Romesberg F.E. Efforts toward expansion of the genetic alphabet: replication of DNA with three base pairs. J. Am. Chem. Soc. 123:2001;7439-7440 Replication of the d7AI self pair with high efficiency and selectivity by the dual actions of KF and mammalian polymerase β.
39. Berger M., Luzzi S.D., Henry A.A., Romesberg F.E. Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues. J. Am. Chem. Soc. 124:2002;1222-1226.
40. Yu C., Henry A.A., Romesberg F.E., Schultz P.G. Polymerase recognition of unnatural base pairs. Angew. Chem. Int. Ed. Engl. 41:2002;3841-3844.
41. Matsuda S., Henry A.A., Schultz P.G., Romesberg F.E. The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs. J. Am. Chem. Soc. 125:2003;6134-6139.
42. Henry A.A., Yu C., Romesberg F.E. Determinants of unnatural nucleobase stability and polymerase recognition. J. Am. Chem. Soc. 125:2003;9638-9646.
43. Prakash S., Prakash L. Translesion DNA synthesis in eukaryotes: a one- or two-polymerase affair. Genes Dev. 16:2002;1872-1883.
44. Goodman M. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71:2002;17-50.
45. Xia G., Chen L., Sera T., Fa M., Schultz P.G., Romesberg F.E. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 99:2002;6597-6602.
46. Ghadessy F.J., Ong J.L., Holliger P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl. Acad. Sci. U.S.A. 98:2001;4552-4557.
47. Jestin J.-L., Kristensen P., Winter G. A method for the selection of catalytic activity using phage display and proximity coupling. Angew. Chem. Int. Ed. Engl. 38:1999;1124-1127.
48. Huang CC, Couch GS, Pettersen EF, Ferrin TE: Chimera: an extensible molecular modeling application constructed using standard components. In Pacific Symposium on Biocomputing '96. Hunter L, Klein TE (Eds). Singapore: World Scientific Publishing; 1996:724. [See also http://www.cgl.ucsf.edu/ chimera .].
49. Sanner M.F., Olson A.J., Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:1996;305-320.