Enzymatic incorporation of a third nucleobase pair

Nucleic Acids Research

Volumn 35, Issue 13, 2007, Pages 4238-4249

  Yang, Zunyi ^a   Sismour, A Michael ^a   Sheng, Pinpin ^a   Puskar, Nyssa L ^a   Benner, Steven A ^a  

^a FOUNDATION FOR APPLIED MOLECULAR EVOLUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; NUCLEIC ACID BASE; OLIGONUCLEOTIDE; 2 AMINO 8 (1' (2' DEOXYRIBOFURANOSYL))IMIDAZO(1,2 A) 1,3,5 TRIAZIN 4(8H) ONE; 2-AMINO-8-(1'-(2'-DEOXYRIBOFURANOSYL))IMIDAZO(1,2-A)-1,3,5-TRIAZIN-4(8H)-ONE; 6 AMINO 5 NITRO 3 (1' (2' DEOXYRIBOFURANOSYL)) 2(1H) PYRIDONE; 6-AMINO-5-NITRO-3-(1'-(2'-DEOXYRIBOFURANOSYL))-2(1H)-PYRIDONE; DEOXYRIBONUCLEOSIDE; DEOXYRIBONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE; PYRIDONE DERIVATIVE; TRIAZINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; ELECTRON; ENZYME MECHANISM; ENZYME SPECIFICITY; GENE SEQUENCE; HYDROGEN BOND; MISMATCH REPAIR; MOLECULAR MECHANICS; PH; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN FAMILY; BASE MISPAIRING; CHEMISTRY; METABOLISM;

BASE PAIR MISMATCH; DEOXYRIBONUCLEOSIDES; DEOXYRIBONUCLEOTIDES; DNA-DIRECTED DNA POLYMERASE; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; POLYMERASE CHAIN REACTION; PYRIDONES; TRIAZINES;

EID: 34547843669     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm395     Document Type: Article

References (38)

1. Watson,J.D. and Crick,F.H.C. (1953) Molecular structure of nucleic acids. Nature, 171, 737-738.
2. Watson,J.D. and Crick,F.H.C. (1953) General implications of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
3. Rappaport,H.P. (1988) The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucleic Acids Res., 16, 7253-7267.
4. Kool,E.T. (2002) Replacing the nucleobases in DNA with designer molecules. Acc. Chem. Res., 35, 936-943.
5. Ishikawa,M., Hirao,I. and Yokoyama,S. (2000) 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 3931-3934.
6. Hirao,I., Harada,Y., Kimoto,M., Mitsui,T., Fujiwara,T. and Yokoyama,S. (2004) A two unnatural base pair system toward the expansion of the genetic code. J. Am. Chem. Soc., 126, 13298-13305.
7. Minakawa,N., Kojima,N., Hikishima,S., Sasaki,T., Kiyosue,A., Atsumi,N., Ueno,Y. and Matsuda,A. (2003) New Base Pairing Motifs. The synthesis and thermal stability of oligodeoxynucleotides containing imidazopyridopyrimidine nucleosides with the ability to form four hydrogen bonds. J. Am. Chem. Soc., 125, 9970-9982.
8. Henry,A.A. and Romesberg,F.E. (2003) Beyond A. C, G and T: Augmenting Nature's alphabet. Curr. Opin. Chem. Biol., 7, 727-733.
9. Tae,E.L., Wu,Y.Q., 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.
10. 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.
11. Piccirilli,J.A., Krauch,T., Moroney,S.E. and Benner,S.A. (1990) Extending the genetic alphabet. Enzymatic incorporation of a new base pair into DNA and RNA. Nature, 343, 33-37.
12. Benner,S.A. (2004) Understanding nucleic acids using synthetic chemistry. Acc. Chem. Res., 37, 784-797.
13. Gleaves,C.A., Welle,J., Campbell,M., Elbeik,T., Ng,V., Taylor,P.E., Kuramoto,K., Aceituno,S., Lewalski,E. et al. (2002) Multicenter evaluation of the Bayer VERSANT (TM) HTV-1 RNA 3.0 assay: Analytical and clinical performance. J. Clin. Virol., 25, 205-216.
14. Elbeik,T., Surtihadi,J., Destree,M., Gorlin,J., Holodniy,M., Jortani,S.A., Kuramoto,K., Ng,V., Valdes,R. et al. (2004) Multicenter evaluation of the performance characteristics of the Bayer VERSANT HCV RNA 3.0 assay (bDNA). J. Clin. Microbiol., 41, 563-569.
15. Johnson,S.C., Marshall,D.J., Harms,G., Miller,C.M., Sherrill,C.B., Beaty,E.L., Lederer,S.A., Roesch,E.B., Madsen,G. et al. (2004) Multiplexed genetic analysis using an expanded genetic alphabet. Clin. Chem., 50, 2019-2027.
16. Joyce,C.M. and Steitz,T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem., 63, 777-822.
17. Kunkel,T.A. and Bebenek,K. (2000) DNA replication fidelity. Annu. Rev. Biochem., 69, 497-529.
18. Morales,J.C. and Kool,E.T. (2000) Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry, 39, 12979-12988.
19. Hendrickson,C., Devine,K. and Benner,S.A. (2004) Probing the necessity of minor groove interactions with three DNA polymerase families using 3-deaza-2′-deoxyadenosine 5′-triphosphate. Nucleic Acids Res., 32, 2241-2250.
20. McCain,M.D., Meyer,A.S., Schultz,S.S., Glekas,A. and Spratt,T.E. (2005) Fidelity of mispair formation and extension is dependent on the interaction between the minor groove, of the primer terminus and Arg668 of DNA polymerase I of Escherichia coli. Biochemistry, 44, 5647-5659.
21. Piccirilli,J.A., Krauch,T., MacPherson,L.J. and Benner,S.A. (1991) A direct route to 3-(ribofuranosyl)-pyridine nucleosides. Helv. Chim. Acta, 74, 397-406.
22. Voegel,J.J., von Krosigk,U. and Benner,S.A. (1993) Synthesis and tautomeric equilibrium of 6-amino-5-benzyl-3-methylpyrazin-2-one. An acceptor-donor-donor nucleoside base analog. J. Org. Chem., 58 7542-7547.
23. Hutter,D. and Benner,S.A. (2003) Expanding the genetic alphabet. Nonepimerizing nucleoside with the pyDDA hydrogen bonding pattern. J. Org. Chem., 68, 9839-9842.
24. Yang,Z., Hutter,D., Sheng,P., Sismour,A.M. and Benner,S.A. (2006) Artificially expanded genetic information system. A new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res., 34 6095-6101.
25. Ludwig,J. and Eckstein,F. (1989) Rapid and efficient synthesis of nucleoside 5′-O (1-thiotriphosphates), 5′-triphosphates and 2′,3′-cyclophosphorothioates using 2-chloro-4H- 1,3,2-benzo-dioxaphosphorin-4-one. J. Org. Chem., 54, 631-635.
26. Sismour,A.M., Lutz,S., Park,J.-H., Lutz,M.J., Boyer,P.L., Hughes,S.H. and Benner,S.A. (2004) PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1. Nucleic Acids Res., 32, 728-735.
27. Linxweiler,W. and Horz,W. (1982) Sequence specificity of exonuclease III from E. coli. Nucleic Aids Res., 10, 4845-4859.
28. He,K.Z., Porter,K.W., Hasan,A., Briley,D.J. and Shaw,B.R. (1999) Synthesis of 5-substituted 2′-deoxycytidine 5′-(alpha-P-borano) triphosphates, their incorporationinto DNA and effects on exonuclease. Nucleic Aids Res., 27, 1788-1794.
29. Good,N.E., Winget,G.D., Winter,W., Connolly,T.N., Izawa,S. and Singh,R.M.M. (1966) Hydrogen ion buffers for biological research. Biochemistry, 5, 467-477.
30. Day,J.P., Hammer,R.P., Bergstrom,D. and Barany,F. (1999) Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations. Nucleic Acids Res., 27, 1819-1827.
31. Sismour,A.M. and Benner,S.A. (2005) The use of thymidine analogs to improve the replication of an extra DNA base pair: A synthetic biological system. Nucleic Acids Res., 33, 5640-5646.
32. Clark,J.M., Joyce,C.M. and Beardsley,G.P. (1987) Novel blunt-end addition-reactions catalyzed by DNA polymerase I of Escherichia coli. J. Mol. Biol., 198, 123-127.
33. Hu,G.X. (1993) DNA polymerase-catalyzed addition of nontemplated extra nucleotides to the 3′ end of a DNA fragment. DNA Cell Biol., 12, 763-770.
34. Johnson,S.C., Sherrill,C.B., Marshall,D.J., Moser,M.J. and Prudent,J.R. (2004) A third base pair for the polymerase chain reaction: Inserting isoC and isoG. Nucleic Acids Res., 32, 1937-1941.
35. Sepiol,J., Kazimierczuk,Z. and Shugar,D. (1976) Tautomerism of iso guanosine and solvent-induced keto-enol equilibrium. Z. Naturforsch., C 31, 361-370.
36. 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.
37. Lezius,A.G. and Scheit,K.H. (1967) Enzymatic synthesis of DNA with 4-thio- thymidine triphosphate as substitute for dTTP. Eur. J. Biochem., 3, 85-94.
38. Young,L.Y., Krawczyk,S.H., Matteucci,M.D. and Toole,J.J. (1991) Triple helix formation inhibits transcription elongation in vitro. Proc. Natl Acad. Sci. USA, 88, 10023-10026.