PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1

Nucleic Acids Research

Volumn 32, Issue 2, 2004, Pages 728-735

  Sismour, A Michael ^e   Lutz, Stefan ^a   Park, Jeong Ho ^b   Lutz, Michael J ^c   Boyer, Paul L ^d   Hughes, Stephen H ^d   Benner, Steven A ^e  

^a EMORY UNIVERSITY   (United States)

^b Hanbat National University   (South Korea)

^c NOVARTIS PHARMA AG   (Switzerland)

^d NATIONAL CANCER INSTITUTE   (United States)

^e University of Florida ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2,4 DIAMINOPYRIMIDINE DERIVATIVE; 3 [(4,7 DIMETHYL 2 BENZOXAZOLYLMETHYL)AMINO] 5 ETHYL 6 METHYL 2(1H) PYRIDONE; DOUBLE STRANDED DNA; LEUCINE; NEVIRAPINE; OLIGONUCLEOTIDE; RNA DIRECTED DNA POLYMERASE; TYROSINE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME PURIFICATION; GENE AMPLIFICATION; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION;

AMINO ACID SUBSTITUTION; BASE PAIRING; BINDING SITES; DNA; DNA-DIRECTED DNA POLYMERASE; HIV-1; HIV-1 REVERSE TRANSCRIPTASE; HUMANS; HYDROGEN BONDING; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; TAQ POLYMERASE; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 1342327652     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh241     Document Type: Article

References (42)

1. 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.
2. 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.
3. Strazewski,P. and Tamm,C. (1990) Replication experiments with nucleotide base analogs. Int. Ed. Engl., 29, 36-57.
4. Rappaport,H.P. (1993) Replication of the base pair 6-thioguanine/5-methyl-2-pyrimidinone with the large Klenow fragment of Escherichia coli DNA-polymerase-I. Biochemistry, 32, 3047-3057.
5. Kool,E.T. (2001) Hydrogen bonding, base stacking and steric effects in DNA replication. Annu. Rev. Biophys. Biomol. Struct., 30, 1-22.
6. Wu,Y.Q., 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.
7. 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.
8. Goodman,M.F. (1999) On the wagon. DNA polymerase joins 'H-bonds anonymous'. Nat. Biotechnol., 17, 640-641.
9. Service,R. (2000) Creation's Seventh Day. Science, 289, 232-235.
10. Watson,J.D. and Crick,F.H.C. (1953) Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. Nature, 171, 964-967.
11. Collings,M.L, Irvine,B., Tyner,D., Fine,E., Zayati,C., Chang,C., Horn,T., Ahle,D., Detmer,J., Shen,L., Kolberg,J., Bushnell,S., Urdea,M.S. and Ho,D.D. (1997) A branched DNA signal amplification assay for the quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res., 25, 2979-2984.
12. Yu,C.Z., Henry,A.A., Romesberg,F.E. and Schultz,P.G. (2002) Polymerase recognition of unnatural base pairs. Int. Ed. Engl., 41, 3941-3844.
13. Bain,J.D., Chamberlin,A.R., Switzer,C.Y. and Benner,S.A. (1992) Ribosome-mediated incorporation of non-standard amino acids into a peptide through expansion of the genetic code. Nature, 356, 537-539.
14. Horlacher,J., Hottiger,M., Podust,V.N., Hübscher,U. and Benner,S.A. (1995) Expanding the genetic alphabet: recognition by viral and cellular DNA polymerases of nucleosides bearing bases with non-standard hydrogen bonding patterns. Proc. Natl Acad. Sci. USA, 92, 6329-6333.
15. Kiefer,J.R., Mao,C., Braman,J.C. and Beese,L.S. (1998) Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature, 391, 304-307.
16. Hingorani,M.M. and O'Donnell,M. (2000) DNA polymerase structure and mechanisms of action. Current Org. Chem., 4, 887-913.
17. Das,K., Ding,J., Hsiou,Y., Clark,A.D.,Jr, Moereels,H., Koymans,L., Andries,K., Pauwels,R., Janssen,P.A.J., Boyer,P.L., Clark,P., Smith,R.H.,Jr, Kroeger-Smith,M.B., Michejda,C.J., Hughes,S.H. and Arnold,E. (1996) Crystal structure of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181 Cys HIV-1 RT drug-resistant mutant. J. Mol. Biol., 264, 1085-1100.
18. Kohlstaedt,L.A., Wang,J., Friedman,J.M., Rice,P.A. and Steitz,T.A. (1992). Crystal structure at 3.5Å Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor. Science, 256, 1783-1790.
19. Lutz,M.J., Held,H.A., Hottinger,M., Hübscher,U. and Benner,S.A. (1996) Differential discrimination of DNA polymerases 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.
20. Larder,B.A. and Kemp,S.D. (1989). Multiple mutations in HIV-1 reverse transcriptase confer high-level resistance to zidovudine (AZT). Science, 246, 1155-1158.
21. Tantillo,C., Ding,J.P., Jacobomolina,A., Nanni,R.G., Boyer,P.L., Hughes,S.H., Pauwels,R., Andries,K., Janssen,P.A.J. and Arnold,E. (1994) Locations of anti-AIDS drug-binding sites and resistance mutations in the 3-dimensional structure of HIV-1 reverse-transcriptase. Implications for mechanisms of drug-inhibition and resistance. J. Mol. Biol., 243, 369-387.
22. Gu,Z.X., Qing,G., Li,X.G., Parniak,M.A. and Wainberg,M.A. (1992) Novel mutation in the human-immunodeficiency-virus type-1 reverse-transcriptase gene that encodes cross-resistance to 2′,3′-dideoxyinosine and 2′,3′-dideoxycytidine. J. Virol., 66, 7128-7135.
23. Chu,C.K., Wempen,I., Watanabe,K.A. and Fox,J.J. (1976) Nucleosides. 100. General synthesis of pyrimidine C-5 nucleosides related to pseudouridine. Synthesis of 5-(β-D-ribofuranosyl)isocytosine (pseudoisocytosine), 5-(β-D-ribofuranosyl)-2-thiouracil (2-thiopseudouridine) and 5-(β-D-ribofuranosyl)uracil (pseudouridine). J. Org. Chem., 41, 2793-2797.
24. 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.
25. Jurczyk,S.C., Horlacher,J., Devine,K.G., Benner,S.A. and Battersby,T.R. (2000) Synthesis and characterization of oligonucleotides containing 2′-deoxyxanthosine using phosphoramidite chemistry. Helv. Chim. Acta, 83, 1517-1524.
26. VanAerschot,A., Mag,M., Herdewijn,P. and Vanderhaeghe,H. (1989) Double protection of the heterocyclic base of xanthosine and 2′-deoxyxanthosine. Nucl. Nucl., 8, 159-178.
27. Sinha,N.D., Biernat,J. and Köster,H. (1983) Beta-cyanoethyl n,n-dialkylamino/n-morpholinomonochloro phosphoamidites, new phosphitylating agents facilitating ease of deprotection and work-up of synthesized oligonucleotides. Tetrahedron Lett., 24, 5843-5846.
28. 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,,2-benzodioxaphosphorin-4-one. J. Org. Chem., 54, 631-635.
29. Boyer,P.L., Tantillo,C., Jacobo-Molina,A., Nanni,R.G., Ding,J.P., Arnold,E. and Hughes,S.L. (1994) Sensitivity of wild-type human-immunodeficiency-virus type-1 reverse-transcriptase to dideoxynucleotides depends on template length - the sensitivity of drug-resistant mutants does not. Proc. Natl Acad. Sci. USA, 91, 4882-4886.
30. Bryant,F.R., Johnson,K.A. and Benkovic,S.J. (1983). Elementary steps in the DNA polymerase I reaction pathway. Biochemistry, 22, 3537-3546.
31. Kuchta,R.D. (1996). Isotopic assays of viral polymerases and related proteins. Methods Enzymol., 275, 241-257.
32. Reardon,J.E. and Miller,W.H. (1990). Human immunodeficiency virus reverse transcriptase. J. Biol. Chem., 265, 20302-20307.
33. Stahlhut,M.W. and Olsen,D.B. (1996). Expression and purification of retroviral HIV-1 Reverse Transcriptase. Methods Enzymol., 275, 122-132.
34. Williams,K.P. and Bartel,D.P. (1995). PCR products with strands of unequal length. Nucleic Acids Res., 23, 4220-4221.
35. Roy,K.B. and Miles,H.T. (1983) Tautomerism and ionization of xanthosine. Nucl. Nucl., 2, 231-242.
36. Krauch,T. (1989) Ein neues Basenpaar Fur den genetischen Code. PhD Dissertation, ETH No. 8940, Swiss Federal Institute of Technology, Zurich, Switzerland.
37. Arnold,F.H. (1998). Design by directed evolution. Acc. Chem. Res., 31, 125-131.
38. Kinchington,P.R., Araullo-Cruz,T., Vergnes,J.P., Yates,K. and Gordon,Y.J. (2002) Sequence changes in the human adenovirus type 5 DNA polymerase associated with resistance to the broad spectrum antiviral cidofovir. Antivir. Res., 56, 73-84.
39. Seigneres,B., Pichoud,C., Ahmed,S.S., Hantz,O., Trepo,C. and Zoulim,F. (2000) Evolution of hepatitis B virus polymerase gene sequence during famciclovir therapy for chronic hepatitis B. J. Infect. Dis., 184, 1221-1233.
40. Chou,S.W., Miner,R.C. and Drew,W.L. (2000) A deletion mutation in region V of the cytomegalovirus DNA polymerase sequence confers multidrug resistance. J. Infect. Dis., 182, 1765-1768.
41. Witkin,E.M. and Roegner-Maniscalco,V. (1992). Overproduction of DnaE Protein (a-subunit of DNA polymerase III) restores viability in a conditional inviable Escherichia coli strain deficient in DNA polymerase I. J. Bacteriol., 174, 4166-4168.
42. Kim,B. and Loeb,L. (1995) Human immunodeficiency virus reverse transcriptase substitutes for DNA polymerase I in Escherichia coli. Proc. Natl Acad. Sci. USA, 92, 684-688.