Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Apr 1;24(7):1308–1313. doi: 10.1093/nar/24.7.1308

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.

M J Lutz 1, H A Held 1, M Hottiger 1, U Hübscher 1, S A Benner 1
PMCID: PMC145792  PMID: 8614635

Abstract

Mammalian DNA polymerases alpha and epsilon, the Klenow fragment of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase (RT) were examined for their ability to incorporate components of an expanded genetic alphabet in different forms. Experiments were performed with templates containing 2'-deoxyxanthosine (dX) or 2'-deoxy-7-deazaxanthosine (c7dX), both able to adopt a hydrogen bonding acceptor-donor-acceptor pattern on a purine nucleus (puADA). Thus these heterocycles are able to form a non-standard nucleobase pair with 2,4-diaminopyrimidine (pyDAD) that fits the Watson-Crick geometry, but is joined by a non-standard hydrogen bonding pattern. HIV-1 RT incorporated d(pyDAD)TP opposite dX with a high efficiency that was largely independent of pH. Specific incorporation opposite c7dX was significantly lower and also independent of pH. Mammalian DNA polymerases alpha and epsilon from calf thymus and the Klenow fragment from E. coli DNA polymerase I failed to incorporate d(pyDAD)TP opposite c7dX.

Full Text

The Full Text of this article is available as a PDF (110.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  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. Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. Cold Spring Harb Symp Quant Biol. 1987;52:53–63. doi: 10.1101/sqb.1987.052.01.009. [DOI] [PubMed] [Google Scholar]
  2. Chu C. K., Reichman U., Watanabe K. A., Fox J. J. Nucleosides. 104. Synthesis of 4-amino-5-(D-ribofuranosyl)pyrimidine C-nucleosides from 2-(2,3-O-isopropylidene-5-O-trityl-D-ribofuranosyl)acetonitrile. J Org Chem. 1977 Feb 18;42(4):711–714. doi: 10.1021/jo00424a030. [DOI] [PubMed] [Google Scholar]
  3. Hafkemeyer P., Ferrari E., Brecher J., Hübscher U. The p15 carboxyl-terminal proteolysis product of the human immunodeficiency virus type 1 reverse transcriptase p66 has DNA polymerase activity. Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5262–5266. doi: 10.1073/pnas.88.12.5262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hendler S., Fürer E., Srinivasan P. R. Synthesis and chemical properties of monomers and polymers containing 7-methylguanine and an investigation of their substrate or template properties for bacterial deoxyribonucleic acid or ribonucleic acid polymerases. Biochemistry. 1970 Oct 13;9(21):4141–4153. doi: 10.1021/bi00823a017. [DOI] [PubMed] [Google Scholar]
  5. 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. 1995 Jul 3;92(14):6329–6333. doi: 10.1073/pnas.92.14.6329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. McConlogue L., Brow M. A., Innis M. A. Structure-independent DNA amplification by PCR using 7-deaza-2'-deoxyguanosine. Nucleic Acids Res. 1988 Oct 25;16(20):9869–9869. doi: 10.1093/nar/16.20.9869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Milligan J. F., Krawczyk S. H., Wadwani S., Matteucci M. D. An anti-parallel triple helix motif with oligodeoxynucleotides containing 2'-deoxyguanosine and 7-deaza-2'-deoxyxanthosine. Nucleic Acids Res. 1993 Jan 25;21(2):327–333. doi: 10.1093/nar/21.2.327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Mizusawa S., Nishimura S., Seela F. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucleic Acids Res. 1986 Feb 11;14(3):1319–1324. doi: 10.1093/nar/14.3.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Pelletier H., Sawaya M. R., Kumar A., Wilson S. H., Kraut J. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science. 1994 Jun 24;264(5167):1891–1903. [PubMed] [Google Scholar]
  10. 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. 1990 Jan 4;343(6253):33–37. doi: 10.1038/343033a0. [DOI] [PubMed] [Google Scholar]
  11. Piccirilli J. A., Moroney S. E., Benner S. A. A C-nucleotide base pair: methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA polymerase. Biochemistry. 1991 Oct 22;30(42):10350–10356. doi: 10.1021/bi00106a037. [DOI] [PubMed] [Google Scholar]
  12. Pochon F., Michelson A. M. Polynucleotides. VI. Interaction between polyguanylic acid and polycytidylic acid. Proc Natl Acad Sci U S A. 1965 Jun;53(6):1425–1430. doi: 10.1073/pnas.53.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Porter K. W., Tomasz J., Huang F., Sood A., Shaw B. R. N7-cyanoborane-2'-deoxyguanosine 5'-triphosphate is a good substrate for DNA polymerase. Biochemistry. 1995 Sep 19;34(37):11963–11969. doi: 10.1021/bi00037a038. [DOI] [PubMed] [Google Scholar]
  14. Sepiol J., Kazimierczuk Z., Shugar D. Tautomerism of isoguanosine and solvent-induced keto-enol equilibrium. Z Naturforsch C. 1976 Jul-Aug;31(7-8):361–370. doi: 10.1515/znc-1976-7-803. [DOI] [PubMed] [Google Scholar]
  15. Steitz T. A., Smerdon S. J., Jäger J., Joyce C. M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science. 1994 Dec 23;266(5193):2022–2025. doi: 10.1126/science.7528445. [DOI] [PubMed] [Google Scholar]
  16. Switzer C. Y., Moroney S. E., Benner S. A. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Biochemistry. 1993 Oct 5;32(39):10489–10496. doi: 10.1021/bi00090a027. [DOI] [PubMed] [Google Scholar]
  17. WATSON J. D., CRICK F. H. Genetical implications of the structure of deoxyribonucleic acid. Nature. 1953 May 30;171(4361):964–967. doi: 10.1038/171964b0. [DOI] [PubMed] [Google Scholar]
  18. Weiser T., Gassmann M., Thömmes P., Ferrari E., Hafkemeyer P., Hübscher U. Biochemical and functional comparison of DNA polymerases alpha, delta, and epsilon from calf thymus. J Biol Chem. 1991 Jun 5;266(16):10420–10428. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES