Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1995 Jan 11;23(1):123–129. doi: 10.1093/nar/23.1.123

On the mechanism of preferential incorporation of dAMP at abasic sites in translesional DNA synthesis. Role of proofreading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site.

H Ide 1, H Murayama 1, S Sakamoto 1, K Makino 1, K Honda 1, H Nakamuta 1, M Sasaki 1, N Sugimoto 1
PMCID: PMC306639  PMID: 7870577

Abstract

DNA polymerase preferentially incorporate dAMP opposite abasic sites (A-rule). The mechanism of the A-rule can be studied by analyzing three dissected stages of the reaction including (i) initial nucleotide insertion, (ii) proofreading excision of the inserted nucleotide and (iii) extension of the nascent primer terminus. To assess the role of the stage (ii) in the A-rule, kinetic parameters of the proofreading excision of primer terminus nucleotides opposite abasic sites were determined using E.coli DNA polymerase I Klenow fragment. The relative efficiency of the excision (Vmax/Km) revealed that removal of A was the least favored of the four nucleotides, but the differences in the efficiencies between excision of A and the other nucleotides was less than 2-fold. In addition, in an attempt to reconcile kinetic data associated with the stage (i) or (ii), the differences in free energy changes (delta delta G degrees) for the formation of model template-primer termini containing XN pairs (X = abasic site, N = A, G, C or T) were determined by temperature dependent UV-melting measurements. The order of delta delta G degrees was XG > XA = XC > or = XT, with delta delta G degrees being 0.5 kcal/mol for the most stable XG and the least stable XT. Based on these data, the role of the stage (ii) and energetic aspects of the A-rule are discussed.

Full text

PDF
123

Images in this article

125Image
on p.125

Selected References

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

  1. Bertrand J. R., Vasseur J. J., Rayner B., Imbach J. L., Paoletti J., Paoletti C., Malvy C. Synthesis, thermal stability and reactivity towards 9-aminoellipticine of double-stranded oligonucleotides containing a true abasic site. Nucleic Acids Res. 1989 Dec 25;17(24):10307–10319. doi: 10.1093/nar/17.24.10307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boiteux S., Laval J. Coding properties of poly(deoxycytidylic acid) templates containing uracil or apyrimidinic sites: in vitro modulation of mutagenesis by deoxyribonucleic acid repair enzymes. Biochemistry. 1982 Dec 21;21(26):6746–6751. doi: 10.1021/bi00269a020. [DOI] [PubMed] [Google Scholar]
  3. Brenowitz S., Kwack S., Goodman M. F., O'Donnell M., Echols H. Specificity and enzymatic mechanism of the editing exonuclease of Escherichia coli DNA polymerase III. J Biol Chem. 1991 Apr 25;266(12):7888–7892. [PubMed] [Google Scholar]
  4. Cai H., Bloom L. B., Eritja R., Goodman M. F. Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase. J Biol Chem. 1993 Nov 5;268(31):23567–23572. [PubMed] [Google Scholar]
  5. Derbyshire V., Freemont P. S., Sanderson M. R., Beese L., Friedman J. M., Joyce C. M., Steitz T. A. Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I. Science. 1988 Apr 8;240(4849):199–201. doi: 10.1126/science.2832946. [DOI] [PubMed] [Google Scholar]
  6. Donlin M. J., Patel S. S., Johnson K. A. Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry. 1991 Jan 15;30(2):538–546. doi: 10.1021/bi00216a031. [DOI] [PubMed] [Google Scholar]
  7. Hevroni D., Livneh Z. Bypass and termination at apurinic sites during replication of single-stranded DNA in vitro: a model for apurinic site mutagenesis. Proc Natl Acad Sci U S A. 1988 Jul;85(14):5046–5050. doi: 10.1073/pnas.85.14.5046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ide H., Murayama H., Murakami A., Morii T., Makino K. Effects of base damages on DNA replication--mechanism of preferential purine nucleotide insertion opposite abasic site in template DNA. Nucleic Acids Symp Ser. 1992;(27):167–168. [PubMed] [Google Scholar]
  9. Ide H., Okagami M., Murayama H., Kimura Y., Makino K. Synthesis and characterization of oligonucleotides containing the alpha-anomer of deoxyadenosine to study its influence on DNA replication. Biochem Mol Biol Int. 1993 Nov;31(3):485–491. [PubMed] [Google Scholar]
  10. Ide H., Tedzuka K., Shimzu H., Kimura Y., Purmal A. A., Wallace S. S., Kow Y. W. Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry. 1994 Jun 28;33(25):7842–7847. doi: 10.1021/bi00191a011. [DOI] [PubMed] [Google Scholar]
  11. Kamiya H., Suzuki M., Komatsu Y., Miura H., Kikuchi K., Sakaguchi T., Murata N., Masutani C., Hanaoka F., Ohtsuka E. An abasic site analogue activates a c-Ha-ras gene by a point mutation at modified and adjacent positions. Nucleic Acids Res. 1992 Sep 11;20(17):4409–4415. doi: 10.1093/nar/20.17.4409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Klinedinst D. K., Drinkwater N. R. Mutagenesis by apurinic sites in normal and ataxia telangiectasia human lymphoblastoid cells. Mol Carcinog. 1992;6(1):32–42. doi: 10.1002/mc.2940060107. [DOI] [PubMed] [Google Scholar]
  13. Kuchta R. D., Benkovic P., Benkovic S. J. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry. 1988 Sep 6;27(18):6716–6725. doi: 10.1021/bi00418a012. [DOI] [PubMed] [Google Scholar]
  14. Kunkel T. A. Mutational specificity of depurination. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1494–1498. doi: 10.1073/pnas.81.5.1494. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kunz B. A., Henson E. S., Roche H., Ramotar D., Nunoshiba T., Demple B. Specificity of the mutator caused by deletion of the yeast structural gene (APN1) for the major apurinic endonuclease. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8165–8169. doi: 10.1073/pnas.91.17.8165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Laspia M. F., Wallace S. S. Excision repair of thymine glycols, urea residues, and apurinic sites in Escherichia coli. J Bacteriol. 1988 Aug;170(8):3359–3366. doi: 10.1128/jb.170.8.3359-3366.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lawrence C. W., Borden A., Banerjee S. K., LeClerc J. E. Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vector. Nucleic Acids Res. 1990 Apr 25;18(8):2153–2157. doi: 10.1093/nar/18.8.2153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lindahl T., Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry. 1972 Sep 12;11(19):3610–3618. doi: 10.1021/bi00769a018. [DOI] [PubMed] [Google Scholar]
  19. Martin F. H., Uhlenbeck O. C., Doty P. Self-complementary oligoribonucleotides: adenylic acid-uridylic acid block copolymers. J Mol Biol. 1971 Apr 28;57(2):201–215. doi: 10.1016/0022-2836(71)90341-x. [DOI] [PubMed] [Google Scholar]
  20. Miller J. H., Low K. B. Specificity of mutagenesis resulting from the induction of the SOS system in the absence of mutagenic treatment. Cell. 1984 Jun;37(2):675–682. doi: 10.1016/0092-8674(84)90400-8. [DOI] [PubMed] [Google Scholar]
  21. Millican T. A., Mock G. A., Chauncey M. A., Patel T. P., Eaton M. A., Gunning J., Cutbush S. D., Neidle S., Mann J. Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: a possible approach to the problem of mixed base oligodeoxynucleotide synthesis. Nucleic Acids Res. 1984 Oct 11;12(19):7435–7453. doi: 10.1093/nar/12.19.7435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Neto J. B., Gentil A., Cabral R. E., Sarasin A. Mutation spectrum of heat-induced abasic sites on a single-stranded shuttle vector replicated in mammalian cells. J Biol Chem. 1992 Sep 25;267(27):19718–19723. [PubMed] [Google Scholar]
  23. Ng L., Weiss S. J., Fisher P. A. Recognition and binding of template-primers containing defined abasic sites by Drosophila DNA polymerase alpha holoenzyme. J Biol Chem. 1989 Aug 5;264(22):13018–13023. [PubMed] [Google Scholar]
  24. Osborne M., Merrifield K. Depurination of benzo[a]pyrene-diolepoxide treated DNA. Chem Biol Interact. 1985 Feb-Apr;53(1-2):183–195. doi: 10.1016/s0009-2797(85)80095-8. [DOI] [PubMed] [Google Scholar]
  25. Petersheim M., Turner D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):256–263. doi: 10.1021/bi00271a004. [DOI] [PubMed] [Google Scholar]
  26. Petruska J., Goodman M. F., Boosalis M. S., Sowers L. C., Cheong C., Tinoco I., Jr Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6252–6256. doi: 10.1073/pnas.85.17.6252. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Petruska J., Sowers L. C., Goodman M. F. Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc Natl Acad Sci U S A. 1986 Mar;83(6):1559–1562. doi: 10.1073/pnas.83.6.1559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Puglisi J. D., Tinoco I., Jr Absorbance melting curves of RNA. Methods Enzymol. 1989;180:304–325. doi: 10.1016/0076-6879(89)80108-9. [DOI] [PubMed] [Google Scholar]
  29. Randall S. K., Eritja R., Kaplan B. E., Petruska J., Goodman M. F. Nucleotide insertion kinetics opposite abasic lesions in DNA. J Biol Chem. 1987 May 15;262(14):6864–6870. [PubMed] [Google Scholar]
  30. Sagher D., Strauss B. Insertion of nucleotides opposite apurinic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides. Biochemistry. 1983 Sep 13;22(19):4518–4526. doi: 10.1021/bi00288a026. [DOI] [PubMed] [Google Scholar]
  31. Schaaper R. M., Kunkel T. A., Loeb L. A. Infidelity of DNA synthesis associated with bypass of apurinic sites. Proc Natl Acad Sci U S A. 1983 Jan;80(2):487–491. doi: 10.1073/pnas.80.2.487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schaaper R. M., Loeb L. A. Depurination causes mutations in SOS-induced cells. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1773–1777. doi: 10.1073/pnas.78.3.1773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Singer B. All oxygens in nucleic acids react with carcinogenic ethylating agents. Nature. 1976 Nov 25;264(5584):333–339. doi: 10.1038/264333a0. [DOI] [PubMed] [Google Scholar]
  34. Strauss B. S. The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions? Bioessays. 1991 Feb;13(2):79–84. doi: 10.1002/bies.950130206. [DOI] [PubMed] [Google Scholar]
  35. Takeshita M., Chang C. N., Johnson F., Will S., Grollman A. P. Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J Biol Chem. 1987 Jul 25;262(21):10171–10179. [PubMed] [Google Scholar]
  36. Tarpley W. G., Miller J. A., Miller E. C. Rapid release of carcinogen-guanine adducts from DNA after reaction with N-acetoxy-2-acetylaminofluorene or N-benzoyloxy-N-methyl-4-aminoazobenzene. Carcinogenesis. 1982;3(1):81–88. doi: 10.1093/carcin/3.1.81. [DOI] [PubMed] [Google Scholar]
  37. Turner D. H., Sugimoto N., Freier S. M. RNA structure prediction. Annu Rev Biophys Biophys Chem. 1988;17:167–192. doi: 10.1146/annurev.bb.17.060188.001123. [DOI] [PubMed] [Google Scholar]
  38. Vesnaver G., Chang C. N., Eisenberg M., Grollman A. P., Breslauer K. J. Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data. Proc Natl Acad Sci U S A. 1989 May;86(10):3614–3618. doi: 10.1073/pnas.86.10.3614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Wallace S. S. AP endonucleases and DNA glycosylases that recognize oxidative DNA damage. Environ Mol Mutagen. 1988;12(4):431–477. doi: 10.1002/em.2860120411. [DOI] [PubMed] [Google Scholar]

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

RESOURCES