Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1989 May;86(10):3614–3618. doi: 10.1073/pnas.86.10.3614

Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data.

G Vesnaver 1, C N Chang 1, M Eisenberg 1, A P Grollman 1, K J Breslauer 1
PMCID: PMC287188  PMID: 2726738

Abstract

We report a complete thermodynamic characterization of the impact of abasic and anucleosidic lesions on the stability, conformation, and melting behavior of a DNA duplex. The requisite thermodynamic data were obtained by using a combination of spectroscopic and calorimetric techniques to investigate helix-to-coil transitions in a family of DNA duplexes of the form d(CGCATGAGTACGC).d(GCGTACXCATGCG), where X corresponds to a thymidine residue in the parent Watson-Crick duplex and to an abasic or anucleosidic site in the modified duplexes. The data derived from these studies reveal that incorporation of an abasic site into a DNA duplex dramatically reduces the duplex stability, transition enthalpy, and transition entropy. The magnitudes of these lesion-induced effects are greater than one would expect based on simple nearest-neighbor considerations. Nearly identical thermodynamic data are obtained when the modified duplex contains an anucleosidic site rather than an abasic site. This observation suggests that the thermodynamic impact of these lesions primarily results from removal of the base rather than the sugar ring. Significantly, the melting cooperativities of the abasic and anucleosidic derivatives are identical with each other and with the corresponding unmodified Watson-Crick parent duplex. This result suggests that the phosphodiester backbone, rather than the base-sugar network, serves as the primary propagation path for the communication of cooperative melting effects. We propose molecular interpretations for the thermodynamic data based on the structural picture that has emerged from the NMR studies of Patel and coworkers on the same family of modified and unmodified DNA duplexes [Kalnik, M.W., Chang, C.-N., Grollman, A.P. & Patel, D.J. (1988) Biochemistry 27, 924-931].

Full text

PDF
3614

Selected References

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

  1. Arnold F. H., Wolk S., Cruz P., Tinoco I., Jr Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2. Biochemistry. 1987 Jun 30;26(13):4068–4075. doi: 10.1021/bi00387a049. [DOI] [PubMed] [Google Scholar]
  2. Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cuniasse P., Sowers L. C., Eritja R., Kaplan B., Goodman M. F., Cognet J. A., LeBret M., Guschlbauer W., Fazakerley G. V. An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Nucleic Acids Res. 1987 Oct 12;15(19):8003–8022. doi: 10.1093/nar/15.19.8003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kalnik M. W., Chang C. N., Grollman A. P., Patel D. J. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose. Biochemistry. 1988 Feb 9;27(3):924–931. doi: 10.1021/bi00403a013. [DOI] [PubMed] [Google Scholar]
  5. Lindahl T. DNA repair enzymes. Annu Rev Biochem. 1982;51:61–87. doi: 10.1146/annurev.bi.51.070182.000425. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Loeb L. A., Kunkel T. A. Fidelity of DNA synthesis. Annu Rev Biochem. 1982;51:429–457. doi: 10.1146/annurev.bi.51.070182.002241. [DOI] [PubMed] [Google Scholar]
  8. Loeb L. A., Preston B. D. Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet. 1986;20:201–230. doi: 10.1146/annurev.ge.20.120186.001221. [DOI] [PubMed] [Google Scholar]
  9. Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987 Sep;26(9):1601–1620. doi: 10.1002/bip.360260911. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Dallas J., Itakura K., Breslauer K. J. Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry. 1982 Feb 2;21(3):437–444. doi: 10.1021/bi00532a003. [DOI] [PubMed] [Google Scholar]
  12. Raap J., Dreef C. E., van der Marel G. A., van Boom J. H., Hilbers C. W. Synthesis and proton-NMR studies of oligonucleotides containing an apurinic (AP) site. J Biomol Struct Dyn. 1987 Oct;5(2):219–247. doi: 10.1080/07391102.1987.10506391. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. Seela F., Kaiser K. Oligodeoxyribonucleotides containing 1,3-propanediol as nucleoside substitute. Nucleic Acids Res. 1987 Apr 10;15(7):3113–3129. doi: 10.1093/nar/15.7.3113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Weiss B., Grossman L. Phosphodiesterases involved in DNA repair. Adv Enzymol Relat Areas Mol Biol. 1987;60:1–34. doi: 10.1002/9780470123065.ch1. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES