Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 May 12;14(9):3773–3790. doi: 10.1093/nar/14.9.3773

Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies.

H Werntges, G Steger, D Riesner, H J Fritz
PMCID: PMC339814  PMID: 3714496

Abstract

The helix-coil transitions of the 16 octadecameric DNA duplexes dCGTCGTTTXACAACGTCG X dCGACGTTGTX1AAACGACG with A, T, G, and C for X and X1 were measured by UV-absorption. This sequence was taken from former studies of in vivo determination of efficiencies of mismatch repair (Kramer, Kramer, and Fritz (1984) Cell 38, 879-887). The thermodynamic parameters for double strand and mismatch formation have been obtained by evaluating the partition function of a stack model which allowed for loop formation. As a result the mismatches could be classified into wobble base pairs (T/G, G/G, C/A, A/A, A/G), open base pairs, i.e. permanent loops (T/T, C/T, T/C, C/C), and intermediate or weak base pairs (G/T, A/C, G/A). There is no correlation between Tm and the biological repair efficiency of X/X1. The structure classes, however, as described above show a close correlation: Open base pairs show the lowest repair efficiencies, whereas mismatches with high repair efficiency always belong to the structural class of wobble base pairs. Because of the palindromic nearest neighbors of the variation site X/X1, the influence of next-nearest neighbor interactions could be detected and be estimated to about 1 kJ/mol for one stack.

Full text

PDF
3776

Selected References

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

  1. Brown T., Kennard O., Kneale G., Rabinovich D. High-resolution structure of a DNA helix containing mismatched base pairs. Nature. 1985 Jun 13;315(6020):604–606. doi: 10.1038/315604a0. [DOI] [PubMed] [Google Scholar]
  2. Chuprina V. P., Poltev V. I. Possible conformations of double-helical polynucleotides containing incorrect base pairs. Nucleic Acids Res. 1983 Aug 11;11(15):5205–5222. doi: 10.1093/nar/11.15.5205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dohet C., Wagner R., Radman M. Repair of defined single base-pair mismatches in Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jan;82(2):503–505. doi: 10.1073/pnas.82.2.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fersht A. R., Knill-Jones J. W. DNA polymerase accuracy and spontaneous mutation rates: frequencies of purine.purine, purine.pyrimidine, and pyrimidine.pyrimidine mismatches during DNA replication. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4251–4255. doi: 10.1073/pnas.78.7.4251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fersht A. R., Knill-Jones J. W., Tsui W. C. Kinetic basis of spontaneous mutation. Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J Mol Biol. 1982 Mar 25;156(1):37–51. doi: 10.1016/0022-2836(82)90457-0. [DOI] [PubMed] [Google Scholar]
  6. Fritz H. J., Belagaje R., Brown E. L., Fritz R. H., Jones R. A., Lees R. G., Khorana H. G. High-pressure liquid chromatography in polynucleotide synthesis. Biochemistry. 1978 Apr 4;17(7):1257–1267. doi: 10.1021/bi00600a020. [DOI] [PubMed] [Google Scholar]
  7. Gotoh O. Prediction of melting profiles and local helix stability for sequenced DNA. Adv Biophys. 1983;16:1–52. doi: 10.1016/0065-227x(83)90007-2. [DOI] [PubMed] [Google Scholar]
  8. Gralla J., Crothers D. M. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. J Mol Biol. 1973 Aug 5;78(2):301–319. doi: 10.1016/0022-2836(73)90118-6. [DOI] [PubMed] [Google Scholar]
  9. Kan L. S., Chandrasegaran S., Pulford S. M., Miller P. S. Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4263–4265. doi: 10.1073/pnas.80.14.4263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Keepers J. W., Schmidt P., James T. L., Kollman P. A. Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG). Biopolymers. 1984 Dec;23(12):2901–2929. doi: 10.1002/bip.360231214. [DOI] [PubMed] [Google Scholar]
  11. Kramer B., Kramer W., Fritz H. J. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell. 1984 Oct;38(3):879–887. doi: 10.1016/0092-8674(84)90283-6. [DOI] [PubMed] [Google Scholar]
  12. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  13. Patel D. J., Kozlowski S. A., Ikuta S., Itakura K. Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA X dC mismatch site. Biochemistry. 1984 Jul 3;23(14):3218–3226. doi: 10.1021/bi00309a016. [DOI] [PubMed] [Google Scholar]
  14. Poland D. Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations. Biopolymers. 1974;13(9):1859–1871. doi: 10.1002/bip.1974.360130916. [DOI] [PubMed] [Google Scholar]
  15. Pukkila P. J., Peterson J., Herman G., Modrich P., Meselson M. Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli. Genetics. 1983 Aug;104(4):571–582. doi: 10.1093/genetics/104.4.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Randles J. W., Steger G., Riesner D. Structural transitions in viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and Solanum nodiflorum mottle virus. Nucleic Acids Res. 1982 Sep 25;10(18):5569–5586. doi: 10.1093/nar/10.18.5569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Schumacher J., Randles J. W., Riesner D. A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids. Anal Biochem. 1983 Dec;135(2):288–295. doi: 10.1016/0003-2697(83)90685-1. [DOI] [PubMed] [Google Scholar]
  18. Topal M. D., Fresco J. R. Base pairing and fidelity in codon-anticodon interaction. Nature. 1976 Sep 23;263(5575):289–293. doi: 10.1038/263289a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES