An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations

Ph Cuniasse, Lawrence Sowers, R. Eritja, B. Kaplan, M. F. Goodman, J. A H Cognet, M. Lebret, W. Guschlbauer, G. V. Fazakerley

Research output: Contribution to journalArticle

99 Citations (Scopus)

Abstract

We have determined the three-dimensional structure of a non-self complementary nonanucleotide duplex which contains an abasic (apyrimi-dinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assiggned by NOESY, COSY and 2DQF spectra in D2O and H2O. We have measured the initial slope of buildup of NOEs in NOESY spectra at very short mixing times (25 to 50 ms), and -from these were able to establish interproton distances for the central part of the duplex. We propose a different strategy for proton-proton distance determinations which takes into account the observed variations in correlation times for particular proton-proton vectors. A set of 31 measured interproton distances was incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. Two structures were obtained which retain all aspects of a classical B DNA in which the unpaired adenine and the abastic deoxyribose lie inside the helix. We observe that the non-hydrogen bonded adenine is held well in the helix, the Tm of this base being the same as that of the A.T base pairs in the same duplex.

Original languageEnglish (US)
Pages (from-to)8003-8022
Number of pages20
JournalNucleic Acids Research
Volume15
Issue number19
DOIs
StatePublished - Oct 12 1987
Externally publishedYes

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Molecular Mechanics
Molecular mechanics
Mechanics
Conformation
Conformations
Protons
DNA
Nuclear magnetic resonance
Helix
Deoxyribose
Adenine
Mixing Time
Adenosine
Sugars
Slope
Refinement
Oligonucleotides
Three-dimensional
Molecular Structure
Base Pairing

ASJC Scopus subject areas

  • Statistics, Probability and Uncertainty
  • Applied Mathematics
  • Health, Toxicology and Mutagenesis
  • Toxicology
  • Genetics(clinical)
  • Genetics

Cite this

Cuniasse, P., Sowers, L., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., ... Fazakerley, G. V. (1987). An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Nucleic Acids Research, 15(19), 8003-8022. https://doi.org/10.1093/nar/15.19.8003

An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. / Cuniasse, Ph; Sowers, Lawrence; Eritja, R.; Kaplan, B.; Goodman, M. F.; Cognet, J. A H; Lebret, M.; Guschlbauer, W.; Fazakerley, G. V.

In: Nucleic Acids Research, Vol. 15, No. 19, 12.10.1987, p. 8003-8022.

Research output: Contribution to journalArticle

Cuniasse, P, Sowers, L, Eritja, R, Kaplan, B, Goodman, MF, Cognet, JAH, Lebret, M, Guschlbauer, W & Fazakerley, GV 1987, 'An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations', Nucleic Acids Research, vol. 15, no. 19, pp. 8003-8022. https://doi.org/10.1093/nar/15.19.8003
Cuniasse, Ph ; Sowers, Lawrence ; Eritja, R. ; Kaplan, B. ; Goodman, M. F. ; Cognet, J. A H ; Lebret, M. ; Guschlbauer, W. ; Fazakerley, G. V. / An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. In: Nucleic Acids Research. 1987 ; Vol. 15, No. 19. pp. 8003-8022.
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AB - We have determined the three-dimensional structure of a non-self complementary nonanucleotide duplex which contains an abasic (apyrimi-dinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assiggned by NOESY, COSY and 2DQF spectra in D2O and H2O. We have measured the initial slope of buildup of NOEs in NOESY spectra at very short mixing times (25 to 50 ms), and -from these were able to establish interproton distances for the central part of the duplex. We propose a different strategy for proton-proton distance determinations which takes into account the observed variations in correlation times for particular proton-proton vectors. A set of 31 measured interproton distances was incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. Two structures were obtained which retain all aspects of a classical B DNA in which the unpaired adenine and the abastic deoxyribose lie inside the helix. We observe that the non-hydrogen bonded adenine is held well in the helix, the Tm of this base being the same as that of the A.T base pairs in the same duplex.

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