The pH dependent configurations of the C.A mispair in DMA

Y. Boulard, J. A H Cognet, J. Gabarro-Arpa, M. Le Bret, Lawrence Sowers, G. V. Fazakerley

Research output: Contribution to journalArticle

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Abstract

The structure of the cytosine-adenine mispair in a 7 base pair duplex has been investigated by proton NMR spectroscopy. At low pH, the predominant structure is protonated on the A residue and assumes a wobble conformation consistent with previous findings. The C residue of the mispair is found in a C2′-C3′ endo eqilibrium. This is confirmed by molecular dynamics calculations which suggest that the conformation of the protonated wobble is flexible and not as rigid as a normal base pair. As the solution pH is raised, a structural transition is observed with an apparent pK of 7.54 at 23°C. At higher pH the predominant structure is one in which both the C and A residues are intrahelical. Evidence is presented that this structure corresponds to a reverse wobble in which the two bases are held together by one hydrogen bond. This structure is much less stable than the protonated form and even at low temperature single strands are observed in slow exchange with the neutral duplex form.

Original languageEnglish (US)
Pages (from-to)1933-1941
Number of pages9
JournalNucleic Acids Research
Volume20
Issue number8
StatePublished - 1992
Externally publishedYes

Fingerprint

Dynamic mechanical analysis
Conformations
Base Pairing
Configuration
Dependent
Cytosine
Adenine
Nuclear magnetic resonance spectroscopy
Molecular dynamics
Protons
Hydrogen bonds
Conformation
Molecular Dynamics Simulation
Hydrogen
Magnetic Resonance Spectroscopy
Normal Basis
Hydrogen Bonds
Temperature
Molecular Dynamics
Spectroscopy

ASJC Scopus subject areas

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

Cite this

Boulard, Y., Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., Sowers, L., & Fazakerley, G. V. (1992). The pH dependent configurations of the C.A mispair in DMA. Nucleic Acids Research, 20(8), 1933-1941.

The pH dependent configurations of the C.A mispair in DMA. / Boulard, Y.; Cognet, J. A H; Gabarro-Arpa, J.; Le Bret, M.; Sowers, Lawrence; Fazakerley, G. V.

In: Nucleic Acids Research, Vol. 20, No. 8, 1992, p. 1933-1941.

Research output: Contribution to journalArticle

Boulard, Y, Cognet, JAH, Gabarro-Arpa, J, Le Bret, M, Sowers, L & Fazakerley, GV 1992, 'The pH dependent configurations of the C.A mispair in DMA', Nucleic Acids Research, vol. 20, no. 8, pp. 1933-1941.
Boulard Y, Cognet JAH, Gabarro-Arpa J, Le Bret M, Sowers L, Fazakerley GV. The pH dependent configurations of the C.A mispair in DMA. Nucleic Acids Research. 1992;20(8):1933-1941.
Boulard, Y. ; Cognet, J. A H ; Gabarro-Arpa, J. ; Le Bret, M. ; Sowers, Lawrence ; Fazakerley, G. V. / The pH dependent configurations of the C.A mispair in DMA. In: Nucleic Acids Research. 1992 ; Vol. 20, No. 8. pp. 1933-1941.
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AB - The structure of the cytosine-adenine mispair in a 7 base pair duplex has been investigated by proton NMR spectroscopy. At low pH, the predominant structure is protonated on the A residue and assumes a wobble conformation consistent with previous findings. The C residue of the mispair is found in a C2′-C3′ endo eqilibrium. This is confirmed by molecular dynamics calculations which suggest that the conformation of the protonated wobble is flexible and not as rigid as a normal base pair. As the solution pH is raised, a structural transition is observed with an apparent pK of 7.54 at 23°C. At higher pH the predominant structure is one in which both the C and A residues are intrahelical. Evidence is presented that this structure corresponds to a reverse wobble in which the two bases are held together by one hydrogen bond. This structure is much less stable than the protonated form and even at low temperature single strands are observed in slow exchange with the neutral duplex form.

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