Abasic frameshift 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. Le Bret, W. Guschlbauer, G. V. Fazakerley

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

We have determined the three-dimensional structure of a non-self-complementary oligodeoxynucleotide duplex that contains a model abasic site. The duplex contains six GC base pairs plus the abasic site at the center of one strand and corresponds to an abasic frameshift. Two-dimensional NMR studies on the nonexchangeable protons show that the guanine bases on either side of the abasic site are stacked over each other and that the abasic site is rotated out of the helix. Close proton-proton interactions are observed between the H4′ proton of the abasic site and sugar protons of the guanosine in the 5′ direction, which allows the position of the free sugar to be well-defined. NOE buildup curves from NOESY spectra recorded at very short mixing times were used to calculate a set of interproton distances. This data set was incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. Two conformations that differ in the sugar conformation of the guanosine next to the abasic site in the 3′ direction were necessary to fit all the NMR data. One of these two conformations could only be stabilized by addition of counterions at specific sites.

Original languageEnglish (US)
Pages (from-to)2018-2026
Number of pages9
JournalBiochemistry
Volume28
Issue number5
StatePublished - 1989
Externally publishedYes

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Molecular mechanics
Mechanics
Conformations
Protons
Nuclear magnetic resonance
Sugars
DNA
Guanosine
Oligodeoxyribonucleotides
Guanine
Molecular Structure
Oligonucleotides
Base Pairing

ASJC Scopus subject areas

  • Biochemistry

Cite this

Cuniasse, P., Sowers, L., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., ... Fazakerley, G. V. (1989). Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Biochemistry, 28(5), 2018-2026.

Abasic frameshift 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; Le Bret, M.; Guschlbauer, W.; Fazakerley, G. V.

In: Biochemistry, Vol. 28, No. 5, 1989, p. 2018-2026.

Research output: Contribution to journalArticle

Cuniasse, P, Sowers, L, Eritja, R, Kaplan, B, Goodman, MF, Cognet, JAH, Le Bret, M, Guschlbauer, W & Fazakerley, GV 1989, 'Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations', Biochemistry, vol. 28, no. 5, pp. 2018-2026.
Cuniasse, Ph ; Sowers, Lawrence ; Eritja, R. ; Kaplan, B. ; Goodman, M. F. ; Cognet, J. A H ; Le Bret, M. ; Guschlbauer, W. ; Fazakerley, G. V. / Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. In: Biochemistry. 1989 ; Vol. 28, No. 5. pp. 2018-2026.
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AU - Cognet, J. A H

AU - Le Bret, M.

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