Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations

Journal Article · Tue Mar 07 04:00:00 EST 1989 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00431a009· OSTI ID:5717965

Cuniasse, P; Sowers, L C; Eritja, R; Kaplan, B; Goodman, M F; Cognet, J A.H.; Le Bret, M; Guschlbauer, W; Fazakerley, G V ^[1]

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1. Centre d'Etudes Nucleaires de Saclay, Gif-sur-Yvette (France)

The authors 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.

• OSTI ID: 5717965
• Journal Information: Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 28:5; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550601* -- Medicine-- Unsealed Radionuclides in Diagnostics
62 RADIOLOGY AND NUCLEAR MEDICINE
AQUEOUS SOLUTIONS
BARYONS
CONFORMATIONAL CHANGES
DISPERSIONS
DNA
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
MATHEMATICAL MODELS
MIXTURES
MOLECULAR STRUCTURE
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
OLIGONUCLEOTIDES
ORGANIC COMPOUNDS
OVERHAUSER EFFECT
PROTONS
RESONANCE
SOLUTIONS
SPECTRA