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Nucleic Acids Research, Vol 25, Issue 19 3855-3862, Copyright © 1997 by Oxford University Press

ARTICLES

Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics

A Lefebvre, S Fermandjian and B Hartmann
Departement de Biologie Structurale, URA 147 C.N.R.S., Institut Gustave Roussy, P.R.2, 39 rue C. Desmoulins, F-94805 Villejuif Cedex, France.

Nuclear magnetic resonance (NMR) spectroscopy, combining correlated spectroscopy (COSY) coupling constant measurements with nuclear Overhauser effect spectroscopy (NOESY) interatomic distances, should make it possible to determine an averaged solution structure for DNA oligomers. However, even if such data could be obtained with high accuracy, it is not clear which structural parameters of DNA would be determined. Here, the relationships between measurable internucleotide distances and helical parameters are systematically studied through molecular modelling. Investigations are carried out using four representative sequences, (ACGT)n, (TCGA)n, (AGCT)n and (TGCA)n, composed of repeated tetranucleotides belonging to oligomers previously studied by NMR. Correlations between interatomic distances become evident and strong connections between distances and inter-base helical parameters are observed. Results imply that twist, roll, shift and slide values can be accurately determined from NMR data. Sequence independent mechanical coupling which link backbone and sugar conformations to helical twist are also described.
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