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Nucleic Acids Research, 2003, Vol. 31, No. 20 5930-5940
© 2003 Oxford University Press

Structural study of DNA duplex containing an N-(2-deoxy-ß-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics

C. Maufrais, G. V. Fazakerley, J. Cadet1 and Y. Boulard*

CEA, Département de Biologie Joliot Curie, Service de Biochimie et de Génétique Moléculaire, Bat 144, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France and 1 CEA, Service de Chimie Inorganique et Biologique & FRE2600, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 38054 Grenoble Cedex 9, France

*To whom correspondence should be addressed. Tel: +33 01 69 08 35 84; Fax: +33 01 69 08 47 12; Email: yboulard{at}cea.fr

The presence of an N-(2-deoxy-ß-D-erythro-pentofuranosyl) formamide (F) residue, a ring fragmentation product of thymine, in a frameshift context in the sequence 5'-d-(AGGACCACG)·d(CGTGGFTCCT) has been studied by 1H and 31P nuclear magnetic resonance (NMR) and molecular dynamics. Two-dimensional NMR studies show that the formamide residue, whether the cis or trans isomer, is rotated out of the helix and that the bases on either side of the formamide residue in the sequence, G14 and T16, are stacked over each other in a way similar to normal B-DNA. The cis and trans isomers were observed in the ratio 3:2 in solution. Information extracted from 31P NMR data reveal a modification of the phosphodiester backbone conformation at the extrahelical site, which is also observed during the molecular dynamics simulations.


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