1osr

From Proteopedia

Structural study of dna duplex containaing a n-(2-deoxy-beta-erytho-pentofuranosyl) formamide frameshift by nmr and restrained molecular dynamics

Overview

The presence of an N-(2-deoxy-beta-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.

About this Structure

1OSR is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics., Maufrais C, Fazakerley GV, Cadet J, Boulard Y, Nucleic Acids Res. 2003 Oct 15;31(20):5930-40. PMID:14530441

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