DSSR-PyMOL cartoon-block schematics: PDB entry 1osr

PDB-id

1osr; SNAP-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

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

Reference

Maufrais C, Fazakerley GV, Cadet J, Boulard Y (2003): "Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics." Nucleic Acids Res., 31, 5930-5940. doi: 10.1093/nar/gkg803.

Abstract

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.