DSSR-PyMOL cartoon-block schematics: PDB entry 1ht4

PDB-id

1ht4; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Solution structure of a bistrand abasic site lesion staggered in a 3'-orientation.

Reference

Lin Z, de los Santos C (2001): "NMR characterization of clustered bistrand abasic site lesions: effect of orientation on their solution structure." J.Mol.Biol., 308, 341-352. doi: 10.1006/jmbi.2001.4587.

Abstract

A unique characteristic of ionizing radiation and radiomimetic anticancer drugs is the induction of clustered damage: two or more DNA lesions (oxidized bases, abasic sites, or strand breaks) occurring in the same or different strands of the DNA molecule within a single turn of the helix. In spite of arising at a lower frequency than single lesions, clustered DNA damage represents an exotic challenge to the repair systems present in the cells and, in some cases, these lesions may escape detection and/or processing. To understand the structural properties of clustered DNA lesions we have prepared two oligodeoxynucleotide duplexes containing adjacent tetrahydrofuran residues (abasic site analogues), positioned one in each strand of the duplex in a 5' or 3' orientation, and determined their solution structure by NMR spectroscopy and molecular dynamics simulations. The NMR data indicate that both duplex structures are right-handed helices of high similarity outside the clustered damage site. The thermal stability of the duplexes is severely reduced by the presence of the abasic residues, especially in a 5' orientation where the melting temperature is 5 degrees C lower. The structures show remarkable differences at the lesion site where the extrahelical location of the tetrahydrofuran residues in the (AP)(2)-5'-staggered duplex contrasts with their smooth alignment along the sugar-phosphate backbone in the (AP)(2)-3'-staggered duplex.