NMR characterization of clustered bistrand abasic site lesions: Effect of orientation on their solution structure

A unique characteristic of ionizing radiation and radiomimetic anticancer d rugs is the induction of clustered damage: two or more DNA lesions (oxidize d 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 rep resents an exotic challenge to the repair systems present in the cells and, in some cases, these lesions may escape detection and/ or processing. To u nderstand the structural properties of clustered DNA lesions we have prepar ed two oligodeoxynucleotide duplexes containing adjacent tetrahydrofuran re sidues (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 severe ly reduced by the presence of the abasic residues, especially in a 5' orien tation where the melting temperature is 5 degreesC lower. The structures sh ow remarkable differences at the lesion site where the extrahelical locatio n of the tetrahydrofuran residues in the (AP)(2)-5'-staggered duplex contra sts with their smooth alignment along the sugar-phosphate backbone in the ( AP)(2)-3'-staggered duplex. (C) 2001 Academic Press.