Refined solution structure of a DNA heteroduplex containing an aldehydic abasic site

Abstract

The solution structure of the DNA duplex d(C1G2C3G4 A5D6A7C8G9C10C11)- d(G22C21G20C19T18A17T16G15C14G13-G12), with D indicating a deoxyribose aldehyde abasic site and numbering from 5' to 3', has been determined by the combined use of NMR and restrained molecular dynamics. The 31P and 31P-1H correlation data indicate that the backbones of these duplex DNAs are regular. One- and two-dimensional 1H NMR data indicate that the duplexes are right-handed and B-form. Conformational changes due to the presence of the abasic site extends to the base pairs adjacent to the lesion site with the local conformation of the DNA being dependent on whether the abasic site is in the α or β configuration. When the sugar of the abasic site is in the β configuration the deoxyribose is within the helix, whereas when the sugar is in the α configuration the deoxyribose is out of the helix. The base of residue A17 in the position opposite the abasic site is predominantly stacked in the helix in both cases. A water molecule can apparently form a hydrogen bond bridge between the β abasic site and A17.