Stereoelectronic effects of deoxyribose O4' on DNA conformation.

Abstract

While B-DNA, the most common DNA conformation, displays rather regular twist angles and base stacking between successive base pairs, left-handed Z-DNA is characterized by the alternation of two different dinucleotide conformations with either a large twist and a small slide or a small twist and a large slide between adjacent base pairs. This results in poor stacking within the latter dinucleotide repeat that is in apparent contradiction to the rigidity and conformational stability of Z-DNA at high ionic strength. However, at d(CpG) steps the cytidine deoxyribose is situated such that its O4' sits directly over the six-membered ring of the guanine. We show here that the particular positionings of the two O4' lone-pair electrons provide stability through an intracytidine O4'...H6--C6 hydrogen bond and an n-->pi* interaction with the guanidinium system of the stacked base. Our model is based on the assumption of a strong polarization of the guanine bases in Z-DNA that is consistent with the Z-DNA-specific guanine O6 and N7 coordination to metal and organic cations and the proximity of its N2 and C8 positions to neighboring phosphate groups, as well as several other Z-DNA-specific conformational features.