Stereoelectronic effects of deoxyribose O4' on DNA conformation.

• DOI: 10.1073/pnas.92.1.180
• Publication Date: 2006-05-31T13:09:12Z
• Authors: M Egli; R V Gessner
• Keywords: Deoxyribose; Lone pair; Nucleobase; Cytosine

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