Removal of a single minor-groove functional group eliminates A-tract curvature.

Much of the work in studying the phenomenon of A-tract curvature has involved the insertion of modified residues into the A-tract sequence and then cross-correlation of the structural differences with the resulting curvature effects. In the A-tract sequence d(A-T)5, removal of a single functional group (the O2-carbonyl of the central dT residue) by its replacement with hydrogen completely eliminates the curvature properties. This atom-specific change was accomplished by using the C-nucleoside dm32P in which the O2-carbonyl is replaced with -H but normal Watson-Crick hydrogen bonding is maintained. Similar derivatives with -F (dF62P) or -CH3 (dm62P) when present for the central dT residue also eliminate curvature. Finally, we have shown that the extent of curvature for sequences containing this carbonyl are sensitive to the [Mg2+], while those lacking the carbonyl show little to no Mg2+ dependence, strongly suggesting, we believe, a role for Na+/Mg2+ cooperative interactions in the minor groove to explain the curvature phenomenon.