[Base interaction and conformation manifestations of repetitive nucleotide sequences]

Abstract

To understand why different nucleotide sequences prefer different double helical conformations and to predict conformational behaviour of definite sequences the base-base interaction energy in regular helices consisting of A:U, A:T, G:C and I:C (hypoxanthine-cytosine) base pairs was calculated. Interaction energy was assumed to be a function of eight conformational parameters: H, the distance between adjacent pairs along helix axes; tau, turn angle of one pair relative to the neighbouring one; angles between base planes in a pair (TW, propeller twist and BL, buckle) and position of pairs with respect to helix axes (D and SL, displacements in the plane normal to helix axes, and TL and RL, inclinations to this plane, tilt and roll, respectively). For H and tau characteristic of A- and B-families of nucleic acid conformations (2.5 A less than H less than or equal to 3.5 A, 30 degrees less than or equal to tau less than or equal to 45 degrees) the ranges of conformational parameters corresponding to energy values close to minimal ones (valleys) and correlations between conformational parameters were revealed. Valleys for different sequences largely coincide but have distinctive characteristics for each sequence. Reasons for base pair planarity distortion in double-stranded helices were considered. The calculations permit to account for A-phility of G:C sequences and B-phility for A:T sequences. The valley for I:C sequence branches. This corresponds to A:T-like behaviour in some cases and G:C-like in the others.