Principles of sequence-dependent flexure of DNA

Abstract

The curvature of a bent rod may be defined in several different, but equivalent ways. The best way of describing the curvature of double-helical DNA is by an angle of turning per base step. Curvature comes mainly from the angle of roll between successive base-pairs, and this is defined as positive when the angle opens up on the minor groove side of the bases. DNA forms a plane curve if the roll angle values along the molecule alternate periodically between positive and negative, with a complete period equal to the helical repeat. It is known from studies of crystallized oligomers that the roll angles for particular dinucleotide steps have preferred values, or lie in preferred ranges of values. Therefore the formation of a plane curve will be easier with some base sequences of DNA than with others. We set up a computer algorithm for determining the ease with which DNA of given sequence will adopt a curved form. The algorithm has two different sets of constants: in model 1 the base step parameters come from an inspection of crystallized oligomers, and in model 2 data from a statistical survey of the incidence of dinucleotide steps in a large number of samples of chicken erythrocyte core DNA is incorporated. Both forms of the algorithm successfully locate the dyad of the nucleosome sequence (modulo 10) in a frog gene, and suggest strongly that sequence-dependent flexural properties of DNA play a part in the recognition of binding sites by nucleosome cores.