Prediction of Modes with Dominant Base Roll and Propeller Twist in B-DNA poly(dA)-poly(dT).

摘要

The polymer poly(dA)-poly(dT) is a one-dimensional infinite lattice with the nucleotide pair adenine (A)-thymine (T) for a unit cell. Both bases are planar ringed structures.The orientation of these planar structures is described in terms of two parameters. One is the angle between the bases in a pair, referred to as the propeller twist. The other is the base roll which describes the rotation of the base pair as a whole. We calculate the absolute base roll which is the change of angle the base pair, rolling as one unit, makes with the mean base pair plane. Structural investigations by the Klug and Rich3groups of single crystals of DNA dodecamers have identified a propeller twist conformation for regions containing a homopolymeric run of A-T base pairs. Austin has suggested that propeller twist and base pair roll are temperature dependent in solutions of poly(dA)- poly(dT) 4 Liu et al 5 suggest that the onset of these departures from a more regular structure could be soft mode mediated. To explore this possibility we examine the eigenvectors of our dynamical matrix for dominant base roll and propeller twist.