Identification of effects of YOYO-1 intercalation on the topological states of circular DNA

Abstract

YOYO-1 intercalation leads to the reduction of twist rigidity, unwinding of DNA, elongation of DNA contour length and YOYO-1 concentration-dependent persistence length, until now few works identified their roles in determining the topological states of circular DNA. Based on the convolution of the writhe distribution of circular DNA obtained by using Monte Carlo simulation and the twist distribution, effects of YOYO-1 intercalation on the linking number distribution of circular DNA are predicted and identified. YOYO-1 intercalation leads to larger fluctuation, but not to the obvious enlargement of the writhe distribution, so that the variance of the linking number distribution mainly depends on the variance of the twist distribution. The unwinding angle contributes to the drifting of the linking number distribution away from the original equilibrium value of zero and has no effects on the variance of the linking number distribution, converse to the roles of the reduced twist rigidity in the linking number distribution. Furthermore, the method used in the work can be generalized to detect the effects of other intercalators on the topological states of circular DNA.