Terminal Twist-Induced Writhe of DNA with Intrinsic Curvature

Abstract

Supercoiling of a closed circular DNA rod may result from an application of terminal twist to the DNA rod by cutting the rod, rotating one of the cut faces as the other being fixed and then sealing the cut. According to White's formula, DNA supercoiling is probably accompanied by a writhe of the DNA axis. Deduced from the elastic rod model for DNA structure, an intrinsically straight closed circular DNA rod does not writhe as subject to a terminal twist, until the number of rotation exceeds a rod-dependent threshold. By contrast, a closed circular DNA rod with intrinsic curvature writhes instantly as subject to a terminal twist. This noteworthy character in fact belongs to many intrinsically curved DNA rods. By solving the dynamic equations, the linearization of the Euler-Lagrange equations governing intrinsically curved DNA rods, this paper shows that almost every clamped-end intrinsically curved DNA rod writhes instantly when subject to a terminal twist (clamped-end DNA rods include closed circular DNA rods and topological domains of open DNA rods). In terms of physical quantities, the exceptions are identified with points in R(6) whose projections onto R(5) (through ignoring the total energy density of a rod) form a subset of a quadratic hypersurface. This paper also suggests that the terminal twist induced writhe is due to the elasticity and the clamped-end boundary conditions of the DNA rods.