Mechanical behavior of a wormlike chain with variable bending rigidity along the chain contour in free space

TL;DR

This paper develops a theory to analyze the mechanical properties of heterogeneous wormlike chains with variable bending rigidity, validated by simulations and applied to DNA sequence-dependent behavior.

Contribution

It introduces a novel theoretical framework for variable persistence length in polymer chains and provides experimental methods for measurement, advancing understanding of heterogeneous biopolymer mechanics.

Findings

Theory agrees with Brownian dynamics simulations

Exact persistence lengths for DNA dinucleotide steps determined

Application to DNA sequence dependence demonstrated

Abstract

In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function, under the condition of varying persistence length (a measure of bending rigidity) along the chain contour. Additionally, we give the specifically experimental method to measure the variable persistence length to examine our theory. In order to verify the theoretical predictions, we also performed large numbers of Brownian dynamics simulations based on the Generalized Bead-Rod (GBR) model and showed that our theory is in good agreement with simulation results. As an application, sequence dependence of the mechanical behavior of DNA chains is successfully analyzed and we have given the exact persistence length of basic dinucleotide steps, which is verified through using the basic steps to design other DNA fragments.