Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer

TL;DR

This paper derives simple models for bending and base-stacking energies in double-stranded semiflexible biopolymers like DNA, and validates them against experimental data on extension and supercoiling.

Contribution

It introduces a Schrödinger equation-based approach to model folding angles and provides analytical expressions for biopolymer energetics and mechanics.

Findings

Theoretical extension-force and supercoiling relations match experimental data.

Derived energy expressions accurately describe DNA behavior.

Model offers a new framework for understanding biopolymer flexibility.

Abstract

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schr\"{o}dinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DNA chain are in good agreement with the experimental observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it ibid.} {\bf 271}, 1835 (1996)].