Effects of Kinks on DNA Elasticity

TL;DR

This paper investigates how reversible kink-like defects affect the elastic properties of DNA modeled as a worm-like chain, revealing force-dependent changes in persistence length and the significance of multi-kink structures at high rigidity.

Contribution

It introduces a generalized analytical and numerical model for DNA elasticity incorporating reversible kinks, extending the classical worm-like chain model.

Findings

Persistence length is renormalized by kinks at low forces.

High-force response is dominated by the bare persistence length with exponential kink corrections.

Multi-kink structures become relevant in highly rigid chains.

Abstract

We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of trans-gauche rotations in the backbone of the single-stranded DNA. The problem is solved both analytically and numerically by generalizing the well-known analogy to the Quantum Rotator. In the small stretching force regime, we find that the persistence length is renormalized due to the presence of the kinks. In the opposite regime, the response to the strong stretching is determined solely by the bare persistence length with exponential corrections due to the ``ideal gas of kinks''. This high-force behavior changes significantly in the limit of high bending rigidity of the chain. In that case, the leading corrections to the mechanical response are likely to be due to the formation of multi-kink structures, such as kink pairs.