Sequence Effects on DNA Entropic Elasticity

TL;DR

This paper clarifies how sequence-dependent effects influence DNA's measured elastic properties, showing that the persistence length from stretching experiments combines bend stiffness and sequence effects, unlike torsional measurements.

Contribution

It provides a simple analytic model demonstrating how sequence effects alter DNA persistence length measurements, resolving discrepancies between different experimental methods.

Findings

Persistence length from stretching includes sequence effects.

Torsional persistence length remains unaffected by sequence.

Analytic model applies to DNA and similar polymers with weak disorder.

Abstract

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.