A generalized theory of semiflexible polymers

TL;DR

This paper develops a generalized semiflexible polymer theory to better understand DNA bending, showing that while the wormlike chain model works at long scales, new models can capture short-scale behaviors and experimental anomalies.

Contribution

It introduces a class of generalized semiflexible polymer models and demonstrates their ability to describe DNA bending across different length scales, including deviations from the WLC model.

Findings

WLC model accurately describes long-length-scale DNA statistics.

New models can reproduce short-length-scale experimental anomalies.

Force-extension, scattering, and cyclization experiments are explained by both models.

Abstract

DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biological length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific toy model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by the Renormalization Group. In particular, we show that either the WLC or our new model adequate describes force-extension, solution scattering, and long-contour-length cyclization experiments, regardless of the details of DNA bend elasticity. In contrast, experiments sensitive to short-length-scale chain behavior can in principle reveal dramatic departures from the linear elastic behavior assumed in the WLC model. We demonstrate this explicitly by showing that our toy model can reproduce the anomalously large short-contour-length cyclization J factors observed by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments.