A generalized theory of semiflexible polymers

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.

References in corpus (4)

• Exact theory of kinkable elastic polymers
• Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules
• The distribution function of a semiflexible polymer and random walks with constraints
• Effects of Kinks on DNA Elasticity

Cited by in corpus (15)

• Probing the elastic limit of DNA bending
• Entropic Spectral Broadening in Carbon Nanotube Resonators
• The Worm-Like Chain Theory And Bending Of Short DNA
• DNA flexibility on short length scales probed by atomic force microscopy
• Effect of supercoiling on formation of protein mediated DNA loops
• Microscopic mechanism for experimentally observed anomalous elasticity of DNA in 2D
• Computing the elastic mechanical properties of rod-like DNA nanostructures
• Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops
• Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
• Extreme bendability of DNA double helix due to bending asymmetry
• Conformations and diffusion of flexibly linked colloidal chains
• Self-avoiding worm-like chain model for dsDNA loop formation
• Bimodal distribution function of a 3d wormlike chain with a fixed orientation of one end
• Conformational transformations induced by the charge-curvature interaction at finite temperature
• Colloidal particle motion as a diagnostic of DNA conformational transitions