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Generalized theory of semiflexible polymers

Wiggins, Paul A. and Nelson, Philip C. (2006) Generalized theory of semiflexible polymers. Physical Review E, 73 (3). Art. No. 031906. ISSN 1539-3755.

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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 biologically relevant 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, illustrative model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by renormalization group arguments. In particular, we show that either the WLC or our present model adequately 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 recently measured by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments.

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Additional Information:©2006 The American Physical Society (Received 5 August 2005; published 7 March 2006) We thank N. R. Dan, Cees Dekker, M. Inamdar, Igor Kulic, Richard Lavery, J. Maddocks, John Marko, Fernando Moreno-Herrero, Rob Phillips, Ashok Prasad, Prashant Purohit, J. M. Schurr, A. Spakowitz, Thijn van der Heijden R. James, Z.-G. Wang, Jonathan Widom, and Yongli Zhang, for helpful discussions and correspondence. P.A.W. acknowledges financial support from the NSF and the Keck Foundation and from NSF Grant No. CMS-0301657, and the NSF-funded Center for Integrative Multiscale Modeling and Simulation. P.N. acknowledges NSF Grant No. DMR04-04674 and the NSF-funded NSEC on Molecular Function at the Nano/Bio Interface Grant No. DMR04-25780.
Subject Keywords:DNA; molecular biophysics; bending; biomechanics; elasticity; free energy; genetics
Issue or Number:3
Record Number:CaltechAUTHORS:WIGpre06
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:3841
Deposited By: Archive Administrator
Deposited On:14 Jul 2006
Last Modified:02 Oct 2019 23:07

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