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arXiv · 0911.3661

A Generalized Theory of DNA Looping and Cyclization

David P. Wilson·Alexei V. Tkachenko·Jens-Christian Meiners
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Abstract

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length scales $(\sim \ell_{p})$ entropic effects are significant. We propose a simple analytic formula to describe our numerical results for a homogenous DNA in planar loops, which can be used to predict experimental cyclization and loop formation rates as a function of loop size and binding geometry. We also introduce an effective torsional persistence length that describes the coupling between twist and bending of DNA when looped.

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David P. Wilson, Alexei V. Tkachenko, Jens-Christian Meiners. 2009-11-18. A Generalized Theory of DNA Looping and Cyclization. https://doi.org/10.1209/0295-5075%2F89%2F58005

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