Modeling the Entropic Cost of DNA Looping

Platform Presentation in Biophysical Society Meeting, Baltimore

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Abstract

We have developed a mechanical model of DNA, which computes free energy and entropy of the inter-operator DNA segment of a larger DNA-protein complexes, common in prokaryotic gene regulation systems. We model the DNA using a non-linear rod model, which captures the sequence-dependent intrinsic curvature, to determine its mechanical equilibrium. We then construct a Hamiltonian to describe the linear perturbations from equilibrium in order to calculate the system stiffness. The change in system stiffness then allows us to calculate the change in entropy, free energy and the Stockmayer J-factor (looping probability). Our work shows that these entropic effects can be important when considering loop stability and formation. This work is part of a larger multi-scale modeling effort to quantitatively describe the interaction of DNA with regulatory proteins. Presented here is a Free Energy calculation for a nearly straight segment of DNA bent into a semi-circle and clamped.

 

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