Modeling the Entropic Cost of DNA Looping
Platform Presentation in Biophysical Society Meeting, Baltimore 

David P. Wilson, Todd D. Lillian, Bachelors, Sachin Goyal, PhD, Noel C. Perkins, Alexei Tkachenko, Jens C. Meiners.
University of Michigan, Ann Arbor, MI, USA Mar 37, 2007
AbstractWe have developed a mechanical model of DNA, which computes free energy and entropy of the interoperator DNA segment of a larger DNAprotein complexes, common in prokaryotic gene regulation systems. We model the DNA using a nonlinear rod model, which captures the sequencedependent 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 Jfactor (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 multiscale 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 semicircle and clamped.

