Understanding the role of thermal fluctuations in DNA looping

David P. Wilson; Todd Lillian; Sachin Goyal; Alexei V. Tkachenko; Noel C. Perkins; Jens-Christian Meiners

doi:10.1117/12.724717

8 June 2007 Understanding the role of thermal fluctuations in DNA looping

David P. Wilson, Todd Lillian, Sachin Goyal, Alexei V. Tkachenko, Noel C. Perkins, Jens-Christian Meiners

Proceedings Volume 6602, Noise and Fluctuations in Biological, Biophysical, and Biomedical Systems; 660208 (2007) https://doi.org/10.1117/12.724717
Event: SPIE Fourth International Symposium on Fluctuations and Noise, 2007, Florence, Italy

Abstract

Protein-mediated DNA loop formation is an important biological process that regulates key functions such as transcription. We present a mechanical model for these DNA-protein complexes that can take effects of the DNA sequence such induced curvature into account. This model provides the equilibrium shape and elastic energy of the DNA loop, using boundary conditions from the protein crystal structure. We then construct a Hamiltonian for small perturbations of the DNA around the equilibrium shape, which in turn allows us to calculate the eigenmodes and the entropic contributions of the thermal fluctuations to the free energy of the DNA loop. Here we present computations related to the short wild-type lactose repressor loop of Escheria coli (E. coli), and find that the entropic contributions are significant and amount to up to 3.9 k_BT of the free energy. We also show that this entropic contribution from the stiffening of the DNA loop depends strongly on the phase angle between the two operator sites, which adds to the known phasing effect of the elastic energy of the loop.

Citation Download Citation

David P. Wilson, Todd Lillian, Sachin Goyal, Alexei V. Tkachenko, Noel C. Perkins, and Jens-Christian Meiners "Understanding the role of thermal fluctuations in DNA looping", Proc. SPIE 6602, Noise and Fluctuations in Biological, Biophysical, and Biomedical Systems, 660208 (8 June 2007); https://doi.org/10.1117/12.724717

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