Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks
arXiv:cond-mat/0508288 · doi:10.1103/PhysRevE.72.061902
Abstract
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.
arXiv commentcorrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev. E
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- Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules
- Extreme bendability of DNA double helix due to bending asymmetry
- Kinetics of rare events for non-Markovian stationary processes and application to polymer dynamics
- Bending short DNAs as transversely isotropic rings in series
- Colloidal particle motion as a diagnostic of DNA conformational transitions