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• W1983201119 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 wormlike 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 $24phantom{rule{0.3em}{0ex}}{k}_{mathrm{B}}T$ to $13phantom{rule{0.3em}{0ex}}{k}_{mathrm{B}}T$ when the loop is closed by a protein of $r=10phantom{rule{0.3em}{0ex}}mathrm{nm}$ length. It further decreases to $5phantom{rule{0.3em}{0ex}}{k}_{mathrm{B}}T$ when the loop has a kink of 120ifmmode^circelsetextdegreefi{} at half-length." @default.
• W1983201119 created "2016-06-24" @default.
• W1983201119 creator A5041457778 @default.
• W1983201119 creator A5050420323 @default.
• W1983201119 date "2005-12-02" @default.
• W1983201119 modified "2023-09-27" @default.
• W1983201119 title "Protein-mediated DNA loops: Effects of protein bridge size and kinks" @default.
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• W1983201119 doi "https://doi.org/10.1103/physreve.72.061902" @default.
• W1983201119 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16485969" @default.
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