Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks
| dc.creator | Douarche, Nicolas | |
| dc.creator | Cocco, Simona | |
| dc.date | 2005-08-11 | |
| dc.date | 2005-11-16 | |
| dc.date.accessioned | 2026-07-07T06:41:34Z | |
| dc.date.available | 2026-07-07T06:41:34Z | |
| dc.description | 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. | |
| dc.description | corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev. E | |
| dc.identifier | https://arxiv.org/abs/cond-mat/0508288 | |
| dc.identifier | http://arxiv.org/abs/cond-mat/0508288 | |
| dc.identifier | Physical Review E 72, 061902 (2005) | |
| dc.identifier | doi:10.1103/PhysRevE.72.061902 | |
| dc.identifier.uri | http://salesiana.dossiersoluciones.com/handle/123456789/101710 | |
| dc.subject | Soft Condensed Matter | |
| dc.title | Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks | |
| dc.type | text |