DNA bending potentials for loop-mediated nucleosome repositioning
Nucleosome repositioning is a fundamental process in gene function. DNA elasticity is a key element of loop-mediated nucleosome repositioning. Two analytical models for DNA elasticity have been proposed: the linear sub-elastic chain (SEC), which allows DNA kinking, and the worm-like chain (WLC), wit...
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| Main Authors: | , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
6 February 2012
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| In: |
epl
Year: 2012, Volume: 97, Issue: 3 |
| ISSN: | 1286-4854 |
| DOI: | 10.1209/0295-5075/97/38004 |
| Online Access: | Verlag, Volltext: http://dx.doi.org/10.1209/0295-5075/97/38004 Verlag, Volltext: http://stacks.iop.org/0295-5075/97/i=3/a=38004 |
| Author Notes: | M. Biswas, T. Wocjan, J. Langowski and J.C. Smith |
MARC
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| 520 | |a Nucleosome repositioning is a fundamental process in gene function. DNA elasticity is a key element of loop-mediated nucleosome repositioning. Two analytical models for DNA elasticity have been proposed: the linear sub-elastic chain (SEC), which allows DNA kinking, and the worm-like chain (WLC), with a harmonic bending potential. In vitro studies have shown that nucleosomes reposition in a discontiguous manner on a segment of DNA and this has also been found in ground-state calculations with the WLC analytical model. Here we study using Monte Carlo simulation the dynamics of DNA loop-mediated nucleosome repositioning at physiological temperatures using the SEC and WLC potentials. At thermal energies both models predict nearest-neighbor repositioning of nucleosomes on DNA, in contrast to the repositioning in jumps observed in experiments. This suggests a crucial role of DNA sequence in nucleosome repositioning. | ||
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