Abstract
We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled double-stranded DNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test our results in vitro, and discuss the possible role played by plectoneme localization in the search process of transcription factors for their targets (promoter regions) on the bacterial genome.
Original language | English |
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Article number | 135101 |
Journal | Journal of Chemical Physics |
Volume | 144 |
Issue number | 13 |
DOIs | |
State | Published - 7 Apr 2016 |
Bibliographical note
Publisher Copyright:© 2016 AIP Publishing LLC.
Funding
This work was supported by the ICORE Program of the Planning and Budgeting committee and the Israel Science Foundation and by the US-Israel Binational Science Foundation.
Funders | Funder number |
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United States-Israel Binational Science Foundation | |
Israel Science Foundation |