Journal article
Coarse-grained modelling of supercoiled RNA
- Abstract:
- We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Accepted manuscript, pdf, 3.0MB, Terms of use)
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- Publisher copy:
- 10.1063/1.4933066
Authors
- Publisher:
- American Institute of Physics
- Journal:
- Journal of Chemical Physics More from this journal
- Volume:
- 143
- Issue:
- 24
- Article number:
- 243122
- Publication date:
- 2015-01-01
- DOI:
- EISSN:
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1089-7690
- ISSN:
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0021-9606
- Keywords:
- Pubs id:
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pubs:527452
- UUID:
-
uuid:f332898a-657d-41cd-aaad-398ebfef5275
- Local pid:
-
pubs:527452
- Source identifiers:
-
527452
- Deposit date:
-
2015-12-07
Terms of use
- Copyright holder:
- AIP Publishing LLC
- Copyright date:
- 2015
- Notes:
- Copyright 2015 AIP Publishing. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in Matek, C., Šulc, P., Randisi, F., Doye, J. P. K., and Louis, A. A. (2015, December 28). Coarse-grained modelling of supercoiled RNA. The Journal of Chemical Physics. AIP Publishing. and may be found at http://dx.doi.org/10.1063/1.4933066.
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