Journal article
Modelling toehold-mediated RNA strand displacement
- Abstract:
- We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5′ end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
-
-
(Preview, Accepted manuscript, pdf, 648.8KB, Terms of use)
-
(Supplementary materials, zip, 842.1KB, Terms of use)
-
- Publisher copy:
- 10.1016/j.bpj.2015.01.023
Authors
- Publisher:
- Cell Press
- Journal:
- Biophysical Journal More from this journal
- Volume:
- 108
- Issue:
- 5
- Pages:
- 1238-1247
- Publication date:
- 2015-03-10
- Acceptance date:
- 2015-01-26
- DOI:
- EISSN:
-
1542-0086
- ISSN:
-
0006-3495
- Language:
-
English
- Pubs id:
-
pubs:490973
- UUID:
-
uuid:3d606bca-c491-4ada-af54-8b41f1236204
- Local pid:
-
pubs:490973
- Source identifiers:
-
490973
- Deposit date:
-
2014-11-22
Terms of use
- Copyright holder:
- Biophysical Society
- Copyright date:
- 2015
- Rights statement:
- Copyright © 2015 by the Biophysical Society.
- Notes:
- This is the accepted manuscript version of the article. The final version is available online from Cell Press at https://dx.doi.org/10.1016/j.bpj.2015.01.023
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