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.
Original language | English (US) |
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Pages (from-to) | 1238-1247 |
Number of pages | 10 |
Journal | Biophysical journal |
Volume | 108 |
Issue number | 5 |
DOIs | |
State | Published - Mar 10 2015 |
Externally published | Yes |
ASJC Scopus subject areas
- Biophysics