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.
- Pub Date:
- March 2015
- Physics - Biological Physics;
- Condensed Matter - Soft Condensed Matter;
- Physics - Chemical Physics;
- Quantitative Biology - Biomolecules
- Biophysical Journal , Volume 108 , Issue 5 , 1238 - 1247, 2015