  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.

Biological Physics;Soft Condensed Matter;Chemical Physics;Biomolecules