  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.
