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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.

SUBMITTER: Sulc P

PROVIDER: S-EPMC4375624 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Modelling toehold-mediated RNA strand displacement.

Šulc Petr P Ouldridge Thomas E TE Romano Flavio F Doye Jonathan P K JP Louis Ard A AA

Biophysical journal 20150301 5

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 ...[more]

PMID: 25762335

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