Modelling toehold-mediated RNA strand displacement
arXiv:1411.3239 · doi:10.1016/j.bpj.2015.01.023
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.
References in corpus (10)
- Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
- Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales
- Forward Flux Sampling for rare event simulations
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- DNA hybridization kinetics: zippering, internal displacement and sequence dependence
- DNA nanotweezers studied with a coarse-grained model of DNA
- A nucleotide-level coarse-grained model of RNA
- The role of collective motion in examples of coarsening and self-assembly
- DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
- Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Cited by in corpus (6)
- Studying Rare Events using Forward-Flux Sampling: Recent Breakthroughs and Future Outlook
- Coarse-grained modelling of DNA-RNA hybrids
- First passage time study of DNA strand displacement
- Coarse-grained modelling of supercoiled RNA
- Strand displacement: a fundamental mechanism in RNA biology?
- Robust control of biochemical reaction networks via stochastic morphing