Coarse-grained modelling of nucleic acids for biology and nanotechnology

We present a nucleotide-level model of RNA designed to reproduce structural, mechanical and thermodynamic properties of single-stranded
as well as double-stranded RNA.

We test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, the unzipping of a hairpin motif, and formation of a plectoneme.

We further use the model to study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction. Strand displacement is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo.

Furthermore, recent experiments have demonstrated promising application of RNA strand displacement systems to bionanotechnology. We obtain the rate of displacement reactions as a function of the length of the toehold and temperature and find that the displacement is faster if the toehold is placed at the 5' end of the substrate, thus suggesting a plausible mechanism for improvement of yields of strand displacement reaction cascades.

We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The further improvements to the model will aim to combine the known thermodynamic properties with information about the interactions inferred from covariance analysis of multiple sequence alignments.