A nucleotide-level coarse-grained model of RNA

Abstract

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, 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, and the unzipping of a hairpin motif. 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 source code implementing the model is released for public use.

25 pages

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Cited by in corpus (9)

• Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
• A nucleotide-level coarse-grained model of RNA
• A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect
• Studying Rare Events using Forward-Flux Sampling: Recent Breakthroughs and Future Outlook
• Modelling toehold-mediated RNA strand displacement
• Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
• DNA nanotechnology: understanding and optimisation through simulation
• The role of loop stacking in the dynamics of DNA hairpin formation
• Ab initio RNA folding