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.

arXiv comment25 pages

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Cited by in corpus (20)

• 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
• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent and divalent ion solutions
• Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
• Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
• A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
• DNA nanotechnology: understanding and optimisation through simulation
• The oxDNA coarse-grained model as a tool to simulate DNA origami
• SAT-assembly: A new approach for designing self-assembling systems
• The role of loop stacking in the dynamics of DNA hairpin formation
• Coarse-grained modelling of DNA-RNA hybrids
• Ab initio RNA folding
• Coarse-grained modelling of supercoiled RNA
• Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs
• Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular Dynamics
• Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model