Sequence-Dependent Properties of the RNA Duplex

Sequence-dependentproperties of the DNA duplex havebeen accuratelydescribed using extensive molecular dynamics simulations. The RNAduplex meanwhile which is typically represented as a sequence-averagedrigid rod does not benefit from having equivalent moleculardynamics simulations. In this paper, we present a massive simulationeffort using a set of ABC-optimized duplexes from which we derivedtetramer-resolution properties of the RNA duplex and a simple mesoscopicmodel that can represent elastic properties of long RNA duplexes.Despite the extreme chemical similarity between DNA and RNA, the localand global elastic properties of the duplexes are very different.DNA duplexes show a complex and nonelastic pattern of flexibility,for instance, while RNA duplexes behave as an elastic system whosedeformations can be represented by simple harmonic potentials. InRNA duplexes (RNA(2)), not only are intra- and interbasepair parameters (equilibrium and mechanical) different from thosein the equivalent DNA duplex sequences (DNA(2)) but the correlationsbetween movements also differ. Simple statements on the relative flexibilityor stability of both polymers are meaningless and should be substitutedby a more detailed description depending on the sequence and the typeof deformation considered.

Automated summary

The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.