RNA solvation: a molecular dynamics simulation perspective

Biopolymers
P Auffinger, E Westhof

Abstract

With the availability of accurate methods to treat the electrostatic long-range interactions, molecular dynamics simulations have resulted in refined dynamical models of the structure of the hydration shell around RNA motifs. The models reviewed here range from basic Watson-Crick to more specific noncanonical base pairs, from "simple" double helices to RNA molecules displaying more complex tertiary folds, and from DNA/RNA hybrid double helices to RNA hybrids formed with a chemically modified strand.

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Related Concepts

In Silico
Hydrogen Bonding
Ions
RNA
Solvents
Thermodynamics
Base Pairing
Static Electricity

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