The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.

Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 612 65 Brno Czech Republic

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Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

Long-timescale dynamics of the Drew-Dickerson dodecamer

Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Extended molecular dynamics of a c-kit promoter quadruplex

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations