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Theoretical studies of nucleic acids folding

The mechanism of how RNA and DNA molecules fold into defined three‐dimensional (3D) structures is still not well understood. Molecular simulation approaches are increasingly being used to study structure formation processes of nucleic acids and to understand the driving forces for folding. It is possible to use molecular dynamics (MD) simulations based on a classical force field to follow the dynamics of nucleic acids at atomic resolution and high time resolution and including surrounding solvent molecules and ions explicitly. Recent studies indicate that it is possible to investigate folding of small motifs such as hairpin structures using MD simulations. However, this approach is still limited by the currently accessible time scales and force field accuracy. Advanced sampling methods such as the replica‐exchange MD (REMD) approach allow significant enhancement of conformational sampling of nucleic acids and could help to systematically study structure formation processes and to refine force fields. In case of large RNAs or RNA containing macromolecular structures, coarse‐grained representations can help to overcome current computational limitations. In combination with experimentally derived constraints and predicted secondary structure, several approaches have been developed to fold RNA molecules into possible 3D structures. Such structural model can often be helpful to plan experiments or to interpret experimental results.