Molecular Dynamics Simulation in RNA Interference

RNA interference (RNAi) is a mechanism that utilizes small RNA molecules to silence gene expression after the gene has been transcribed. To understand the mechanisms of small RNA biogenesis, target nucleic acid recognition and cleavage, and how they are influenced by other regulators, one needs to know the structures and dynamics of the proteins or/and nucleic acids in these processes. Molecular dynamics (MD) simulation is a powerful tool for understanding motions and dynamics of macro-biomolecules at an atomic-scale via theoretical and empirical principles in physical chemistry. With its application to RNAi, an excellent overview of structural and dynamical mechanistic of RNAi processes has already emerged. In this review, we summarize the recent advances in MD simulations in the study of functional modules and their assemblies and target recognition and cleavage in RNAi processes. Additionally, we also present some perspectives on this technique.