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.
Keywords: Biogenesis, miRNA, molecular dynamics simulation, RNA interference, siRNA.
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