RNA plays numerous roles in the cell. Messenger RNAs serve as templates to transfer genetic information from DNA to the ribosomes. The ribosome itself is built of RNA that has both a structural and catalytic role. There is also a plethora of non-coding RNAs, that do not carry genetic information, but have various other functions, including regulatory ones.
The complicated three-dimensional architectures of RNA result from its sequence, secondary and tertiary structure and are required for such diverse functions. Internal dynamics of RNA hierarchical structure is needed for its biological function, which is related to RNA flexibility. Some RNAs adopt multiple folds depending on environmental conditions or the presence of ligands.
We apply molecular dynamics simulations to investigate the dynamics of RNA structures and relate the dynamics to function. I will discuss the difficulties in visualizing such three-dimensional all-atom dynamics of RNAs. I will describe RNA flexibility based on biologically-relevant RNA motifs. The examples will include large RNAs, such as the ribosomes, whose dynamics is altered by binding of small antibiotics. Another example will be a small RNA thermal switch, a short mRNA sequence responding to temperature changes, whose melting regulates gene expression.