Modeling ligand docking to RNA in the design of RNA-based nanostructures

RNA has grown in biological importance as the discovery of its many functional roles in the cellular machinery has revealed the potential for targeting it to disrupt cancer pathways. RNA structure underlies its functionality and suitability as a nanoparticle building material. Advances in modelling methods have been achieved by the recognition of common structural motifs in natural RNA molecules that can be employed in the prediction of new structures based on sequence information and in design of functional nanostructures. Ligand docking prediction programs and RNA dynamics adds an important and non-trivial aspect to the modeling and characterization of the RNA structures. This short review introduces the issues involved in RNA structure prediction and modeling, dynamics of RNA structures, the influence of ligands on the structure and the dynamics, and ways to incorporate this information in the design of RNA-based nanostructures.