Modeling Nucleic Acids at the Residue–Level Resolution

Coarse–grained models and force fields have become useful in the studies of the dynamics and physicochemical properties of nucleic acids. Reduced representations of DNA or RNA allow saving computational cost of a few orders of magnitude in comparison with full–atomistic simulations. In this chapter we describe a few selected coarse–grained models of nucleic acids in which one nucleotide is represented as either one, two or three beads. We present the examples of the models designed to investigate the internal dynamics and temperature-dependent denaturation of nucleic acids, as well as created to predict the tertiary structure of RNA or used for large ribonucleoprotein complexes. We describe how the purpose of the model affects the design of the potential energy function and the choice of the simulation method. We also address the limitations of these models.