ABSTRACT
This chapter focuses on a selection of coarse-grained (CG) deoxyribonucleic acid (DNA) models that have established a continuous line of research and are part of an ongoing effort to go beyond simple characteristics of the double helix and into the realm of protein–DNA interactions, chromatin packaging, and nanomaterial assembly. It also focuses on three CG DNA models, namely Molecular Renormalization CG (MRG-CG) DNA, three sites per nucleotide (3SPN), and oxDNA, all of which have their strengths and weaknesses. Among computational approaches, classical molecular dynamics simulations are a powerful way of treating and visualizing various phases of DNA and their transformations. Double-stranded DNA is the carrier of hereditary information that is physically involved in template-based synthesis and regulation of vast array of biomolecules in the cell. Newly developed CG molecular models of DNA chains proved to be instrumental in supplying microscopic explanations for the behaviors observed in the single molecule experiments.
