ABSTRACT
DNA is a highly charged, semi-flexible polyelectrolyte. In eukaryotic
cells, DNA chains are packed inside the microscopic volume of
the nucleus in an ordered, yet dynamical way. To overcome the
electrostatic repulsion that hinders compaction, DNA molecules
associate with a variety of counterions and proteins to condensate
into a hierarchical and tunable architecture named chromatin.
Besides DNA condensation, chromatin also plays a key role in
gene regulation by making DNA accessible for transcription in
a dynamical and specific way. Consequently, understanding the
physicochemical properties of DNA chains at the molecular and
mesoscopic scales is a required step to elucidate how cells regulate
critical events such as DNA transcription, replication, repair, and
recombination in vivo. In this chapter, we first briefly describe some of themost salient challenges ofmodeling the biophysical properties
of DNA molecules and their solution environment. Following, we
review a selection of recently developed coarse-grained models and
computational approaches that may be used to investigate the DNA
structure, dynamics, and association with proteins.
