Abstract

DNA in living cells of both bacteria and eukaryotes associates with proteins that continuously bind and dissociate. Some proteins affect local structure (such as histones and histone-like proteins), whereas others act globally to compact whole chromosomal segments (such as CCCTC -binding factors).

Brownian dynamics simulations are used here to model both DNA and DNA -bindin proteins. In the absence of any explicit interaction between proteins, or between templates, we find that binding of protein which are able to bridge the DNA , spontaneously induces local DNA compaction and protein aggregation. Small proteins interacting with naked DNA form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], and large proteins into quasi-spherical aggregates (as on nanoparticle binding). We also explore how these ideas apply to the self-assembly, or reconstitution, of chromatin, which can be made in vitro from DNA and histone octamers, provided that appropriate experimental protocols are followed accurately.