Multi-Scale Models of Genomic Bacterial DNA

Abstract

Detailed structural models of genomic bacterial DNA were developed using multi-scale modeling methods. Initial models were generated using a coarse-grained representation of supercoiled plectonemic DNA informed by experimental data. Conformational sampling was carried out using a Monte Carlo procedure to generate ensembles of nucleoid structures for complete genomic DNA within the constraints of known nucleoid sizes. The resulting models suggest that nucleoids are porous structures that may allow the diffusion of most proteins and protein complexes, in particular those involved in transcription and replication. The coarse-grained models were further refined with increasingly detailed representations of helical DNA up to quasi-atomistic models to serve as starting structures for realistic models of cellular environments.