Coarse-Grained LAMMPS Simulations of Supercoiled DNA

Through modeling we can visualize and understand how DNA is folded and stored within bacterial cells. Prokaryotic DNA is compacted almost 1000 fold and is highly organized, this conformation having a direct impact on gene expression in cells. DNA-binding proteins known as NAPs bind to DNA and create a highly dense, supercoiled structure that allows the lengthy bacterial DNA to both fit in the small cellular space as well as unwind and separate when it comes time for replication. We have performed coarse-grained simulations modeling varying amounts and kinds of NAPs binding to helical DNA, demonstrating their influence on its spatial organization and density. These visual representations shed light on the underlying factors behind transcription and replication. Understanding the compaction process might eventually help medicine to target DNA replication and suggest new strategies for designing antibiotics.