Current models of genomic DNA are still far from atomistic or even base pair resolution. Genomic DNA is highly dynamic, with its structure stabilized by a multitude of proteins in vivo and topological complexities reaching from atomistic to cellular scales. We are applying multi-scale modeling techniques to build high-resolution models of bacterial nucleoids that combine topological knowledge with base pair distance restraints from chromosome conformation capture (3C-5C, Hi-C) experiments.
The nucleoid models serve as the basis for gene-structure-function studies at the DNA level and for exploring protein interactions with genomic DNA.
|1.||Asli Yildirim, Monika Sharma, Bradley Varner, Liang Fang, Michael Feig: Conformational Preferences of DNA in Cellular Environments Journal of Physical Chemistry B (2014) 118, 10874-10881 Abstract PDF|