Chemical and Biological Engineering Graduate Program

Faculty Advisor: Juan de Pablo


Confinement of genomic sequences plays a crucial role in all biological species, both free living and otherwise (viruses). Very long segments of double stranded (ds)DNA must be packaged within a small volume such as a cellular nucleus or a viral capsid in order to perform its biological functions. Such confinement presents an interesting problem as dsDNA possesses a negatively charged backbone, which generates a strong self-repulsion in highly confined environments.  A well-studied example of such confinement is the packaging of dsDNA in bacteriophage. These viruses possess viral capsid with dimensions on the order of the persistence length of dsDNA. In addition, a volume compaction of nearly 1000 times over free solution is achieved during packaging.  These conditions result in high curvature and strongly repulsive self-interactions required to confine the viral genome. I am using molecular simulation to explore the mechanism for confinement of dsDNA within linear, dsDNA viruses, specifically a coarse-grained model for a capsid-genome system which I and colleagues have applied it to the study of DNA encapsidation.