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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.
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