Lecturer: Prof. Avinoam Ben-Shaul
Affiliation: Institute of Chemistry
and the Fritz Haber Research Center
The Hebrew University of Jerusalem
Abstract:
From a physical point of view, double-
stranded (ds) DNA is a stiff (semiflexible)
linear polymer. Single-stranded (ss) RNA,
on the other hand, is a relatively flexible
polymer that partially folds on itself with
secondary structure giving rise to an
effectively branched polymer. Long
dsDNA and ssRNA molecules serve as
viral genomes and thus need to be
efficiently packaged into the small confines
of the viral protein shells. The packaged
dsDNA is generally extremely densely
packed, exerting very high pressure
(reaching ~100 atm) on the capsid walls.
Although ssRNA is less tightly packed,
there is also a limit to its packaged length,
and experiments reveal clear correlations
between viral RNA length and capsid size
(and charge). I will describe some of the
basic physical properties of dsDNA in
solution and inside viral capsids, outlining
and comparing theoretical and simulation
studies of the force required to load it into
the capsid, and its resulting structure,
energy and pressure. Representing the
branched ssRNA polymers as tree graphs,
we show that viral RNAs are more compact
than non-viral ones, and that random-
sequence RNAs are more compact than
randomly-branched polymers involving
equal numbers of monomers. Further,
neglecting self-interaction, their 3D size
varies with the 1/3 power of their length, in
contrast to the 1/4 power that holds for
randomly-branched polymers. If time
permits I will also outline the Prüfer
shuffling procedure used to arrive at these
conclusions.