  Under many in vitro conditions, some small viruses spontaneously encapsidate
a single stranded (ss) RNA into a protein shell called the capsid. While viral
RNAs are found to be compact and highly branched because of long distance
base-pairing between nucleotides, recent experiments reveal that in a
head-to-head competition between a ssRNA with no secondary or higher order
structure and a viral RNA, the capsid proteins preferentially encapsulate the
linear polymer! In this paper, we study the impact of genome stiffness on the
encapsidation free energy of the complex of RNA and capsid proteins. We show
that an increase in effective chain stiffness because of base-pairing could be
the reason why under certain conditions linear chains have an advantage over
branched chains when it comes to encapsidation efficiency. While branching
makes the genome more compact, RNA base-pairing increases the effective Kuhn
length of the RNA molecule, which could result in an increase of the free
energy of RNA confinement, that is, the work required to encapsidate RNA, and
thus less efficient packaging.
