D. Marenduzzo and C. Micheletti
Thermodynamics of DNA packaging inside a viral capsid: The role of DNA intrinsic thickness
J. Mol. Biol., 330, 485-492 (2003).
Link to online article.
We characterize the equilibrium thermodynamics of a thick polymer
confined in a spherical region of space. This is used to gain insight
into the DNA packaging process. The experimental reference system for
the present study is the recent characterization of the loading
process of the genome inside the $\phi$29 bacteriophage capsid. Our
emphasis is on the modelling of double-stranded DNA as a flexible
thick polymer (tube) instead of a beads-and-springs chain. By using
finite-size scaling to extrapolate our results to genome lengths
appropriate for $\phi$29, we find that the thickness-induced force may
account for up to half the one measured experimentally at high packing
densities. An analogous agreement is found for the total work that
has to be spent in the packaging process. Remarkably, such agreement
can be obtained in the absence of any tunable parameters and is a mere
consequence of the DNA thickness. Furthermore, we provide a
quantitative estimate of how the persistence length of a polymer
depends on its thickness. The expression accounts for the significant
difference in the persistence lengths of single- and double-stranded
DNA (again with the sole input of their respective sections and
natural nucleotide/base-pair spacing).