Speaker
Prof.
Cristian Micheletti
(International school for Advanced Studies (SISSA), Trieste, Italy)
Description
The packing of DNA inside bacteriophages arguably yields the
simplest example of genome organisation in living organisms
[1, 2]. An indirect indication of how DNA is packaged is
provided by the detected spectrum of knots formed by DNA
that is circularised inside the P4 viral capsid [3, 4]. The
experimental results on the knot spectrum of the P4 DNA are
compared to results of coarse-grained simulation of DNA
knotting in confined volumes. We start by considering a
standard coarse-grained model for DNA which is known to be
capable of reproducing the salient physical aspects of free
(unconstrained) DNA [5]. Specificallty the model accounts
for DNA bending rigidity and excluded volume interactions.
By subjecting the model DNA molecules to spatial confinement
it is found that confinement favours chiral knots over
achiral ones, as found in the P4 experiments. However, no
significant bias of torus over twist knots is found,
contrary to what found in P4 experiments [6, 7]. A good
agreement with experiment is found, instead, upon
introducing an additional interaction potential that
accounts for tendency of contacting DNA portions to order as
in cholesteric liquid crystals. Accounting for this local
potential allows us to reproduce the main experimental data
on DNA organisation in phages, including the cryo-EM
observations and detailed features of the spectrum of
DNAknots formed inside viral capsids. The DNA knots we
observe are strongly delocalized and, intriguingly, this is
shown not to interfere with genome ejection out of the phage
[8].
[1] Earnshaw WC, Harrison SC (1977) DNA arrangement in
isometric phage heads. Nature 268:598-602.
[2] Gelbart WM, Knobler CM (2009) Virology. pressurized
viruses. Science 323:1682-1683.
[3] Arsuaga J, Vazquez M, Trigueros S, Sumners D, Roca J
(2002) Proc Natl Acad Sci U S A 99:5373-5377.
[4] Arsuaga, J et al. (2005) Proc Natl Acad Sci U S A
102:9165-9169.
[5] Rybenkov VV, Cozzarelli NR, Vologodskii AV (1993) Proc
Natl Acad Sci U S A 90:5307-5311.
[6] Micheletti C, Marenduzzo D, Orlandini E, Sumners DW
(2006) J Chem Phys 124:64903-64903.
[7] Micheletti C, Marenduzzo D, Orlandini E, Sumners DW
(2008) Biophys J 95:3591-3599.
[8] Marenduzzo D, Orlandini E, Stasiak A, Sumners DW,
Tubiana L, Micheletti C (2009) Proc Natl Acad Sci U S A
106:22269-22274.
