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Date:03-04-2020 Print

Viruses come in a range of shapes and sizes, from the tiny, icosahedral rhinovirus (common cold) to the much larger, brick-shaped orthopoxvirus (smallpox). How DNA is packed inside a virus, however, remains a controversial question. In a recent work published in Physical Review Letters, researchers from IoP and UCAS addressed this packing problem with a combination of analytical theory and simulations.

Compartmentalization of confined
viral DNA. Image by J.D. Farrell, IoP.

We postulated a simplified model of an elastic filament confined to a sphere with three competing interactions: elasticity, which prefers the filament to be straight; excluded volume, which prevents the filament from overlapping with itself; and the spherical confinement, which frustrates the other two interaction terms. This simple model gives rise to a surprisingly great deal of complexity. We observe that at high densities the preferred structure is a complex arrangement of intertwined rings and that compartmentalization into multiple domains is always preferred to a single, donut-shaped domain proposed in previous works.

Multidomain ordering is known from the structure of chromatin, where the complex protein-DNA interactions drive the segregation of DNA. Here, we have shown that it can emerge in a much simpler and smaller system, in the absence of specific structural constraints. In making the leap to predict the exact packing in real viruses, the specific interactions between the DNA and the viral shell, and within the DNA molecule itself, should naturally be considered. However, our results give a general context in which viral DNA packing can be discussed, offering fresh insight into the fundamental mechanisms that govern this process.

Tine Curk, James D. Farrell, Jure Dobnikar, Rudi Podgornik, Spontaneous Domain Formation in Spherically-Confined Elastic Filaments, Phys. Rev. Lett. 123 047801 (2019)

Institute of Physics, CAS
Jure Dobnikar

Physics of viruses, self-assembly, polymer topology, elastic forces, confinement

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.