[DBS seminar] Jure Dobnikar, "DNA packing in viral capsids"

Thursday 9 Apr 2026, 14:15 → 15:15 Europe/Ljubljana

Seminar room of physics (106) (IJS)

Assembly of viral capsids containing genetic material, is a key process in viral reproduction cycle. The bacteriophages and double stranded DNA viruses assemble their capsids prior to genome packaging and actively push DNA inside by ATP-driven packaging motors. The genome is typically densely packed in the capsid and understanding its spatial configuration presents a challenging problem, which is not completely understood despite its obvious importance.

To elucidate the mechanism of DNA packing, we first explored a simple model of elastic filament confined to a sphere with three competing interactions [1]. The simple phenomenological theory supported by extensive parallel tempering MD simulations of the wormlike chain (WLC) model show that the optimal ground state packing is not an inverse spool configuration as previously assumed; it is a more complex structure where the filament is compartmentalized into multiple domains, resembling nested tori or topological links. While this suggests that DNA will also form multidomain structures in a viral capsid, it is important to realize that DNA cannot be completely described by the linear elastic model. Under sufficient local torsion, the base pairs of the double helix can locally melt creating regions with large flexibility that can easily form kinks. We incorporated this effect into a meltable WLC model and explored nonequilibrium process of pushing such kinkable chains into a capsid by molecular motors [3]. It turns out that the kink formation crucially affects the structure: for sufficiently slow packing process we observe a coexistence of outer spool domain and a twisted nematic core – in a perfect agreement with available cryo-EM experimental observations. Our findings suggest that the nonlinear elasticity of biological molecules plays an important role in their spatial structuring in confined biological systems. 

References

[1] T. Curk, J.D. Farrell, J. Dobnikar, R. Podgornik, Spontaneous Domain Formation in Spherically Confined Elastic Filaments, Phys. Rev. Lett. 123 047801 (2019)

[2] J.D. Farrell, J. Dobnikar, R. Podgornik, T. Curk: Spool-nematic ordering of dsDNA and dsRNA under confinement, Phys. Rev. Lett. 133 148101 (2024)