engleski

Non-toroidal conformations of DNA condensed in spherical confinement

When condensed in free space, long DNA typically assumes a shape of a toroid. The geometry of the toroid, its inner and outer radii and the shape of its cross-section can be understood from a phenomenological model, describing condensation as an interplay between the (unfavorable) surface energy of the toroid and the (unfavorable) bending energy of the DNA strands in it – the only favorable contribution to the free energy is the volume term, requiring that the DNA strands be next to each other [1]. When condensed in confinement, e.g. in virus capsids, it is known that the, sufficiently short, DNA also assumes toroidal conformations, but the free energy balance is in that case additionally complicated by the adsorption energy (DNA-capsid interaction) and by the capsid confinement [2]. It has been proposed in the literature that the, sufficiently long DNA, may condense in conformations which are non-toroidal, i.e. which do not have the cylindrical axis of symmetry [3]. Nevertheless, such propositions were never tested in a suitable model, explaining the free energies of all the conformations that can be envisioned. I will show a generalization of the previously proposed models [1] to account for non-toroidal conformations of DNA condensed in spherical confinement. Such conformations may occur in viruses when they are completely filled. The model that I will present reproduces conformations that were previously predicted [3], but also several intriguing conformations that were never predicted in the context of viruses. [1] J. Ubbink and T. Odijk, Europhys. Lett. 33, 353 (1996). [2] A. Leforestier, A. Šiber, F. Livolant, and R. Podgornik, Biophys. J. 100, 2209 (2011). [3] N. V. Hud, Biophys. J. 69, 1355 (1995).

DNA; condensation; virus; confinement; elasticity; writhe

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