BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Memento EPFL// BEGIN:VEVENT SUMMARY:Conformations of DNA Bundles in Viruses DTSTART:20150915T141500 DTSTAMP:20260429T231836Z UID:de2f81e5406a38922e6a447a83bc07fcd96e2df43804108343b71036 CATEGORIES:Conferences - Seminars DESCRIPTION:Antonio Šiber\, Ph.D.\, University of Zagreb (HR)\nBIOENGINEE RING SEMINARAbstract:\nSome sort of DNA “compression” is required to p ack the long DNA strand in a small space\, such as the cell nucleus or bac teria. Viruses have\, in particular\, developed several strategies to phys ically compress the DNA genome molecule. In presence of basic proteins [1] or multi-valent counterions\, DNA can be “condensed”\, i.e. brought t o a state where it self-attracts. When condensed in free space\, long DNA typically assumes a shape of a toroid. The geometry of the toroid can be u nderstood from a phenomenological model\, describing condensation as an in terplay between the (unfavorable) surface energy of the toroid and the (un favorable) bending energy of the DNA strands in it – the only favorable contribution to the free energy is the volume term\, requiring that the DN A strands be next to each other [2]. When condensed in confinement\, e.g. in virus protein coatings (capsids)\, it is known that the\, sufficiently short\, DNA also assumes toroidal conformations\, but the free energy bala nce is in that case additionally complicated by the adsorption energy (DNA -capsid interaction) and by the capsid confinement [3]. It has been propos ed in the literature that the\, sufficiently long DNA\, may condense in co nformations which are non-toroidal\, i.e. which do not have the cylindrica l axis of symmetry [4]. Nevertheless\, such propositions were never tested in a suitable model\, explaining the free energies of all the conformatio ns that can be envisioned. Furthermore\, it is not known how the conformat ions depend on the geometry of a virus\, in particular whether its capsid is icosahedral or elongated\, as is often the case for bacteriophage virus es. I will show a generalization of the previously proposed models [2] to account for non-toroidal conformations of DNA condensed in spherical confi nement. Such conformations may occur in viruses when they are completely f illed. The model that I will present reproduces conformations that were pr eviously predicted [4]\, but also several intriguing conformations that we re never predicted in the context of viruses.\n[1] A. J. Perez-Berna\, S. Marion\, F. J. Chichon\, J. J. Fernandez\, D. C. Winkler\, J. L. Carrascos a\, A. C. Steven\, A. Šiber\, and C. San Martin\, Nucl. Acids Res. 43\, 4 274 (2015).\n[2] J. Ubbink and T. Odijk\, Europhys. Lett. 33\, 353 (1996). \n[3] A. Leforestier\, A. Šiber\, F. Livolant\, and R. Podgornik\, Biophy s. J. 100\, 2209 (2011).\n[4] N. V. Hud\, Biophys. J. 69\, 1355 (1995).Bio :\nEDUCATION\nJanuary 2007 – January 2008\, Postdoc at Jožef Stefan Ins titute\, Slovenia. Worked with Prof. dr. Rudolf Podgornik.\nJuly 2002\, Ph .D. in solid state physics\, University of Zagreb\, Croatia. “Theory of thermal energy atom scattering from (sub)monolayers on solid surfaces”\, thesis advisor: Dr. Branko Gumhalter\nEMPLOYMENT\n2010 - \, scientific ad visor\, Institute of physics\, Zagreb\, Croatia\n2007 - \, higher scientif ic associate\, Institute of physics\, Zagreb\, Croatia\n2007 /2008\, postd octoral research associate\, Institute Jožef Stefan\, Ljubljana\, Sloveni a\n2003 - 2007\, scientific associate\, Institute of physics\, Zagreb\, Cr oatia\n2002 – 2003\, higher research assistant\, Institute of physics\, Zagreb\, Croatia\n1997 – 2002\, research assistant\, Institute of physic s\, Zagreb\, Croatia LOCATION:SV1717a http://map.epfl.ch/?room=sv1717a STATUS:CONFIRMED END:VEVENT END:VCALENDAR