Conformations of DNA Bundles in Viruses
Event details
| Date | 15.09.2015 |
| Hour | 14:15 |
| Speaker | Antonio Šiber, Ph.D., University of Zagreb (HR) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
Some sort of DNA “compression” is required to pack the long DNA strand in a small space, such as the cell nucleus or bacteria. Viruses have, in particular, developed several strategies to physically compress the DNA genome molecule. In presence of basic proteins [1] or multi-valent counterions, DNA can be “condensed”, i.e. brought to 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 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 [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 balance is in that case additionally complicated by the adsorption energy (DNA-capsid interaction) and by the capsid confinement [3]. 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 [4]. Nevertheless, such propositions were never tested in a suitable model, explaining the free energies of all the conformations that can be envisioned. Furthermore, it is not known how the conformations depend on the geometry of a virus, in particular whether its capsid is icosahedral or elongated, as is often the case for bacteriophage viruses. I will show a generalization of the previously proposed models [2] 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 [4], but also several intriguing conformations that were never predicted in the context of viruses.
[1] A. J. Perez-Berna, S. Marion, F. J. Chichon, J. J. Fernandez, D. C. Winkler, J. L. Carrascosa, A. C. Steven, A. Šiber, and C. San Martin, Nucl. Acids Res. 43, 4274 (2015).
[2] J. Ubbink and T. Odijk, Europhys. Lett. 33, 353 (1996).
[3] A. Leforestier, A. Šiber, F. Livolant, and R. Podgornik, Biophys. J. 100, 2209 (2011).
[4] N. V. Hud, Biophys. J. 69, 1355 (1995).
Bio:
EDUCATION
January 2007 – January 2008, Postdoc at Jožef Stefan Institute, Slovenia. Worked with Prof. dr. Rudolf Podgornik.
July 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
EMPLOYMENT
2010 - , scientific advisor, Institute of physics, Zagreb, Croatia
2007 - , higher scientific associate, Institute of physics, Zagreb, Croatia
2007 /2008, postdoctoral research associate, Institute Jožef Stefan, Ljubljana, Slovenia
2003 - 2007, scientific associate, Institute of physics, Zagreb, Croatia
2002 – 2003, higher research assistant, Institute of physics, Zagreb, Croatia
1997 – 2002, research assistant, Institute of physics, Zagreb, Croatia
Abstract:
Some sort of DNA “compression” is required to pack the long DNA strand in a small space, such as the cell nucleus or bacteria. Viruses have, in particular, developed several strategies to physically compress the DNA genome molecule. In presence of basic proteins [1] or multi-valent counterions, DNA can be “condensed”, i.e. brought to 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 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 [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 balance is in that case additionally complicated by the adsorption energy (DNA-capsid interaction) and by the capsid confinement [3]. 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 [4]. Nevertheless, such propositions were never tested in a suitable model, explaining the free energies of all the conformations that can be envisioned. Furthermore, it is not known how the conformations depend on the geometry of a virus, in particular whether its capsid is icosahedral or elongated, as is often the case for bacteriophage viruses. I will show a generalization of the previously proposed models [2] 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 [4], but also several intriguing conformations that were never predicted in the context of viruses.
[1] A. J. Perez-Berna, S. Marion, F. J. Chichon, J. J. Fernandez, D. C. Winkler, J. L. Carrascosa, A. C. Steven, A. Šiber, and C. San Martin, Nucl. Acids Res. 43, 4274 (2015).
[2] J. Ubbink and T. Odijk, Europhys. Lett. 33, 353 (1996).
[3] A. Leforestier, A. Šiber, F. Livolant, and R. Podgornik, Biophys. J. 100, 2209 (2011).
[4] N. V. Hud, Biophys. J. 69, 1355 (1995).
Bio:
EDUCATION
January 2007 – January 2008, Postdoc at Jožef Stefan Institute, Slovenia. Worked with Prof. dr. Rudolf Podgornik.
July 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
EMPLOYMENT
2010 - , scientific advisor, Institute of physics, Zagreb, Croatia
2007 - , higher scientific associate, Institute of physics, Zagreb, Croatia
2007 /2008, postdoctoral research associate, Institute Jožef Stefan, Ljubljana, Slovenia
2003 - 2007, scientific associate, Institute of physics, Zagreb, Croatia
2002 – 2003, higher research assistant, Institute of physics, Zagreb, Croatia
1997 – 2002, research assistant, Institute of physics, Zagreb, Croatia
Practical information
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