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Modeling DNA in viral capsids: liquid crystal with bending

The problem of the encapsidation and subsequent ejection of DNA in bacteriophages is still an unsolved problem. It is known that, depending on both the length of the encapsidated genome as well as the physicochemical environment, the viral DNA undergoes several phase transitions[A. Leforestier, J. Biol. Phys. 39, 201 (2013)]. There are currently two predominant models of the DNA packaging and ejection in bacteriophages[I. Molineux and D. Panja, Nature Rev. Microbiol. 11, 194 (2013)]: the continuum mechanics model and the hydrodynamic model. Both models do not take into account the phase changes seen in the conformation of DNA in partially filled capsids – as the capsid is emptied DNA undergoes a series of transitions from a densely packed hexagonal state trough a liquid crystal and ending in an isotropic state before the last of the DNA is ejected. The problem of the DNA organization in the presence of monovalent and divalent counterions at low packing densities is approached using the Onsager approach to lyotropic polymer liquid crystals[T. Odijk, Macromolecules 19, 2313 (1986)]. We obtain the free energy of the encapsidated genome in confinement with added contributions from DNA bending. Implications for DNA ejection in bacteriophages are discussed.

viral capsid; liquid crystal; phase transition; DNA

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