Knotted DNA Configurations in Bacteriophage Capsids: A Liquid Crystal Theory Approach

Abstract

Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement of DNA that corresponds to a hexagonal chromonic liquid-crystalline phase, and increase the topological complexity of the genome in the form of knots. A mathematical model that implements a chromonic liquid-crystalline phase and that captures the changes in topology has been lacking. We adopt a mathematical model that represents the viral DNA as a pair of a vector field and a line. The vector field is a minimizer of the total Oseen-Frank energy for nematic liquid crystals under chromonic constraints, while the line is identified with the tangent to the field at selected locations, representing the central axis of the DNA molecule. The fact that the Oseen-Frank functional assigns infinite energy to topological defects (point defects in two dimensions and line defects in three dimensions) precludes the presence of singularities and, in particular, of knot structures. To address this issue, we begin with the optimal vector field and helical line, and propose a new algorithm to introduce knots through stochastic perturbations associated with splay and twist deformations, modeled by means of a Langevin system. We conclude by comparing knot distributions generated by the model and by interpreting them in the context of previously published experimental results. Altogether, this work relies on the synergy of modeling, analysis and computation in the study of viral DNA organization in capsids.