title: Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation.
abstract: DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10(5)μm. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily detectable. In double-stranded DNA condensation experiments, the signature of the presence of rod-like structures was not unambiguously detected, suggesting that the polyamines used to condense DNA may protect it from bending sharply as needed in the rod-like structures.
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600,Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France.
authors.forename: Ruggero
authors.initials: R
authors.lastname: Cortini
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600,Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France.
authors.forename: Bertrand R
authors.initials: BR
authors.lastname: Caré
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600,Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Victor
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600,Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Barbi
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA