Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation

TL;DR

This study combines analytical modeling and simulations to understand the structures and forces involved in DNA condensation, revealing length-dependent effects and differences in force-extension behavior between toroidal and rod-like formations.

Contribution

The paper introduces an analytical model and Langevin dynamics simulations to predict DNA condensation structures and forces, highlighting finite-size effects and structural signatures.

Findings

Critical condensation force depends on DNA length

Force-extension behavior differs between toroidal and rod-like structures

Rod-like structures are difficult to detect in experiments due to protective effects of polyamines

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 {\mu}m. 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