Model of elastic responses of single DNA molecules in collapsing transition

Nonlinear elasticity of single collapsed polyelectrolytes

Nonlinear elastic responses of short and stiff polyelectrolytes are investigated by dynamic simulations on a single-molecule level. When a polyelectrolyte condensate undergoes a mechanical unfolding, two types of force-extension curves--i.e., a force plateau and a stick-release pattern--are observed depending on the strength of the electrostatic interaction. We provide a physical interpretation of such force-extension behavior in terms of intramolecular structures of the condensates. We also describe charge distributions of counterions condensed onto a polyelectrolyte, which clarify formation of one-dimensional strongly correlated liquid at large Coulomb coupling regime. These findings may provide significant insights into the relationship between a molecular elasticity and a molecular mechanism of like-charge attractions observed in a wide range of charged biopolymer systems.

Stepwise unfolding of collapsed polymers

Motivated by recent experimental data on DNA stretching in presence of polyvalent counterions, we study the force-induced unfolding of a homopolymer on and off lattice. In the fixed force ensemble the globule unravels via a series of steps due to surface effects which play an important role for finite-size chains. This holds both for flexible and stiff polymers. We discuss in a qualitative way how this result may impact on the interpretation of DNA stretching experiments showing peaks in the characteristic curves, by extracting from the raw data the corresponding elongation- versus-force characteristic curves. Furthermore, approximate analytical and numerical calculations, valid in a quasi-equilibrium fixed stretch ensemble, and if the initial low-temperature state is ordered in a spool, show that the average force versus elongation displays peaks related to the geometry of the initial configuration. We finally argue how the proposed mechanisms identified for the arising of peaks may couple in the experiments, and comment on the role of dynamic effects.

Elastic response of single DNA molecules exhibits a reentrant collapsing transition

We measured the elastic response of single DNA molecules at various concentrations of the trivalent cation, spermidine. When added spermidine caused the DNA to collapse, the force-extension curves showed either plateaus or stick-release patterns depending on the concentration. The periodic stick-release response determines a characteristic length, which may reflect toroidal supercoiling. At high concentrations of spermidine, we observed the reelongation of single molecules of collapsed DNA. Thus condensation occurs between lower and upper critical concentrations, verifying that the transition is reentrant as theoretically predicted.