Collapse of DNA under alternating electric fields

Compression of a confined semiflexible polymer under direct and oscillating fields

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.

Polyelectrolyte in Electric Field: Disparate Conformational Behavior along an Aminopolysaccharide Chain

Electrical signals are increasingly used in fabrication of hydrogels (e.g., based on aminopolysaccharide chitosan) to guide the emergence of complex and anisotropic structure; however, how an imposed electric field affects the polymer chain conformation and orientation during the self-assembly process is not understood. Here, we applied nonequilibrium all-atom molecular dynamics simulations to explore the response of a charged chitosan chain comprising 5- or 20-monomer units to a constant uniform electric field in water and salt solution. While no conformational or orientational response was observed for the polyelectrolyte (PE) chains under the small electric fields within the simulation time, a field strength of 400 mV/nm induced significant changes. In water, a 5-mer chain is found to be slightly bent and oriented parallel to the field; however, surprisingly, a 20-mer chain displays candy-cane-like conformations whereby one half of the chain is collapsed and flexible, while the other half of the chain is stretched along the electric field. In salt solution, the disparity remains between the two halves of the 20-mer chain, although the backbone is extremely flexible with multiple bent regions and non-native conformations occur near the chain center in one of the three trajectories. The disparate conformational response along the polyelectrolyte chain may be attributed to the balancing forces between chain dynamics, electric polarization, counterion binding, and hydrodynamic pressure as well as friction. These findings reconcile existing experiments and theoretical studies and represent an important step toward understanding the complex roles of electric field and salt in controlling the structure and properties of soft matter.