Non-equilibrium cyclic conformations of DNA under electrokinetic confinement

Abstract

Classic nanofluidic devices harness geometric confinement to modulate single polymer conformation and control chain dynamics. While classic nanofluidic devices have given rise to a range of applications, they are fundamentally limited by the static nature of their construction, which restricts real time control over molecular conformations. The reversible electrokinetic confinement (RECON) technique enables time-dependent control of DNA conformations in nanowells via dynamic modulation of field-induced confinement. Here, we demonstrate that applying dynamically varying confinement using stochastic and periodic signals can drive the confined polymer to access a range of non-equilibrium states, with the distinct configurations quantified via their radius of gyration tensor. For periodic driving, the device allows controlled cycling across conformational states, with distinct hysteresis observed in the shape anisotropy modulation. We quantify the interplay between the driving frequency, driving amplitude, and resulting hysteresis. Overall, our results establish RECON as a platform for active manipulation of single molecules, opening new avenues for studying non-equilibrium polymer physics and developing high-throughput, dynamically tunable nanofluidic devices.