Sustained, Reversible, and Adaptive Non-Equilibrium Steady States of a Dissipative DNA-Based System

Abstract

Inspired by nature, researchers have developed several chemical fuel-driven supramolecular systems aimed at achieving improved kinetic control over their formation and functions. Alongside, DNA-based systems regulated by energy-dissipating mechanisms have been reported. However, the majority of these systems rely on batchwise additions of chemical fuels to closed reactors, resulting in transient non-equilibrium states that differ fundamentally from the sustained and highly adaptable non-equilibrium steady states (NESS) maintained by living systems through continuous energy dissipation. Here, we demonstrate sustained NESS of a dissipative DNA strand-displacement reaction achieved through the continuous supply of an RNA fuel to an open semi-batch reactor, using a custom automated setup that enables tunable fuel infusion rates and in situ analysis. Similar to biological NESS, our system dynamically adapts in real-time to subtle variations in fuel supply, achieving different steady-state levels of the strand-displacement reaction. Our approach demonstrates remarkable on-the-fly control over a dissipative DNA nanosystem, unachievable when working under batch conditions. Importantly, by fitting the experimental data to a kinetic model of the reaction network, we were able to confirm that the observed steady states correspond to true non-equilibrium compositions of the system.