A DNA Rotary Pump

Biological transmembrane molecular machines such as ATP synthase and flagellar motors couple chemical gradients to rotary motion and are essential to life. These biological pumps utilize energy and information ratchet mechanisms to overcome Brownian motion and directionally transport solutes across membranes. By contrast, fluid flow can be attained at the macroscopic level by continuous rotary motion. Here we explore the limits of rotary pump miniaturization by investigating the possibility of constructing a nanoscale Archimedes screw pump from a rapidly rotating DNA helix within a nanopore. Atomistic molecular dynamics simulations revealed that MHz rotational frequencies would be needed to surpass Brownian motion. Net water and ion translocation was driven in the same direction, irrespective of the charge on the DNA or nanopore, which was consistent with a nanoscale screw-pump mechanism. The efficiency of transduction of mechanical rotational input to the direction mechanical transport of water and ions was <0.00001%. Species flux followed the order water ≫ K+ > Na+ > Cl- ≫ Mg2+ ≈ Ca2+. The transport selectivity between cations and anions generated ionic currents (<100 pA). Altering the charges on the DNA, nanopore, and electrolyte modulated ion selectivity, and even reversed the generated streaming current in some scenarios. These simulations underscore the requirement for ratchet-based mechanisms in molecular machines operating at low velocities, while also providing insights that might be exploited in the design of advanced nanofluidic devices for ion separation or energy transduction.