DNA Dynamics in Dual-Nanopore Tug-of-War

Solid-state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of a molecule through the pore remains a key limitation. We have previously demonstrated that an active dual-nanopore system, consisting of two closely spaced pores operated via feedback-controlled biasing, shows promise in achieving controlled, slowed-down translocation. In this dual-pore device, translocation control is achieved via capturing the DNA in a special tug-of-war configuration, whereby opposing electrophoretic forces at each pore are applied to a DNA molecule cocaptured at the two pores. Here, we systematically explore translocation physics during DNA tug-of-war, focusing on genomically relevant longer dsDNA using a T4-DNA model (166 kbp). We find that longer molecules can be trapped in tug-of-war states with an asymmetric partitioning of the contour between the pores. Second, we extend dual-nanopore control to regulate DNA disengagement from the tug-of-war configuration, demonstrating the ability to tune the velocity of the disengaged DNA free end. We further investigate the physics of DNA free-end escape, in particular how the free-end velocity depends on DNA size and the presence of additional DNA strands between the pores (i.e., arising in the presence of folded translocation). These findings validate theoretical predictions from a first-passage model and demonstrate control over both the translocation and disengagement phases while providing insight into DNA disengagement in tug-of-war.