Integrating biological components into artificial devices establishes an interface to understand and imitate the superior functionalities of the living systems. One challenge in developing biohybrid nanosystems mimicking the gating function of the biological ion channels is to enhance the gating efficiency of the man-made systems. Herein, we demonstrate a DNA supersandwich and ATP gated nanofluidic device that exhibits high ON-OFF ratios (up to 106) and a perfect electric seal at its closed state (∼Gω). The ON-OFF ratio is distinctly higher than existing chemically modified nanofluidic gating systems. The gigaohm seal is comparable with that required in ion channel electrophysiological recording and some lipid bilayer-coated nanopore sensors. The gating function is implemented by self-assembling DNA supersandwich structures into solid-state nanochannels (open-to-closed) and their disassembly through ATP-DNA binding interactions (closed-to-open). On the basis of the reversible and all-or-none electrochemical switching properties, we further achieve the IMPLICATION logic operations within the nanofluidic structures. The present biohybrid nanofluidic device translates molecular events into electrical signals and indicates a built-in signal amplification mechanism for future nanofluidic biosensing and modular DNA computing on solid-state substrates.