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SummaryBiological membrane channels mediate information exchange between cells and facilitate molecular recognition1-4. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout5-8. This challenge at the biotic-abiotic interface results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices9. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces that resolve the ‘iono-electronic’ disparity between the biotic environment and electronics. Through simulations and experiments, we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioelectronic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin, without disrupting the native environment of the biomolecule. We anticipate this robust biotic-abiotic interface will allow facile electronic measurement of inter-cellular ionic communication and also open the door for active control of cell behavior through externally controlled selective gating of the channels.