Graphene nanopore device, since its proposal, has witnessed tremendous progress toward the goal of single-molecule detection. However, one central challenge of preparing electrodes with nanometer precision on the graphene remains unsolved. Here we show theoretically the feasibility of graphene/hexagonal BN (h-BN)/graphene structure where top graphene layer acts as one electrical contact while the bottom layer as the other. Based on quantum chemistry/nonequilibrium Green’s function investigation, we give clear physical pictures why ABC stacking of the above heterogeneous layers results in excellent insulating of the top and bottom graphene electrodes. On the other hand, when the target molecule is inside the nanopore the background conductance through the h-BN dielectric will not keep decreasing even though more layers of h-BN are inside the nanopore. The mechanism is illustrated as that the presence of the molecule will enhance the vertical transmission through the h-BN dielectric via quantum interference. We employ a single-level molecule model, and show quantitatively that the discussed effect can be utilized as a powerful signal amplifier for the molecule conductance, thus enhancing the measurability of single molecules by 3–4 orders. We report a novel design of graphene as electrical sensor for single-molecule detection, by employing natural self-assembly properties of graphene/multilayered h-BN/graphene for single-molecule detection. The novelty of our design is that we use the top and bottom graphene layers as two separate electrodes while the sandwiched h-BN layers as the insulating dielectric. Our theoretical study indicates that the ordered stacking of h-BN dielectric in the nanopore will result in intriguing quantum interference effects, which can be utilized for enhancing the sensitivity of the proposed device. The astonishing electrical capabilities of graphene films make them ideal for use in ‘nanopore’ sensors that detect minute conductance fluctuations from single molecules, such as DNA, passing through small openings. Masateru Taniguchi and co-workers from Osaka University, Japan, have now calculated a way to improve these devices using hexagonal boron nitride (h-BN), a substance with an atomically flat structure similar to graphene but practically no electric conductivity. Quantum simulations reveal that when h-BN multilayers are sandwiched between two graphene electrodes with a symmetry that repeats every three layers – a so-called ‘ABC’ stacking – the sensor’s background conductance is minimized. The introduction of single molecules into this arrangement causes the amplification of conductance signals by three to four orders of magnitude – a sensitivity boost that may prove invaluable to future biosensing applications.