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The RNA-SCAN mechanism proceeds as follows (where the complementary strand regions indicated by matching colours). A hairpin-like nanolatch is first captured and opened by an overhang on the RNA/DNA carrier (self-assembled from a long RNA scaffold and short DNA oligos) through toehold-mediated strand displacement, exposing its target site-complementary segment. Molecular fluctuations in solution then bring the nanolatch’s free end into proximity to the target site, forming a metastable loop structure referred to as the ‘on the latch’ state, a configuration that is formed but not yet fastened. The subsequent stability of the loop depends on base-pairing strength between the nanolatch and target site, resulting in either a ‘latched’ state (where strong complementarity fastens the loop) or an ‘unlatched’ state (where weak binding leads to loop opening). During nanopore detection, the translocation of the carrier generates a characteristic baseline current drop. A six-dumbbell structure (marked in green) positioned next to the target site consistently produces a small spike of approximately half the amplitude of the first-level current drop generated by the carrier alone, serving as a reference. In comparison, a latched loop typically generates a spike larger than the reference spike, approaching the magnitude of the first-level current drop, while an unlatched loop yields minimal current fluctuation beyond the plateau.

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