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Surface-plasmon resonance (SPR)-induced enhanced fluorescence was used to detect the presence of fluorescent TOTO-1 bis-intercalated lambda-DNA complexes introduced into a periodic nanopore array. As we show, the proposed technique allows a high detection sensitivity by providing a strong fluorescence-signal efficiency from nano-confined fluorescent complexes. This novel platform could be used for sensing applications, or to detect and investigate the unique behaviors of nano-confined molecular systems.