Scheme 1.

Design of deoxyribozyme (DZ) probes that produce fluorescent signal upon hybridization to specific nucleic acid analytes. A) Parent RNA-cleaving DZ can cleave a fluorophore- and quencher-labelled substrate (F_ sub), thus producing high fluorescence. B) Switch design for DZ hybridization probes: the catalytic core and/or substrate binding arms of DZ are inactivated by binding to the ‘inhibitory fragment’; hybridization of the analyte to the analyte binding domain releases the substrate binding arms of the DZ construct and enables cleavage of F_sub; C) Split design: two DNA strands DZa and DZb hybridize to the analyte sequence and form catalytically active DZ, which cleaves F_sub.