Abstract: Objective: The enhanced performance of molecular sensors for diagnostics by utilizing a DNA-cassette nanostructure can improve the delivery of fluorogenic substrates to the catalytic core of a binary (split) DNAzyme (BiDz), resulting in reduced background noise compared to traditional designs. Methods: In vitro methods of fluorescence measurement and gel shifts to assess secondary structures, sensitivity and selectivity of the designs were used. Results and Discussion: The modified sensor had reduced background than DNA-cassette-free BiDz sensor of traditional design. Conclusions: This innovation aims to increase the sensitivity and reliability of nucleic acid-based sensors in future in vivo diagnostic applications.