Cerasome Spherical Nucleic Acid Nanostructure-Based AND Logic Gate-Guided Dual-DNAzyme Walker for Accurate Cancer Cell Identification

Spherical nucleic acids that consist of high-density oriented strands allow for tailoring of DNA computation and nanomachines and provide a unique nanoscale platform for biosensing and bioimaging. Herein, we report the construction of a core-shell-nanostructured dual-emission quantum dot-loaded cerasome spherical nucleic acid (QD2@C-SNA), and its use as an intracellular nanobiosensor via AND gate-guided dual-DNAzyme walker-mediated resonance energy transfer at the spherical nanoscale interface. QD2@C-SNA has an inner core (similar to 123 nm) of red- and green-emission quantum dot-layered cerasome and an outer shell (similar to 6 nm) of DNAzyme-AP site-DNAzyme/cDNA probe and a quencher-labeled substrate. In the presence of dual markers (inputs), namely, apurinic/apyrimidinic endonuclease 1 (APE1) and miRNA, the SNA shell performs an operation of AND gate-guided dual-DNAzyme walking: APE1 cleaves the AP site on DNAzyme-AP site-DNAzyme, exposing a middle toehold on cDNA; the middle toehold-mediated miRNA/cDNA hybridization displaces dual strands of DNAzyme from the duplex; the dual-DNAzyme walkers stochastically move along the substrate tracks, leaving the quenchers away from the SNA. This operation eliminates resonance energy transfer at the nanoscale core-shell interface, and the cerasome core outputs dual quantum dot-based ratiometric fluorescence: the reactivated green fluorescence relative to the constant red fluorescence, which is imaged by confocal laser scanning microscopy. As such, single-entity detection of dual endogenous markers is accomplished by the QD2@C-SNA nanobiosensor, and cancer/normal cells as well as cancer cell subtypes are well differentiated, showing improved imaging contrast and accuracy.

Automated summary

This study reports the construction of a core-shell-nanostructured dual-emission quantum dot-loaded cerasome spherical nucleic acid that acts as an intracellular nanobiosensor. The nanobiosensor uses AND gate-guided dual-DNAzyme walker-mediated resonance energy transfer to detect dual endogenous markers and differentiate cancer/normal cells and cancer cell subtypes with improved imaging contrast and accuracy.