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

Abstract

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 (∼123 nm) of red-and green-emission quantum dot-layered cerasome and an outer shell (∼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.

Dual miRNA-Triggered DNA Walker Assisted by APE1 for Specific Recognition of Tumor Cells

“…Recently, many efforts have been made to achieve specific discrimination of cells. 11,12 However, the rapid and accurate identification of tumor cells by imaging disease-related biomarkers remains a challenge due to some non-negligible drawbacks. (a) Low contrast.…”

“…In situ imaging disease-related biomarkers, such as ions, small molecules, proteins, and RNA, have seen significant progress and sparked widespread interest. Recently, many efforts have been made to achieve specific discrimination of cells. , However, the rapid and accurate identification of tumor cells by imaging disease-related biomarkers remains a challenge due to some non-negligible drawbacks. (a) Low contrast.…”

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

“…To tackle the present problems with DNA storage, it is essential to develop a platform that can support the repeated reading of DNA information while also protecting it. Spherical nucleic acids (SNAs) are composed of a particle core and a shell of densely arranged, oriented oligonucleotides. − Oligonucleotides can be attached to the particle core in a covalent or noncovalent manner through a linker moiety. − The unique three-dimensional (3D) architecture of SNAs protects the oligonucleotides from nuclease-mediated degradation, increases oligonucleotide bioavailability, and facilitates special molecular recognition with a binding affinity a hundred times higher for complementary sequences compared with their linear counterparts. , SNAs also offer a practical and suitable vector for a variety of nucleic acid amplifications, including the polymerase chain reaction (PCR). , These advantages make SNAs an excellent biomedicine platform that has been widely used for gene/immune therapy, biosensing, and bioimaging in the past. − To the best of our knowledge, the applications of SNAs as reliable DNA storage platforms are seldom.…”