Photoactivatable Engineering of CRISPR/Cas9-Inducible DNAzyme Probe for In Situ Imaging of Nuclear Zinc Ions

DNAzyme-based fluorescent probes for imaging metal ions in living cells have received much attention recently. However, employing in situ metal ions imaging within subcellular organelles, such as nucleus, remains a significant challenge. We developed a three-stranded DNAzyme probe (TSDP) that contained a 20-base-pair (20-bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure. With this design, the CRISPR/Cas9-inducible imaging of nuclear Zn2+ is demonstrated in living cells. Moreover, the superiority of CRISPR-DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn2+ in both HeLa cells and mice. Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal-associated biology.

Endogenous Enzyme-Operated Spherical Nucleic Acids for Cell-Selective Protein Capture and Localization Regulation

Precise regulation of protein activity and localization in cancer cells is crucial to dissect the function of the protein-involved cellular network in tumorigenesis, but there is a lack of suitable methodology. Here we report the design of enzyme-operated spherical nucleic acids (E-SNAs) for manipulation of the nucleocytoplasmic translocation of proteins with cancer-cell selectivity. The E-SNAs are constructed by programmable engineering of aptamer-based modules bearing enzyme-responsive units in predesigned sites and further combination with SNA nanotechnology. We demonstrate that E-SNAs are able to regulate cytoplasmic-to-nuclear shuttling of RelA protein efficiently and specifically in tumor cells, while they remain inactive in normal cells due to insufficient enzyme expression. We further confirmed the generality of this strategy by investigating the enzyme-modulated inhibition/activation of thrombin activity by varying the aptamer-based design.

Selection of RNA-Cleaving TNA Enzymes for Cellular Mg2+ Imaging

Catalytic DNA-based fluorescent sensors have enabled cellular imaging of metal ions such as Mg²⁺ . However, natural DNA is prone to nuclease-mediated degradation. Here, we report the in vitro selection of threose nucleic acid enzymes (TNAzymes) with RNA endonuclease activities. One such TNAzyme, T17-22, catalyzes a site-specific RNA cleavage reaction with a k_cat of 0.017 min^-1 and K_M of 675 nM. A fluorescent sensor based on T17-22 responds to an increasing concentration of Mg²⁺ with a limit of detection at 0.35 mM. This TNAzyme-based sensor also allows cellular imaging of Mg²⁺ . This work presents the first proof-of-concept demonstration of using a TNA catalyst in cellular metal ion imaging.

Recent Advances on DNAzyme-Based Sensing

DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.

Boronic Acid-Mediated Activity Control of Split 10-23 DNAzymes

The 10-23 DNAzyme is an artificially developed Mg2+ -dependent catalytic oligonucleotide that can cleave an RNA substrate in a sequence-specific fashion. In this study, new split 10-23 DNAzymes made of two nonfunctional fragments, one of which carries a boronic acid group at its 5' end, while the other has a ribonucleotide at its 3' end, were designed. Herein it is demonstrated that the addition of Mg2+ ions leads to assembly of the fragments, which in turn induces the formation of a new boronate internucleoside linkage that restores the DNAzyme activity. A systematic evaluation identified the best-performing system. The results highlight key features for efficient control of DNAzyme activity through the formation of boronate linkages.

Target-Cell-Specific Bioorthogonal and Endogenous ATP Control of Signal Amplification for Intracellular MicroRNA Imaging

A stringent signal amplification method to profile microRNA (miRNA) expression within a specific cell remains a key challenge in biology. To address this issue, we report a target-cell-specific DNA nanosystem for endogenous adenosine-5'-triphosphate (ATP) bioorthogonal activation of the hybridization chain reaction (HCR) to spatiotemporally controlled signal amplification detection of miRNA in vitro and in vivo. The system consists of ATP aptamer-sealed engineered HCR functional units combined with a cancer cell membrane-encapsulated glutathione (GSH)-responsive metal-organic framework (MOF). Once the nanosystem is specifically and efficiently internalized into a cancer cell through membrane-mediated homing targeting, the MOF structure degrades and releases HCR functional units. The endogenous high expressional ATP recognizes the aptamer, allowing the HCR functional units to adopt its active modality. The activated HCR functional units are then able to spatiotemporally and bioorthogonally image miRNA with high sensitivity in vitro and in vivo.