DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

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.

PNA-Guided Peptide Engineering of Aptamer Sensor for Protease-Unlocked Molecular Imaging

Protease-triggered control of functional DNA has remained unachieved, leaving a significant gap in activatable DNA biotechnology. Here we disclose the design of a protease-activatable aptamer technology that can perform molecular sensing and imaging function in a tumor-specific manner. The system is constructed by locking structure-switching activity of aptamer using a rationally designed PNA-peptide-PNA triblock copolymer. Highly selective cleavage of the peptide substrate is achieved by protease-mediated enzymatic reaction that result in reduced binding affinity of PNA to the aptamer module, with the subsequently recovering its biosensing function. We demonstrated that the DNA/peptide/PNA hybrid system not only allows for tumor cell-selective ATP imaging in vitro , but it also produce a fluorescent signal in vivo with improved tumor specificity. This work illustrates the potential of bridging the gap between functional DNA field and peptide area for precise biomedical applications.

[Research progress of solid phase extraction materials in the application of metal ion pretreatment]

Monitoring of trace heavy metal pollutants released during industrial and agricultural processes is essential because of their widespread distribution in the environment and health hazards. Several techniques, including inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-optical emission spectrometry (ICP-OES), electrothermal atomic absorption (ETAAS), and flame atomic absorption spectrometry (FAAS), have been proposed for the determination of heavy metals in serum, plasma, whole blood, and food. All these techniques have earned robust recognition in the field of trace heavy metals and have many advantages such as multi-elemental analysis capability, large dynamic linear range, low detection limits, and high productivity. Nevertheless, most of the recommended techniques require digestion of the sample and extraction with an organic solvent for isolation of the metal ion from the sample solution prior to analysis. Despite improvements in the performance of modern analytical instruments, the direct determination of heavy metal ions in real samples is difficult because of their low concentration levels and matrix interference. Thus, extraction and clean-up steps are required for pre-concentration of the analyte, so that detection and elimination of the interfering matrix component are possible. Solid-phase extraction (SPE) is one of the popular metal ion pretreatment methods. The advantages of SPE include easy cartridge/column regeneration, high analytical frequency, and high preconcentration factors for sorbents with high adsorption capacities. On the other hand, when the analytes are extracted from a complex matrix such as serum and meat samples, large amounts of proteins from the samples can be retained on the sorbent surface, obstructing the binding sites on the sorbent and leading to poor precision and accuracy. The key to metal ion detection is the development of new SPE materials with high efficiency and enrichment factors as well as an effective pretreatment technology. Nanomaterials such as restricted-access carbon nanotubes, nanoadsorbents, nanoparticle carriers, and magnetic nanoparticles have shown great promise in advancing biomedical and environmental analysis because of the unique properties originating from their ultrafine dimensions. Nanomaterials can provide large specific surface areas and tunable functional groups to facilitate metal ion absorption. They could also possess superior optical properties and allow for high sensitivity in simple fluorescent or colorimetric detection methods. Owing to their excellent mechanical and chemical stability, polymer materials have been of great interest as adsorbents for the SPE of metal ions from solution. Moreover, a designed polymeric material can show triple functionality such as physical adsorption, chelate formation, and ion exchange for the target metal ions. A dual-functional nanomaterial-DNAzyme platform can simultaneously allow for the sensitive detection and effective removal of heavy metal ions in water. Thus, this platform can serve as a simple, cost-effective tool for rapid and accurate metal quantification in the determination of human metal exposure and inspection of environmental contamination. Furthermore, the new photocaged chelator can uncage and release the combined metal ions into an aqueous solution that is free of the other components of the matrix. In this manner, we can develop diagnostic tests for metal ions that are often difficult to detect using other methods. In this paper, the characteristics of new SPE materials, including nanomaterials, polymer materials, and functional materials as well as advances in their applications to the preparation of complex samples are summarized, and the direction for future development is proposed.

Detection and Quantification of Tightly Bound Zn2+ in Blood Serum Using a Photocaged Chelator and a DNAzyme Fluorescent Sensor

DNAzymes have emerged as a powerful class of sensors for metal ions due to their high selectivity over a wide range of metal ions, allowing for on-site and real-time detection. Despite much progress made in this area, detecting and quantifying tightly bound metal ions, such as those in the blood serum, remain a challenge because the DNAzyme sensors reported so far can detect only mobile metal ions that are accessible to bind the DNAzymes. To overcome this major limitation, we report the use of a photocaged chelator, XDPAdeCage to extract the Zn2+ from the blood serum and then release the chelated Zn2+ into a buffer using 365 nm light for quantification by an 8-17 DNAzyme sensor. Protocols to chelate, uncage, extract, and detect metal ions in the serum have been developed and optimized. Because DNAzyme sensors for other metal ions have already been reported and more DNAzyme sensors can be obtained using in vitro selection, the method reported in this work will significantly expand the applications of the DNAzyme sensors from sensing metal ions that are not only free but also bound to other biomolecules in biological and environmental samples.

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.