The Two Classic Pb2+ -Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity

Fingerprinting DNAzyme Cross-Reactivity for Pattern-Based Detection of Heavy Metals

Heavy metal contamination in food and water is a major public health concern because heavy metals are toxic in minute amounts. DNAzyme sensors are emerging as a promising tool for rapid onsite detection of heavy metals, which can aid in minimizing exposure. However, DNAzyme activity toward its target metal is not absolute and has cross-reactivity with similar metals, which is a major challenge in the wide-scale application of DNAzyme sensors for environmental monitoring. To address this, we constructed a four DNAzyme array (17E, GR-5, EtNA, and NaA43) and used a pattern-based readout to improve sensor accuracy. We measured cross-reactivity between three metal cofactors (Pb2+, Ca2+, and Na+) and common interferents (Mg2+, Zn2+, Mn2+, UO22+, Li+, K+, and Ag+) and then used t-SNE analysis to identify and quantify the metal ion. We further showed that this method can be used for distinguishing mixtures of metals and detecting Pb2+ in environmental soil samples at micromolar concentrations.

The Programmable Catalytic Core of 8-17 DNAzymes

8-17 DNAzymes (8-17, 17E, Mg5, and 17EV1) are in vitro-selected catalytic DNA molecules that are capable of cleaving complementary RNAs. The conserved residues in their similar catalytic cores, together with the metal ions, were suggested to contribute to the catalytic reaction. Based on the contribution of the less conserved residues in the bulge loop residues (W12, A15, A15.0) and the internal stem, new catalytic cores of 8-17 DNAzymes were programmed. The internal stem CTC-GAG seems to be more favorable for the DNAzymes than CCG-GGC, while an extra W12.0 led to a significant loss of activity of DNAzymes, which is contrary to the positive effect of A15.0, by which a new active DNAzyme 17EM was derived. It conducts a faster reaction than 17E. It is most active in the presence of Pb2+, with the metal ion preference of Pb2+ >> Zn2+ > Mn2+ > Ca2+ ≈ Mg2+. In the Pb2+ and Zn2+-mediated reactions of 17EM and 17E, the same Na+- and pH dependence were also observed as what was observed for 17E and other 8-17 DNAzymes. Therefore, 17EM is another member of the 8-17 DNAzymes, and it could be applied as a potential biosensor for RNA and metal ions.

Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout

Stimuli-responsive DNA hydrogels have shown great potential in sensing applications due to their attractive properties such as programmable target responsiveness, excellent biocompatibility, and biodegradability. In contrast to the extensively developed DNA hydrogel sensing systems based on the stimuli-responsive hydrogel-to-solution phase transition of the hydrogel matrix, the quantitative sensing application of DNA hydrogels exhibiting smart shape deformations has rarely been explored. Moreover, bulk DNA hydrogel-based sensing systems also suffer from high material cost and slow response. Herein, free-standing bilayer polyacrylamide/DNA hybrid hydrogel films with programmable responsive properties directed by the sequence of functional DNA units have been constructed. Compared with bulk DNA hydrogels, these DNA hydrogel films with a thickness at the micrometer scale not only greatly reduce the consumption of DNA materials but also facilitate the mass transfer of biomacromolecular substances within the hydrogel network, thus favoring their sensing applications. Therefore, a target-responsive smart DNA hydrogel film-based sensor system is further demonstrated based on the large amplitude macroscopic shape deformation of the film as a visual signal readout. As a proof of concept, Pb2+ or UO22+ ion-responsive DNA units were introduced into the active layer of the bilayer hydrogel films. In the presence of Pb2+ or UO22+ ions, the occurrence of a cleavage reaction within the DNA units leads to the release of DNA segments from the hydrogel film, inducing a dramatic shape deformation of the film, and thus sensing of Pb2+ or UO22+ ions with high specificity is achieved based on measuring the bending angle changes of these smart free-standing films. These smart DNA hydrogel film sensors with target-programmable responsiveness, simple operation, and ease of storage may hold promise for future rapid on-site testing applications.

Improving the Sensitivity of a Mn(II)-Specific DNAzyme for Cellular Imaging Sensor through Sequence Mutations

Detection of Mn2+ in living cells is important in understanding the roles of Mn2+ in cellular processes and investigating its potential implications in various diseases and disorders. Toward this goal, we have previously selected a Mn2+-specific 11-5 DNAzyme through an in vitro selection method and converted it into a fluorescence sensor for intracellular Mn2+ sensing. Despite the progress, the nucleotides responsible for the activity are unclear, and the performance of the DNAzyme needs to be improved in order for more effective applications in biological systems. To address these issues, we herein report site-specific mutations within the catalytic domain of the selected 11-5 DNAzyme. As a result, we successfully identified a variant DNAzyme, designated as Mn5V, which exhibited a twofold increase in activity compared to the original 11-5 DNAzyme. Importantly, Mn5V DNAzyme maintained its high selectivity for Mn2+ over other competing metal ions. Upon the addition of Mn2+, Mn5V DNAzyme exhibited a higher fluorescence signal within the tumor cells compared to that of the 11-5 DNAzyme. This study therefore provides a better understanding of how the DNAzyme functions and a more sensitive probe for investigating Mn2+ in biological systems.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Electrochemical Biosensor Using Nitrogen-Doped Graphene/Au Nanoparticles/DNAzyme for Ca2+ Determination

An electrochemical biosensor for detecting Ca²⁺ concentration was proposed using glass carbon electrodes (GCEs) modified with nitrogen-doped graphene (NGR), gold nanoparticles (AuNPs) and DNAzyme. The resistance signal was amplified through two methods: electrochemical reduction of AuNPs on the NGR surface to increase the specific surface area of the electrode and strengthen the adsorption of DNAzyme; and increasement of the DNAzyme base sequence. The process of electrode modification was characterized by scanning electron microscopy, Raman spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Experimental parameters’ influence, such as the deposition time of gold nanoparticles and the detection time, were assessed by electrochemical methods. The linear ranges of the electrochemical biosensor were in the range from 5 × 10⁻⁶ to 5 × 10⁻⁵ and 5 × 10⁻⁵ to 4 × 10⁻⁴ M, with a detection limit of 3.8 × 10⁻⁶ M. The concentration of Ca²⁺ in the serum of dairy cows was determined by the biosensor with satisfactory results, which could be potentially used to diagnose subclinical hypocalcemia.

Activation of 8-17 DNAzyme with extra functional group at conserved residues is related to catalytic metal ion

In 8-17 DNAzyme, the end loop A⁶G⁷C⁸ is a highly conserved motif. Here we reported an activation approach by specific chemical modifications on A6 and C8 for more efficient Ca²⁺-mediated reaction. The importance of the end loop was further highlighted and its critical conservation broken for more powerful catalysts.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme

The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb²⁺ giving the fastest cleavage. In this study, the metal-phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni²⁺ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, R_p and S_p, indicated that Mg²⁺, Mn²⁺, Fe²⁺, and Co²⁺ had the highest S_p:R_p activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb²⁺, suggesting inner-sphere coordination. The pH-rate profiles showed that Pb²⁺ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pK_a and the pK_a of metal-bound water. Combining previous reports and our current results, we propose that Pb²⁺ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.

A new Pb2+-specific DNAzyme by revisiting the catalytic core of 10-23 DNAzyme

10-23 DNAzyme is a catalytic DNA molecule from in vitro selection, the 15-mer catalytic core was investigated for more DNAzyme variants by block deletions. DNAzyme DZM01 was selected with metal ion dependence of Pb²⁺ ≫ Mn²⁺, with no activity in the presence of Mg²⁺ (20 mM), Ca²⁺ (20 mM), Zn²⁺ (20 mM, pH 6). The unique binding properties of Pb²⁺ with nucleic acids might be responsible for the formation of the catalytic core, which is different from that of other divalent metal ions. More DNAzyme variants are expected to be derived for specific metal ion dependence by various nucleobase sequences and modifications.

Suppressing the background activity of hemin for boosting the sensitivity of DNAzyme-based biosensors by SYBR Green I

Peroxidase-like DNAzymes have been extensively used to replace horseradish peroxidase (HRP) for developing biosensors for signal amplification. However, the background activity from the cofactor (i.e., free hemin) has limited the sensitivity of such sensors. Herein, we aim to find an inhibitor for hemin to suppress the background signal, and a classic split DNAzyme-based sensor was used to detect a complementary DNA oligonucleotide. After screening a series of dyes, SYBR Green I (SG, one of the DNA stanning dyes) was selected for suppressing the background. Simply by adding 0.84 μM SG, the background from 50 nM hemin was suppressed over 30-fold. The suppression was caused by the interaction between SG and hemin. In the presence of the target DNA, the formed duplex region and G-quadruplex structure can better bind SG and hemin respectively, thus preventing the interaction between them and showing a high activity of the DNAzyme. The optimized sensor showed a detection limit of 3.8 pM for the target DNA (p53 gene). In addition, the backgrounds from chemiluminescence, colorimetric and fluorescence sensing modes can all be reduced by adding SG to the split DNAzyme system. The suppression of the background of peroxidase DNAzymes is a critical step towards practical use of related biosensors.

Pb2+ as a Substrate and a Cofactor of a Porphyrin Metalation DNAzyme

We herein report a DNAzyme named T30695 (sequence: (G₃ T)₄ ) that can catalyze Zn²⁺ insertion into three different porphyrins in the presence of Pb²⁺ as a cofactor. Meanwhile, T30695 with Pb²⁺ alone was found to cause a shift in both the fluorescence and UV-vis spectra of protoporphyrin IX (PPIX), thus suggesting that metalation of Pb²⁺ was also achieved at room temperature. From kinetic measurements, the reaction required two Pb²⁺ ions; this is consistent with one being a cofactor and the other being a substrate. No previous reports inserted Pb²⁺ into porphyrins by using DNAzymes or protein-based enzymes. This reaction was most significantly inhibited in the presence of K⁺ followed by Na⁺ and Li⁺ , suggesting the importance of the Pb²⁺ -stabilized G-quadruplex. When Pb²⁺ is inserted into PPIX, its emission blue shifts from 635 to 590 nm, thus allowing simple ratiometric fluorescent sensing with a detection limit of 1.2 nM Pb²⁺ .

Sensitivity of a classic DNAzyme for Pb2+ modulated by cations, anions and buffers

Both cations and anions in salt strongly affect the activity of a classic Pb²⁺ specific DNAzyme, which in turn can affect the sensitivity of related biosensors.