Cu-DNAzyme facilitates highly sensitive immunoassay

DNAzyme-based ultrasensitive immunoassay: Recent advances and emerging trends

Immunoassay, as the most commonly used method for protein detection, is simple to operate and highly specific. Sensitivity improvement is always the thrust of immunoassays, especially for the detection of trace quantities. The emergence of artificial enzyme, i.e., DNAzyme, provides a novel approach to improve the detection sensitivity of immunoassay. Simultaneously, its advantages of simple synthesis and high stability enable low cost, broad applicability and long shelf life for immunoassay. In this review, we summarized the recent advances in DNAzyme-based immunoassay. First, we summarized the existing different DNAzymes based on their catalytic activities. Next, the common signal amplification strategies used for DNAzyme-based immunoassays were reviewed to cater to diverse detection requirements. Following, the wide applications in disease diagnosis, environmental monitoring and food safety were discussed. Finally, the current challenges and perspectives on the future development of DNAzyme-based immunoassays were also provided.

TMB+-mediated etching of urchin-like gold nanostructures for colorimetric sensing

The morphology-dependent localized surface plasmon resonance of gold nanostructures has been widely utilized for designing sensors. One method relies on the color change of gold nanoparticles upon etching. In previous work, TMB2+oxidized from 3,3',5,5'-tetramethylbenzidine (TMB) was found to etch gold nanorods (AuNRs), leading to a spectrum of different colors. However, the preparation of TMB2+needs the addition of a strong acid and other harsh conditions. Herein, a new colorimetric biosensing platform was developed using urchin-like gold nanoparticles (AuNUs). Compared with AuNRs, the etching of AuNUs can happen under mild conditions by TMB+at pH 6, protecting enzymes and proteins from denaturation. The role of CTAB surfactant was dissected, and its bromide ions were found to be involved in the etching process. Based on these observations, a one-step colorimetric detection of H2O2was realized by using horseradish peroxidase and H2O2to oxidize TMB. Within 30 min, this system achieved a detection limit of 80 nM H2O2. This work offered fundamental insights into the etching of anisotropic gold nanostructures and optimized the etching conditions. These advancements hold promise for broader applications in biosensing and analytical chemistry.

DNAzyme-templated exponential isothermal amplification for sensitive detection of lead pollution and high-throughput screening of microbial biosorbents

Very low concentrations of lead (Pb²⁺) pollution can have far-reaching adverse impacts on human health, due to the cumulative toxicity of Pb²⁺. Herein, we report a DNAzyme-templated exponential isothermal amplification strategy (termed DNAzymee) for the ultrasensitive detection of Pb²⁺ pollution and the high-throughput screening of microbial biosorbents to remove Pb²⁺ pollution. DNAzyme can specifically recognize Pb²⁺, and this recognition event can be amplified by the subsequent exponential isothermal amplification reaction (EXPAR) and monitored by a G-quadruplex specific dye. The proposed design showed a low limit of detection (95 pM) and could identify Pb²⁺ pollution in different real samples with high precision. In particular, the proposed assay was used to screen Pb²⁺ biosorbents, and the results showed that Leuconostoc mesenteroides is a promising microbial biosorbent for removing Pb²⁺ pollution. Thus, the DNAzymee assay can serve as a platform to monitor lead pollution in the environment and screen efficient biosorbents for the control of lead pollution.

Ratiometric Electrochemical Switch for Circulating Tumor DNA through Recycling Activation of Blocked DNAzymes

Circulating tumor DNA (ctDNA) serves as a powerful noninvasive and viable biomarker for the diagnosis of cancers. The abundance of ctDNA in patients with advanced stages is significantly higher than that in patients with early stages. Herein, a ratiometric electrochemical biosensor for the detection of ctDNA is developed by smart design of DNA probes and recycles of DNAzyme activation. The conformational variation of DNA structures leads to the changes of two types of electrochemical species. This enzyme-free sensing strategy promotes excellent amplification efficiency upon target recognition. The obtained results assure good analytical performances and a limit of detection as low as 25 aM is achieved. Additionally, this method exhibits outstanding selectivity and great application prospects in biological sample analysis.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.

Guanosine-rich aptamers@Cu2O nanoparticles: enhanced peroxidase activity and specific recognition capability at neutral pH

The decoration of Cu2O nanoparticles with guanosine-rich aptamers can significantly enhance their peroxidase activity at neutral pH and endow them with specific recognition capabilities. Both the phosphate backbone and guanine of the aptamers contribute to the enhancement. The excellent enzyme-like properties of this Cu2O-aptamer system make it a versatile platform for the development of neutral pH biosensors.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

In vitro Selection of Chemically Modified DNAzymes

DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.