2'-Functional group of adenosine in 10-23 DNAzyme promotes catalytic activity

Exploring the catalytic mechanism of the 10-23 DNAzyme: insights from pH-rate profiles

The 10-23 DNAzyme, a catalytic DNA molecule with RNA-cleaving activity, has garnered significant interest for its potential therapeutic applications as a gene-silencing agent. However, the lack of a detailed understanding about its mechanism has hampered progress. A recent structural analysis has revealed a highly organized conformation thanks to the stabilization of specific interactions within the catalytic core of the 10-23 DNAzyme, which facilitate the cleavage of RNA. In this configuration, it has been shown that G14 is in good proximity to the cleavage site which suggests its role as a general base, by activating the 2'-OH nucleophile, in the catalysis of the 10-23 DNAzyme. Also, the possibility of a hydrated metal acting as a general acid has been proposed. In this study, through activity assays, we offer evidence of the involvement of general acid-base catalysis in the mechanism of the 10-23 DNAzyme by analyzing its pH-rate profiles and the role of G14, and metal cofactors like Mg2+ and Pb2+. By substituting G14 with its analogue 2-aminopurine and examining the resultant pH-rate profiles, we propose the participation of G14 in a catalytically relevant proton transfer event, acting as a general base. Further analysis, using Pb2+ as a cofactor, suggests the capability of the hydrated metal ion to act as a general acid. These functional results provide critical insights into the catalytic strategies of RNA-cleaving DNAzymes, revealing common mechanisms among nucleic acid enzymes that cleave RNA.

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.

Parallel Synthesis of Pyrazolone-Fused Cinnolines by the Palladium-Catalyzed [4 + 2] Annulation of Pyrazol-3-ones with Substituted Allenoates

The synthesis of pyrazolone-fused cinnolines from pyrazol-3-ones and α,γ-substituted allenoates via a palladium-catalyzed C-H activation/annulation cascade was developed. Mechanistic studies revealed the course of the reaction. Initially, N-acyl-valine ligand-assisted ortho-C-H activation gives ortho-alkenylated intermediate. Subsequent cyclopalladation and migratory insertion of allenoate give a seven-membered palladacycle. Reductive elimination finally furnishes pyrazolone-fused cinnolines.

Triple Amplification Strategy of CHA-PER-DNAzyme for Ultrasensitive Detection of circRNA Associated with Hepatocellular Carcinoma

Biological and clinical studies have indicated that aberrant expression of circMTO1 served as a crucial biomarker for the diagnosis and prognosis of hepatocellular carcinoma (HCC) patients as well as a potential therapeutic target. However, the detection of circRNAs currently faces challenges such as homologous linear RNA interference and low-expression abundance of certain circRNAs. Therefore, we developed a triple amplification method based on catalytic hairpin assembly (CHA) activation by back-splice junction (BSJ), resulting in CHA products that triggered primer exchange reaction to generate DNAzyme. Subsequently, DNAzyme cleaved the fluorescent reporter chain, enabling ultrasensitive detection of hepatocellular carcinoma-associated circMTO1 through the output fluorescence signal. The catalytic hairpin opening sequence within CHA specifically targeted the BSJ sequence in circRNA, thereby avoiding false positive signals observed in circRNA assays due to the recognition of homologous linear RNA molecules. Moreover, this triple amplification method facilitated sensitive detection of circRNA and addressed the issue of low-abundance expression levels associated with circMTO1 in HCC samples. Notably, our newly designed assay for detecting circRNA exhibited a linear range from 1 fM to 100 nM with a detection limit of 0.265 fM. Furthermore, it demonstrated excellent and consistent performance even within complex systems. Our proposed method enabled the specific and sensitive detection of circMTO1 in various cancer cells and blood samples from HCC patients, providing an innovative approach for investigating the role of circRNA in tumorigenesis and development while promoting its clinical application.

DNAzymes: Expanding the Potential of Nucleic Acid Therapeutics

Nucleic acids drugs have been proven in the clinic as a powerful modality to treat inherited and acquired diseases. However, key challenges including drug stability, renal clearance, cellular uptake, and movement across biological barriers (foremost the blood-brain barrier) limit the translation and clinical efficacy of nucleic acid-based therapies, both systemically and in the central nervous system. In this study we provide an overview of an emerging class of nucleic acid therapeutic, called DNAzymes. In particular, we review the use of chemical modifications and carrier molecules for the stabilization and/or delivery of DNAzymes in cell and animal models. Although this review focuses on DNAzymes, the strategies described are broadly applicable to most nucleic acid technologies. This review should serve as a general guide for selecting chemical modifications to improve the therapeutic performance of DNAzymes.

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.