Ribozymes, DNAzymes, and Fluorescent Aptamers: Diversity, Mechanisms, and Prospects for Bioanalytical Applications

Ribozymes, DNAzymes, and fluorescent light-up aptamers combine sequence-programmable recognition with catalytic activity or ligand-dependent signal generation. Our review examines their functional diversity, current progress in studies of structure and mechanisms of action, and potential for analytical applications. Natural and in vitro-selected ribozymes and DNAzymes are considered in relation to phosphodiester-bond hydrolysis, ligation, phosphorylation/dephosphorylation, covalent modification, photochemical reactions, and peroxidase-like oxidation. Particular attention is given to the relationship between catalytic core architecture, substrate and cofactor positioning, metal ion coordination, nucleobase participation, and reaction mechanisms. We consider fluorescent aptamer–fluorogen pairs as analogs of catalytic nucleic acids, since they employ RNA or DNA structures to activate fluorescence through fluorogen immobilization, conformational restriction, or chemical transformation. Bioanalytical applications of ribozymes and DNAzymes include the detection of nucleic acids, viral RNA, metal ions, nucleotides, enzymes, pathogens, and small molecules, while aptamer/fluorogen pairs are particularly well-suited for fluorescence imaging of RNA and metabolites in living cells. The review highlights the growing integration of catalytic nucleic acids with amplification strategies, nanomaterials, aptamer domains, and optical or electrochemical reporters. Although functional diversity increases almost every year, structural information and comprehensive structure–function datasets remain limited. Future progress will depend on structural characterization, improved computational modeling, machine-learning-assisted design, and the development of robust, biocompatible systems for broad bioanalytical use.