Ribozymes, DNAzymes, and Fluorescent Aptamers: Diversity, Mechanisms, and Prospects for Bioanalytical Applications
- 1Institute of Biophysics of the Siberian Branch of the Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- 2Knorre Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
Abstract
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.
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BibTeX
@article{shatunova2026ribozymes,
title = {{Ribozymes, DNAzymes, and Fluorescent Aptamers: Diversity, Mechanisms, and Prospects for Bioanalytical Applications}},
author = {Elizaveta A. Shatunova and Mariya A. Vorobyeva and Svetlana V. Markova and Eugene S. Vysotski},
journal = {Molecules},
year = {2026},
month = oct,
doi = {10.3390/molecules31213861},
url = {https://www.mdpi.com/1420-3049/31/21/3861},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Ribozymes, DNAzymes, and Fluorescent Aptamers: Diversity, Mechanisms, and Prospects for Bioanalytical Applications
AU - Elizaveta A. Shatunova
AU - Mariya A. Vorobyeva
AU - Svetlana V. Markova
AU - Eugene S. Vysotski
PY - 2026
DA - 2026/10/26
JO - Molecules
DO - 10.3390/molecules31213861
UR - https://www.mdpi.com/1420-3049/31/21/3861
AB - 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.
SN - 1420-3049
ER -