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Biosensors
Volume 15
Issue 9
10.3390/bios15090562
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

An Isothermal Deoxyribozyme Sensor for Rapid Detection of Enteroviral RNA

by
Begüm Şaş
1,2,*,
Anastasiia Dmitrievna Kirichenko
1,
Marina Anatolyevna Kapitonova
1,
Anna Vyacheslavovna Shabalina
1,
Olga Ilyinichna Kanaeva
3,
Tamer Mohammed El-Messery
2,
Vladimir Georgievich Dedkov
1,4 and
Anna Sergeevna Dolgova
1
1
Laboratory of Pathogen Molecular Genetics, Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
2
Faculty of Biotechnologies, ITMO University, 191002 St. Petersburg, Russia
3
Laboratory of Etiology and Control of Viral Infections, Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
4
Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia
*
Author to whom correspondence should be addressed.
Biosensors 2025, 15(9), 562; https://doi.org/10.3390/bios15090562 (registering DOI)
Submission received: 24 July 2025 / Revised: 20 August 2025 / Accepted: 26 August 2025 / Published: 27 August 2025
(This article belongs to the Section Environmental Biosensors and Biosensing)
Versions Notes

Abstract

Enteric viruses are a major cause of waterborne infections due to their high environmental stability and extremely low infectious dose. Current molecular diagnostic methods, while accurate, often depend on thermal cycling and centralized laboratory facilities, limiting their applicability in decentralized or resource-limited settings. In this study, we developed an isothermal biosensor based on a split deoxyribozyme that reconstitutes its catalytic core upon hybridization with a conserved sequence of enteroviral RNA. This activation leads to site-specific cleavage of a fluorogenic substrate, producing a quantifiable fluorescent signal. The system was experimentally validated using both synthetic enteroviral RNA and RNA extracted from environmental water samples. To enhance detection sensitivity, the DNAzyme-based assay was coupled with isothermal RNA amplification. The results demonstrate high selectivity and compatibility with real-world samples, supporting the sensor’s utility for field-deployable viral RNA detection. Overall, this study highlights the potential of the DNAzyme-based platform as a portable, sequence-specific, and amplification-assisted diagnostic tool for environmental surveillance of enteric viruses.
Keywords: enteroviral RNA detection; environmental water matrices; isothermal biosensor; NASBA-assisted amplification; split DNAzyme enteroviral RNA detection; environmental water matrices; isothermal biosensor; NASBA-assisted amplification; split DNAzyme

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MDPI and ACS Style

Şaş, B.; Kirichenko, A.D.; Kapitonova, M.A.; Shabalina, A.V.; Kanaeva, O.I.; El-Messery, T.M.; Dedkov, V.G.; Dolgova, A.S. An Isothermal Deoxyribozyme Sensor for Rapid Detection of Enteroviral RNA. Biosensors 2025, 15, 562. https://doi.org/10.3390/bios15090562

AMA Style

Şaş B, Kirichenko AD, Kapitonova MA, Shabalina AV, Kanaeva OI, El-Messery TM, Dedkov VG, Dolgova AS. An Isothermal Deoxyribozyme Sensor for Rapid Detection of Enteroviral RNA. Biosensors. 2025; 15(9):562. https://doi.org/10.3390/bios15090562

Chicago/Turabian Style

Şaş, Begüm, Anastasiia Dmitrievna Kirichenko, Marina Anatolyevna Kapitonova, Anna Vyacheslavovna Shabalina, Olga Ilyinichna Kanaeva, Tamer Mohammed El-Messery, Vladimir Georgievich Dedkov, and Anna Sergeevna Dolgova. 2025. "An Isothermal Deoxyribozyme Sensor for Rapid Detection of Enteroviral RNA" Biosensors 15, no. 9: 562. https://doi.org/10.3390/bios15090562

APA Style

Şaş, B., Kirichenko, A. D., Kapitonova, M. A., Shabalina, A. V., Kanaeva, O. I., El-Messery, T. M., Dedkov, V. G., & Dolgova, A. S. (2025). An Isothermal Deoxyribozyme Sensor for Rapid Detection of Enteroviral RNA. Biosensors, 15(9), 562. https://doi.org/10.3390/bios15090562

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