Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors

Bobkov, Gleb A.; Yushkov, Gleb S.; Kuzmin, Andrei D.; Popysheva, Tatiana D.; Stepchenkova, Elena I.; Rubel, Maria S.

doi:10.3390/ijms26199833

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Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors

by

Gleb A. Bobkov

^1,2,3,†

,

Gleb S. Yushkov

^2,†,

Andrei D. Kuzmin

^1,2,

Tatiana D. Popysheva

²,

Elena I. Stepchenkova

^1,3,*

and

Maria S. Rubel

^1,2,*

¹

Laboratory of Amyloid Biology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia

²

Center for Molecular and Biological Technologies, ITMO University, 191002 Saint Petersburg, Russia

³

Vavilov Institute of General Genetics, Saint Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2025, 26(19), 9833; https://doi.org/10.3390/ijms26199833 (registering DOI)

Submission received: 15 September 2025 / Revised: 5 October 2025 / Accepted: 8 October 2025 / Published: 9 October 2025

(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)

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Abstract

‘Light-up’ aptamers are short oligonucleotides that can induce fluorescence of certain organic compounds upon binding. In this study, we compared three crystal violet (CV) aptamers—CV30S, parallel G-quadruplex (G4), and antiparallel G4—regarding their absolute fluorescence intensity, signal-to-background ratio (S/B), and potential as a core component in binary sensors for nucleic acid detection. The G4 antiparallel aptamer exhibited the highest fluorescence intensity and a robust S/B ratio, indicating its effectiveness in stabilizing the CV binding and enhancing fluorescence. In contrast, the G4 parallel aptamer demonstrated poorer performance, suggesting that its structural topology is less suitable for interactions with CV. The CV30S aptamer showed distinct advantages in binary sensor configurations, achieving the best limit of detection at 6 nM.

Keywords: crystal violet; aptamer; ‘light-up’ aptamer; CV30S; G-quadruplex; binary sensor

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MDPI and ACS Style

Bobkov, G.A.; Yushkov, G.S.; Kuzmin, A.D.; Popysheva, T.D.; Stepchenkova, E.I.; Rubel, M.S. Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors. Int. J. Mol. Sci. 2025, 26, 9833. https://doi.org/10.3390/ijms26199833

AMA Style

Bobkov GA, Yushkov GS, Kuzmin AD, Popysheva TD, Stepchenkova EI, Rubel MS. Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors. International Journal of Molecular Sciences. 2025; 26(19):9833. https://doi.org/10.3390/ijms26199833

Chicago/Turabian Style

Bobkov, Gleb A., Gleb S. Yushkov, Andrei D. Kuzmin, Tatiana D. Popysheva, Elena I. Stepchenkova, and Maria S. Rubel. 2025. "Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors" International Journal of Molecular Sciences 26, no. 19: 9833. https://doi.org/10.3390/ijms26199833

APA Style

Bobkov, G. A., Yushkov, G. S., Kuzmin, A. D., Popysheva, T. D., Stepchenkova, E. I., & Rubel, M. S. (2025). Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors. International Journal of Molecular Sciences, 26(19), 9833. https://doi.org/10.3390/ijms26199833

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors

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