Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors
Abstract
1. Introduction
2. Results
2.1. Buffer Optimization
2.2. Aptamer-to-Fluorescent Ratio
2.3. CV30S Aptamer Splitting
2.4. Design of DNA Nanosensors
2.5. Optimization of Fragment Ratios in Binary Sensors
2.6. Limit of Detection (LOD)
3. Discussion
4. Materials and Methods
4.1. Materials
4.2. Buffer Optimization
4.3. Aptamer-to-CV Ratio
4.4. Aptamer Splitting
4.5. Binary Sensor Design
- While selecting the recognition site for the biosensor, the secondary structure of the target DNA region must be taken into account.
- If the target DNA sequence folds into a complex secondary structure forming a loop, the sensor arms should be placed on the same side of the loop.
- The melting temperature should be within the range of 35–40 °C for detection at 37 °C or 50–60 °C for detection at 55 °C.
- Each sequence should be linked to one of the aptamer sequences through a T-linker composed of two to six thymidine residues.
- Each sensor arm must be checked for secondary structure formation at 37 °C and 55 °C. They should not form loop structures, and the overall Gibbs free energy of the structure should not exceed -4 kcal/mol.
4.6. Binary Sensor Arm Ratio Optimization
4.7. Limits of Detection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
CV | Crystal Violet |
G4 | G-Quadruplex |
LOD | Limit of Detection |
S/B | Signal-to-Background |
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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
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 StyleBobkov, 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 StyleBobkov, 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