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

'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.