Fluorescent modifications in aptamer switches—positional, structural, and neighboring pair effects on sensor performance

Aptamers are modular nucleic acid ligands increasingly used as recognition elements in biosensors for precision medicine. Their structure facilitates their adaptation into fluorescent switches through molecular design and conjugation with reporter molecules, which are typically selected based on optimal photophysical compatibility. However, a critical challenge persists: reporter molecules are not inert; their structure and underlying conjugation chemistry can introduce structural perturbations that adversely affect aptamer functional properties and DNA-duplex stability, subsequently impacting biosensing performance. Here, we evaluate the effect of fluorophore-quencher modifications by probing the interplay between reporter identity, local environment, and labeling positions within different switch architectures. We demonstrate that applying a combinatorial array of modifications to an aptamer switch sequence can tune its binding properties over a 2-order-of-magnitude range, with apparent binding affinities from ~230 to 2.3 μM and apparent kinetic response rates from ~1000 s to sub-second resolution, while also influencing the switch's specificity and signal resolution. We also establish that the environment and spatial positioning of a reporter pair are critical design parameters, enabling order-of-magnitude performance differences even at theoretically suboptimal sites. This work provides a comprehensive study to help design optimal switches when using fluorescent modifications, enabling the development of next-generation biosensors with tailored performance.