Uncovering the Impact of a Fluorescent Merocyanine Probe on the Structure and Function of Aptamers for Protein and Small Molecule Detection

Aptamer technology is quickly absorbing the fields of protein and small molecule detection field due to its simple, economical and efficient design. DNA aptamers are functional nucleic acids which engage in target-specific binding which effects changes in the aptamer’s secondary structure. When coupled with a fluorescent probe, target-induced structural changes can alter fluorescence emission thereby signalling binding events. Guanine-quadruplexes are a secondary structure formed by some DNA aptamers which can experience considerable target-induced structural changes and are therefore commonly employed in fluorescent aptamer detection assays. Herein, guanine-quadruplex forming DNA aptamers for the thrombin protein and ochratoxin-A were modified to include a fluorescent merocyanine probe using different labelling strategies. Subsequent investigation of these modified aptamers revealed the effects of different labelling strategies on aptamer structure and stability. Finally, the functionality of these aptamers in detecting their respective targets was evaluated and compared across different labelling strategies using fluorescence spectrometry.