SPR evaluation of binding kinetics and affinity study of modified RNA aptamers towards small molecules

Establishing an efficient method for evaluating the affinity changes after post-SELEX modification of aptamers is essential for broadening the application of these oligonucleotides in biosensing. This is especially challenging when the ligand is a small molecule. Changes in affinity upon partial or total replacement of 2′–OH with 2′-OMe groups in the ribose moieties of a tobramycin binding RNA aptamer are described. The kinetic profile and binding properties of the different anti-tobramycin aptamers were measured by surface plasmon resonance (SPR) experiments through a real-time binding assay with the antibiotic covalently coupled to the gold sensor. This configuration maximizes the changes associated to the recognition event, which is otherwise undetectable. The results indicated that the modification slightly affects the binding characteristics of the parent RNA, while conferring biological stability to the aptamers against nucleases.