Applications of Surface Plasmon Resonance for Advanced Studies Involving Nucleic Acids

Surface plasmon resonance (SPR) is increasingly recognized as one of the most widely used techniques for studying nucleic acid interactions. The main advantage of SPR is its ability to measure the binding affinities and association/dissociation kinetics of complexes in real-time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. In the field of Nucleic Acid, SPR has been intensively used in the study of various artificial and naturally occurring RNA/DNA molecules interaction with large molecular weight mass proteins and small organic molecules because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This mini review aims to provide a short guideline for setting up SPR experiments to identify nucleic acid complexes and assess their binding affinity or kinetics. It covers protocols for (i) nucleic acid immobilization methods, including biotin-streptavidin, metal ion-based affinity, and amine coupling, (ii) analyte-binding analysis, (iii) affinity and kinetic measurements, and (iv) data interpretation. Determining the affinity and kinetics of nucleic acid interactions through SPR is essential for gaining insights into molecular-level binding mechanisms, thus supporting advancements in nucleic acid nanotechnology. The review also highlights the various sections of SPR applications in nucleic acid research, including nucleic acid-probe immobilization, interactions with biomolecules, aptamer studies, and small molecule binding, concluding with perspectives on future developments in the field.