Binding analysis between l-histidine immobilized and oligonucleotides by SPR and NMR

Saturation transfer difference (STD) NMR technique and surface plasmon resonance (SPR) are used to study amino acid affinity supports-nucleotides interactions with l-histidine amino acid immobilized on a surface as model support. We have immobilized l-histidine ligand on a carboxymethyldextran-modified gold surface intended for surface plasmon resonance and we analyze the binding profiles of synthetic polynucleotides (1-6 base, sugar and backbone) by determining the equilibrium dissociation constant (KD). The SPR binding profile (square-shaped) is identical for all the complexes and the highest binding affinity can be found for polyA6 followed by polyG6. As expected, the 5′-mononucleotides have the lowest affinity. To further study the structural aspects of the interaction we investigate the polynucleotide binding preferences to l-histidine chromatography support by STD-NMR spectroscopy. These results revealed that an increase in the number of bases and backbone to 6 units leads to more contacts with the support, where the main driving force for the interaction with polynucleotides are through the base, except for polyC6, which is mainly through sugar-phosphate backbone. Therefore, the combination of SPR measurements with STD-NMR technique allowed to establish fine details of the molecular recognition process involved in amino acid affinity supports-nucleotides complexes.