Quantitative analysis of histamine- and agmatine-DNA interactions using surface plasmon resonance

To exploit the binding affinity for efficient plasmid purification, agmatine and histamine were immobilized on carboxymethylated dextran surface. Their binding strength is evaluated with oligonucleotides and pUC19 (2.69 kbp), pVAX1-LacZ (6.05 kbp) and pcDNA3-myc-FLNa S2152A (14 kbp) isoforms by measuring the KD using SPR-biosensor. The oligonucleotides and plasmid isoforms bind more strongly to histamine than to agmatine. Concerning the oligonucleotides, the highest affinities are found for poly 30, and polyT and polyG series showed lowest affinity with both ligands. These results are corroborating with the hetero-oligonucleotides since the lowest binding affinity is found for GGGTTT, indicating that thymidine and guanosine together decrease the binding strength. The largest plasmid has the highest binding, while pUC19 shows the weaker binding. The linear isoform exhibit the highest binding affinity to both amino acid-derivatives. Decreasing the pH above 6, the interaction strength of linear isoform increases possibly due to positively charged of the surface, which enhances electrostatic interactions. However, no binding response is detected with high salt concentrations (1 M NaCl) and for different buffers. The affinity information accessible with the biosensor offers new insight into nucleic acids-ligand interactions, as well as, new criteria leading the optimization of the novel ligands for preparative plasmid purification.