A surface plasmon resonance method for detecting multiple modes of DNA-ligand interactions

A simple and general surface plasmon resonance (SPR) based method has been developed to detect and quantitate binding of low molecular weight compounds (200-1200 Da) to double stranded DNA. Several compounds were chosen to probe three different modes of binding interactions, intercalation, minor groove binding and electrostatic interactions. Ethidium bromide (MW 390 Da), a probe of intercalative binding, was tested by plotting the steady state SPR responses measured on a DNA modified surface versus ethidium bromide concentration. The best fit of the binding isotherm gave a K-eq of 1.8 x 10(5) M-1. Co-solvents such as DMSO are often used in activity assays to increase the solubility of poorly water-soluble drugs. The effect of DMSO on the ethidium bromide/DNA interaction was also tested by measuring binding in the presence of 0, 1 and 5% DMSO. No effect on the measured K-eq was observed at these DMSO concentrations. The binding of actinomycin (MW 1255 Da), an antibiotic known to bind DNA through intercalation and minor groove binding, was also tested. The K-eq estimated from the steady state responses on a DNA surface was 1.9 x 10(6) M-1. DAPI (MW 350 Da) (4',6-diamidino-2-phenylindole) a fluorescent probe which binds the minor groove of DNA was also tested and gave a K-eq of 1.8 x 10(6) M-1 measured by SPR. Finally, spermine (MW 202) a compound known to bind DNA through ionic interactions gave the weakest K-eq of 1.7 x 10(4) M-1. All the K-eq values measured by SPR and reported for these compounds were in good agreement with literature values measured by other techniques. (C) 2000 Elsevier Science B.V. All rights reserved.