The Interaction of DNA with Intercalating Agents Probed by Sodium-23 NMR Relaxation Rates

Abstract

We have investigated the changes of Na-23 NMR spin-lattice and spin-spin relaxation rates of Na-DNA in dilute aqueous solutions, induced by the intercalating drugs ethidium, propidium, 6,7-dihydro-pyrido[2′,r:3,4]pyrazino[1,2-f]-phenanthridinediium dihydrate (dq2pyp) and by the electrostatic binder Mg2+. It has been found that the Na-23 spin-lattice relaxation is monoexponential, while the spin-spin relaxation follows a biexponential law. From the linear trends of the relaxation rates observed in the titration experiments of Na-DNA with the drugs we inferred the validity of a two-site model in the fast exchange limit: The relaxation rates of sodium in the bound state have been estimated by using the fraction of bound sodium ions per phosphate charge, predicted by the counterion condensation theory, and the number of sodium ions released per bound drug, calculated from salt dependent equilibrium binding studies. The results show that the addition of the competitors slow down the broad component of the spin-spin relaxation rate of bound sodium in the order dq2pyp - propidium < ethidium < Mg2+. This reduction is shown to be due mainly to the decrease of the quadrupolar coupling constant for the slow motions, thus indicating a decrease of the average electric field gradient at the sodium ions close to the DNA surface. We also show that the broad component of the spin-spin relaxation rate linearly correlates with the relative non-polyelectrolyte free energy. This result is discussed in terms of the non-polyelectrolyte interactions affecting R2bB, which can be partitioned into stacking interaction and interactions involving the molecular moieties of the intercalators exposed to the solvent in the minor groove.