Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA

Abstract

4′,6-Diamidino-2-phenylindole (DAPI), netropsin, and pentamidine are minor groove binders that have terminal − C ( N H 2 ) 2 + groups. The hydration changes that accompany their binding to the minor groove of the (AATT) 2 sequence have been studied using the osmotic stress technique with fluorescence spectroscopy. The affinity of DAPI for the binding site decreases with the increasing osmolality of the solution, resulting in acquisition of 35 ± 1 waters upon binding. A competition fluorescence assay was utilized to measure the binding constants and hydration changes of the other two ligands, using the DNA-DAPI complex as the fluorescence reporter. Upon their association to the (AATT) 2 binding site, netropsin and pentamidine acquire 26 ± 3 and 34 ± 2 additional waters of hydration, respectively. The hydration changes are discussed in the context of the terminal functional groups of the ligands and conformational changes in the DNA.