Structure determination and binding kinetics of a DNA aptamer - Argininamide complex

The structure of a DNA aptamer, which was selected for specific binding to arginine, was determined using NMR spectroscopy. The sequence forms a hairp in loop, with residues important for binding occurring in the loop region. Binding of argininamide induces formation of one Watson-Crick and two non-W atson-Crick base pairs, which facilitate generation of a binding pocket. Th e specificity for arginine seems to arise from contacts between the guanidi no end of the arginine and phosphates, with atoms positioned by the shape o f the pocket. Complex binding kinetics are observed suggesting that there i s a slow interconversion of two forms of the DNA, which have different bind ing affinities. These data provide information on the process of adaptive r ecognition of a ligand by an aptamer.