Sequence-specific binding of counterions to B-DNA

Recent studies by x-ray crystallography, NMR, and molecular simulations hav e suggested that monovalent counterions can penetrate deeply into the minor groove of B form DNA, Such groove-bound ions potentially could play an imp ortant role in AT-tract bending and groove narrowing, thereby modulating DN A function in vivo. To address this issue, we report here Na-23 magnetic re laxation dispersion measurements on oligonucleotides, including difference experiments with the groove-binding drug netropsin, The exquisite sensitivi ty of this method to ions in long-lived and intimate association with DNA a llows us to detect sequence-specific sodium ion binding in the minor groove AT tract of three B-DNA dodecamers. The sodium ion occupancy is only a few percent, however, and therefore is not likely to contribute importantly to the ensemble of B-DNA structures. We also report results of ion competitio n experiments, indicating that potassium, rubidium, and cesium ions bind to the minor groove with similarly weak affinity as sodium ions, whereas ammo nium ion binding is somewhat stronger. The present findings are discussed i n the light of previous NMR and diffraction studies of sequence-specific co unterion binding to DNA.