Localization of ammonium lone in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

Monovalent cation binding sites on nucleic acids in solution can be localiz ed using the isotopically labeled ammonium ion ((NH4+)-N-15) as a probe in high resolution NMR spectroscopy experiments. The application of this techn ique to a series of DNA duplexes reveals a preference for the binding of am monium cations in the minor groove of A-tract sequences. These results are consistent with a recent report which indicates that some solvent electron densities previously identified as water molecules in DNA X-ray crystal str uctures are partially occupied by sodium ions. The sequence-specific nature of monovalent cation binding sites demonstrated here for A-tract DNA provi des an explanation for the origin of sequence-directed bending. (C) 1999 Ac ademic Press.