Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending |
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Authors: | Hud N V Sklenár V Feigon J |
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Affiliation: | Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1569, USA. |
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Abstract: | Monovalent cation binding sites on nucleic acids in solution can be localized using the isotopically labeled ammonium ion (15NH4+) as a probe in high resolution NMR spectroscopy experiments. The application of this technique to a series of DNA duplexes reveals a preference for the binding of ammonium 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 structures are partially occupied by sodium ions. The sequence-specific nature of monovalent cation binding sites demonstrated here for A-tract DNA provides an explanation for the origin of sequence-directed bending. |
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