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2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory. J Mol Biol. 294:1999;1135-1147. An application of the Poisson-Boltzmann approach to study diffusive divalent cation binding to a cylindrical model for double-stranded nucleic acids. Good agreement between experimental and calculated magnesium-binding isotherms is observed. The free energy of magnesium binding is partitioned into various salt-dependent ion-ion, ion-DNA and entropic contributions.
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An analysis of the electrostatic potential at the surface of RNA using finite-difference solutions of the nonlinear Poisson-Boltzmann equation. Intermolecular contact regions and ion-binding sites appear to correlate with the magnitude of the electrostatic surface potential
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Chin K., Sharp K.A., Honig B., Pyle A.M. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and functions. Nat Struct Biol. 6:1999;1055-1061. An analysis of the electrostatic potential at the surface of RNA using finite-difference solutions of the nonlinear Poisson-Boltzmann equation. Intermolecular contact regions and ion-binding sites appear to correlate with the magnitude of the electrostatic surface potential.
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This molecular modeling and dynamics study indicates that aminoglycosides can be docked on to the hammerhead ribozyme such that several metal-binding sites are simultaneously replaced by cationic groups of the antibiotics. The result may be important for the identification of RNA ligands. It may give a hint where to place cationic sites on a ligand designed to specifically bind a structural motif in RNA
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Hermann T., Westhof E. Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J Mol Biol. 276:1998;903-912. This molecular modeling and dynamics study indicates that aminoglycosides can be docked on to the hammerhead ribozyme such that several metal-binding sites are simultaneously replaced by cationic groups of the antibiotics. The result may be important for the identification of RNA ligands. It may give a hint where to place cationic sites on a ligand designed to specifically bind a structural motif in RNA.
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