A hydrophobic similarity analysis of solvation effects on nucleic acid bases |
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Authors: | Jordi Muñoz-Muriedas Xavier Barril José María López Modesto Orozco Francisco Javier Luque |
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Institution: | (1) Departament de Fisicoquímica, Facultat de Farmàcia, Avgda. Diagonal 643, Barcelona, 08028, Spain;(2) ICREA and Departament de Fisicoquímica, Facultat de Farmàcia, Avgda. Diagonal 643, Barcelona, 08028, Spain;(3) Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, Barcelona, 08028, Spain;(4) Unitat de Modelització Molecular i Bioinformàtica, Parc Científic de Barcelona, Josep Samitier 1-6, Barcelona, 08028, Spain |
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Abstract: | We investigate the changes in the solvation properties of the natural nucleic acid bases due to the formation of the canonical
Watson–Crick hydrogen-bonded complexes. To this end, the changes in the free energy of solvation of the bases induced upon
hydrogen-bonded dimerization are analyzed by means of the hydrophobic similarity index, which relies on the atomic contributions
to the free energy of solvation determined by the partitioning method implemented in the framework of the MST continuum model.
Such an index is also used to examine the hydrophobic similarity between the canonical nucleic acid bases and a series of
highly apolar analogues, which have been designed as potential candidates to expand the genetic alphabet. The ability of these
analogues to be incorporated into modified DNA duplexes can be related to the large reduction in the hydrophilicity of the
natural bases upon formation of the canonical hydrogen-bonded dimers. The results illustrate the suitability of the hydrophobic
similarity index to rationalize the role played by solvation in molecular recognition.
Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005. |
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Keywords: | Solvation Hydrophobicity Molecular similarity Hydrophobic index Continuum models |
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