A hydrophobic similarity analysis of solvation effects on nucleic acid bases.

TitleA hydrophobic similarity analysis of solvation effects on nucleic acid bases.
Publication TypeJournal Article
Year of Publication2007
AuthorsMuñoz-Muriedas, Jordi, Barril Xavier, López José María, Orozco Modesto, and Luque Francisco Javier
JournalJ Mol Model
Date Published2007 Feb
KeywordsHydrophobic and Hydrophilic Interactions, Models, Molecular, Nucleic Acids, Purines, Pyrimidines

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.