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Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water

AuthorsLucas, Ricardo ; Peñalver, Pablo ; Gomez-Pinto, Irene ; Vengut-Climent, E. ; Matashobya, L.; Cousin, J.; Maldonado, Olivia S.; Reynes, V. Aviñó, A.; Eritja Casadellà, Ramón; González, Carlos ; Linclau, B.; Morales, Juan C.
Issue Date5-Mar-2014
PublisherAmerican Chemical Society
CitationJournal of Organic Chemistry 79(6): 2419-2429 (2014)
AbstractCarbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair. © 2014 American Chemical Society.
Publisher version (URL)http://dx.doi.org/10.1021/jo402700y
Identifiersdoi: 10.1021/jo402700y
issn: 1520-6904
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