title: Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water.
abstract: Carbohydrate-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.
authors.affiliation: Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla , 49 Américo Vespucio, 41092, Sevilla, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Lucas
authors.forename: Pablo
authors.initials: P
authors.lastname: Peñalver
authors.forename: Irene
authors.initials: I
authors.lastname: Gómez-Pinto
authors.forename: Empar
authors.initials: E
authors.lastname: Vengut-Climent
authors.forename: Lewis
authors.initials: L
authors.lastname: Mtashobya
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cousin
authors.forename: Olivia S
authors.initials: OS
authors.lastname: Maldonado
authors.forename: Violaine
authors.initials: V
authors.lastname: Perez
authors.forename: Virginie
authors.initials: V
authors.lastname: Reynes
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Ramón
authors.initials: R
authors.lastname: Eritja
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.forename: Bruno
authors.initials: B
authors.lastname: Linclau
authors.forename: Juan C
authors.initials: JC
authors.lastname: Morales
mesh_terms: D020029:Base Pairing; D002241:Carbohydrates / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006845:Hydrocarbons, Fluorinated / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D002241:Carbohydrates; D006845:Hydrocarbons, Fluorinated; D014867:Water; D004247:DNA