Published October 1, 2018 | Version v1
Publication

Effects of Sugar Functional Groups, Hydrophobicity, and Fluorination on Carbohydrate–DNA Stacking Interactions in Water

Description

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.

Abstract

Ministerio de Economía y Competitividad CTQ2007-68014-C02-02, CTQ2009-13705, CTQ2010-20541-C03-01, CTQ2012-35360

Abstract

Generalida de Cataluña 2009/SGR/208

Abstract

Instituto de Salud Carlos III CIBER-BNN, CB06_01_0019

Additional details

Created:
December 4, 2022
Modified:
December 1, 2023