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Updated: Mar 19, 2026

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water
Published on: August 2, 2012
Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and
Evgeny A Kataev1, Tatiana A Shumilova1, Benjamin Fiedler1
1Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany.
Abstract:
Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.
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