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RESEARCH PRODUCT

Hydrophobic interactions and stacking forces: A convenient model system

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Abstract We consider solvent–biomolecule interactions and the role of solvent structural and isotopic alterations on the thermodynamic stability of biomolecular structures. Approaches to this problem range from the study of biomolecular functional stability, to that of the stability of small structural entities suitable of being taken as model systems for (parts of) larger molecules. We shall focus on this latter case and shall consider the dimerization process of small planar molecules (Methylene Blue). These are a convenient model system for the study of interactions responsible e.g. for base stacking in DNA. As an additional advantage, they do not form hydrogen bonds. The experimental strategy includes H2OD2O substitution and solvent perturbation by means of monohydric alcohols such as methanol, ethanol and propanol. The technique is spectrophotometric, assisted by microprocessor-based data acquisition and high precision, computer-aided data analysis. Simple thermodynamic analysis of results, relative to different temperatures and concentrations, point out the role played in this type of process by solvent structure and perturbation, as well as by hydrophobic interactions and hydrogen mass.