Teaching Upper-Division Biochemistry Students the Role of Noncovalent Interactions and Ligand Structure in DNA Binding

The experiment described here uses the binding. of cyanine. dyes to DNA as a model system for demonstrating the role that both ligand structure and noncovalent interactions play in DNA binding. Upper-division biochemistry laboratory students observe changes in absorbance and fluorescence spectra when small molecules bind either in the minor groove of DNA or by intercalation. Students specifically note that ligand charge, substituents, and flexibility greatly influence binding mode. Based on these observations, students then determine the binding mode of an unknown small molecule. This experiment also fosters independent thought and problem-solving abilities. Students must self-direct binding-mode identification of their unknown without any guidance from the instructor. After completing this experiment, students demonstrate a clear understanding of the factors that influence DNA binding.