Quantifying Small Molecule Binding Interactions with DNA Nanostructures.

Abstract

DNA nanostructures and hybrid DNA-protein materials are attractive solutions to many applications in biotechnology and material science because of their controllable molecule-level features. Critical to a complete description and characterization of these technologies is the quantification of binding affinity between DNA nanostructures and small molecules relevant to the application at hand. This protocols chapter described a series of experimental and in silico analyses that can be used to described and quantify ligand binding interactions between DNA nanostructures (DNA DX tiles), short double stranded DNA fragments, and arbitrary small molecules. The described methods include microscale thermophoresis, ligand completion assays, circular dichroism spectroscopy, and AutoDock simulations. The protocols use organophosphates and model chemical nerve agents as examples, but the methods described here are broadly applicable.