Instrument Free Biomolecular Interaction Measurement with DNA Nanoswitches

Abstract

The quantification of molecular interactions is a cornerstone of almost all aspects of biomedical research, from fundamental cell biology to drug discovery. Yet progress has been impeded by challenges implicit in current approaches: high-cost of equipment and reagents, low throughput of many approaches, and requisite technical expertise. Here we present a new method that solves these challenges, replacing standard equipment with a nanoscale molecular tool. This is accomplished by using DNA origami to place molecules on a strand of DNA effectively creating a “molecular laboratory” that allows us to control both local concentration and binding stoichiometry at a single-molecule level. The binding state of these molecules alters the geometry of the DNA, which can be easily readout using gel electrophoresis. This allows us to make standard binding kinetics measurements in a highly parallel way at low cost. Furthermore these DNA “nanoswitches” provide new capabilities such as the ability to readout the binding state of multi-component systems such as bispecific antibodies or allosteric drugs.