DNA Origami Platform for Protein Interaction Analysis

Abstract

The nanoscale spatial distribution of membrane-bound ligands is thought to play an important role in membrane receptor-mediated signaling. In particular, the formation of protein complexes in the immunological synapse, in the contact area of a T cell and an antigen-presenting cell (APC), plays a key role in the initiation of the immune response. Despite extensive studies, the quantitative molecular details of complex formation, as well as the kinetics are still poorly understood. Here, we use DNA origami nanostructures of 50 nm x 50 nm x 2 nm featuring up to 44 engineered capture sites for a target protein at the top side at well-definded positions. The number of capture sites, their functionalization, their orientation and their distance can be adjusted at will. At the bottom side (opposite of the protein capture sites), the employed DNA rectangles can be functionalized with cholesterol moieties which serve as membrane anchors. The DNA constructs adhere to a lipid bilayer mediated by the cholesterol anchors and serve as mobile platforms for protein recruitment. Here, DNA origami are decorated with recombinant and site-specifically labeled T cell receptor (TCR)β-reactive single chain antibody fragment (scFV) and embedded on planar glass-supported lipid bilayers, which harbors costimulatory molecules and adhesion proteins. This system is used to closely imitate the APC, allowing to re-organize the TCR in living T cells according to the pattern given by the scFv template on the origami. We use this system to address and answer central questions in T cell immunology: the role of TCR clustering in T cell activation, the unknown composition of protein complexes in the T cell plasma membrane as well as the mechanisms of their cohesion.