Membrane-Assisted Growth of DNA Origami Nanostructure Arrays

Abstract

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors—a three-layered rectangular block and a Y-shaped DNA structure—to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins

“…By using high‐speed AFM, the hexagonal dimer was observed to disassemble into monomer units under UV irradiation and reassemble with visible‐light irradiation, owing to the insertion of light‐sensitive azobenzene. The polymerization of both rectangular blocks and Y‐shaped DNA structures into larger 2D assemblies was also observed on the planer lipid layer by Kocabey et al . In this study, the assembly of rectangular origami was implemented on small, spherical unilamellar vesicles up to 300 nm in diameter.…”

“… DNA origami as scaffolds to investigate lipid membranes. A) The assembly of DNA origami on lipid membranes . B) The assembly of DNA origami on lipid vesicles .…”

Design of a molecular support for cryo-EM structure determination

“…For example, one could use commercially available biotin-labeled DNA on the support structure to bind a counterpart to a protein tag attached to a monovalent streptavidin (50,51). For the study of membrane proteins, one might even consider designs where nanodiscs (52) are attached to DNA-origami support structures or where these structures interact directly with patches of membranes (53). Such more generally applicable designs probably would retain even less control over the orientation of the target protein than the design described in this work.…”

Nanotechnology and the Unique Role of DNA

“…Interactions between DNA units can be also directionally driven taking advantage of geometric factors, like the shape-complementarity of the binding surfaces ( Figure 1.4(d)) [71]. Finally, long-range assemblies can also be favored by confining the random Brownian motion of the constituents units to a limited space, helping them to meet and bind [72][73][74]. Both approaches, i.e.…”