DNA Nanostructures on Membranes as Tools for Synthetic Biology

Abstract

Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.

Figure 1

Lipophilic nucleic acids and their assembly on liposomes. (A) Cholesteryl-TEG-nucleotide. (B) Schematic representation of vesicle fusion induced by cholesteryl-TEG-oligonucleotide zippers in analogy to SNARE Fusion complex (reproduced with permission from (43), copyright 2008 American Chemical Society). (C) Hydrodynamic radii (R_H) of liposomes during step-by-step assembly of DNA pseudohexagons on their surface (squares: asymmetric protocol, circles: symmetric protocol) (reproduced with permission from (21), copyright The Royal Society of Chemistry). To see this figure in color, go online.

Figure 2

Switchable partitioning of lipophilic DNA structures on Ld/Lo membrane domains. (A) Oligo DNA/PNA complex colocalized as four-component complexes in the Ld domain, but after cleavage of the complex with restriction endonuclease (EcoR1-HF) the resulting amphipathic components separated from each other. Ratios between the fluorescence intensities in the Lo and Ld phases are given (reproduced with permission from (40), copyright 2012 American Chemical Society). (B) Origami DNA nanorods partition into the Ld phase (marked with DiD), but after addition of Mg²⁺ ions they translocate into the Lo phase, which is fully reversible after removal of the magnesium (with EDTA). Scale bars correspond to 10 μm.

Figure 3

Controllable assembly of lipophilic origami DNA nanostructures on lipid membranes. (A) Origami DNA hexagons with photoresponsive modifications were reversibly assembled or disassembled upon irradiation with light of a different wavelength (reproduced with permission from (73), copyright 2015 American Chemical Society). (B) Origami DNA blocks were polymerized into one-dimensional or two-dimensional complexes via specific DNA oligonucleotides depicted in blue or orange, respectively (reproduced with permission from (60), copyright 2015 American Chemical Society). (C) Two populations of amphipathic origami DNA monoliths (labeled either with Alexa488 (green) or Alexa647 (red)) form regular array, as shown on a transmission electron microscopy (TEM) image (scale bar is 100 nm), which at high surface densities deform a GUV (scale bar is 10 μm) (reproduced with permission from (61), copyright 2015 John Wiley and Sons).

Figure 4

A variety of membrane-anchored origami DNA nanostructures. (A) Cholesteryl-anchored (orange) origami DNA channel consisting of a barrel-like cap (white) and a transmembrane stem (red), which spontaneously dock to liposomes, as shown on a TEM image (B) (reproduced with permission from (64), copyright 2012 The American Association for the Advancement of Science). (C) Virus-inspired membrane-enveloped DNA nanostructures for biomedical applications; color-enhanced TEM image (D) represents the DNA nanostructure (dark blue) tightly wrapped with unilamellar membrane (light blue) (reproduced with permission from (70) copyright 2014 American Chemical Society). Scale bars 50 nm.