Fabricating higher-order functional DNA origami structures to reveal biological processes at multiple scales

Abstract DNA origami technology enables the precise assembly of well-defined two-dimensional and three-dimensional nanostructures with DNA, an inherently biocompatible material. Given their modularity and addressability, DNA origami objects can be used as scaffolds to fabricate larger higher-order structures with other functional biomolecules and engineer these molecules with nanometer precision. Over the past decade, these higher-order functional structures have shown potential as powerful tools to study the function of various bio-objects, revealing the corresponding biological processes, from the single-molecule level to the cell level. To inspire more creative and fantastic research, herein, we highlight seminal works in four emerging areas of bioapplications of higher-order DNA origami structures: (1) assisting in single-molecule studies, including protein structural analysis, biomolecule interaction analysis, and protein functional analysis, (2) manipulating lipid membranes, (3) directing cell behaviors, and (4) delivering drugs as smart nanocarriers. Finally, current challenges and opportunities in the fabrication and application of DNA origami-based functional structures are discussed

Spontaneous Self-Assembly of Silver Nanoparticles into Lamellar Structured Silver Nanoleaves

Uniform lamellar silver nanoleaves (AgNLs) were spontaneously assembled from 4 nm silver nanoparticles (AgNPs) with <i>p</i>-aminothiophenol (PATP) as mediator under mild shaking at room temperature. The compositions of the AgNLs were verified to be ∼1 nm Ag₂₅ nanoclusters and PATP molecules in quinonoid model. The underlying assembly mechanism was systematically investigated and a two-step reaction process was proposed. First, the 4 nm AgNPs were quickly etched to ∼1 nm Ag₂₅ nanoclusters by PATP in the form of [Ag₂₅(PATP)_<i>n</i>]^<i>n</i>+ (<i>n</i> < 12), which were then further electrostatically or covalently interconnected by PATP to form the repeated unit cells of [Ag₂₅(PATP)_<i>n</i>−1]^{(<i>n</i>−1)+}–PATP–[Ag₂₅(PATP)_<i>n</i>−1]^{(<i>n</i>−1)+} (abbreviated as Ag₂₅–PATP–Ag₂₅). Second, these Ag₂₅–PATP–Ag₂₅ complexes were employed as building blocks to construct lamellar AgNLs under the directions of the strong dipole–dipole interaction and the π–π stacking force between the neighboring benzene rings of PATP. Different reaction parameters including the types and concentrations of ligands, solvents, reaction temperature, ionic strength, and pH, <i>etc</i>., were carefully studied to confirm this mechanism. Finally, the preliminary investigations of the applications for AgNLs as “molecular junctions” and SERS properties were demonstrated. We expect that this convenient and simple method can be in principle extended to other systems, or even mixture system with different types of NPs, and will provide an important avenue for designing metamaterials and exploring their physicochemical properties

Photonic Interaction Between Quantum Dots And Gold Nanoparticles In Discrete Nanostructures Through Dna Directed Self-Assembly

Discrete nanostructures of CdSe@ZnS QDs and Au NPs were prepared and the photonic interactions between the QDs and Au NPs were systematically investigated. We found that the Au/QD ratio, separation distances between Au NPs and QDs, and the size of the Au NPs in a given discrete nanostructure all affect the interaction between Au NPs and QDs. © 2010 The Royal Society of Chemistry

Coassembly of Tobacco Mosaic Virus Coat Proteins into Nanotubes with Uniform Length and Improved Physical Stability

Using tobacco mosaic virus coat proteins (TMVcp) from both sources of the plant and bacterial expression systems as building blocks, we demonstrate here a coassembly strategy of TMV nanotubes in the presence of RNA. Specifically, plant-expressed cp (cp_p) efficiently dominates the genomic RNA encapsidation to determine the length of assembled TMV nanotubes, whereas the incorporated <i>Escherichia coli-</i>expressed cp (cp_ec) improves the physical stability of TMV nanotubes by introducing disulfide bonds between the interfaces of subunits. We expect this coassembly strategy can be expanded to other virus nanomaterials to obtain desired properties based on rationally designed protein–RNA and protein–protein interfacial interactions

Selective in Situ Assembly of Viral Protein onto DNA Origami

Engineering hybrid protein–DNA assemblies in a controlled manner has attracted particular attention, for their potential applications in biomedicine and nanotechnology due to their intricate folding properties and important physiological roles. Although DNA origami has served as a powerful platform for spatially arranging functional molecules, <i>in situ</i> assembly of proteins onto DNA origami is still challenging, especially in a precisely controlled and facile manner. Here, we demonstrate <i>in situ</i> assembly of tobacco mosaic virus (TMV) coat proteins onto DNA origami to generate programmable assembly of hybrid DNA origami–protein nanoarchitectures. The protein nanotubes of controlled length are precisely anchored on the DNA origami at selected locations using TMV genome-mimicking RNA strands. This study opens a new route to the organization of protein and DNA into sophisticated protein–DNA nanoarchitectures by harnessing the viral encapsidation mechanism and the programmability of DNA origami