Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard.

DNA origami, in which a long scaffold strand is assembled with a many short staple strands into parallel arrays of double helices, has proven a powerful method for custom nanofabrication. However, currently the design and optimization of custom 3D DNA-origami shapes is a barrier to rapid application to new areas. Here we introduce a modular barrel architecture, and demonstrate hierarchical assembly of a 100 megadalton DNA-origami barrel of ~90 nm diameter and ~250 nm height, that provides a rhombic-lattice canvas of a thousand pixels each, with pitch of ~8 nm, on its inner and outer surfaces. Complex patterns rendered on these surfaces were resolved using up to twelve rounds of Exchange-PAINT super-resolution microscopy. We envision these structures as versatile nanoscale pegboards for applications requiring complex 3D arrangements of matter, which will serve to promote rapid uptake of this technology in diverse fields beyond specialist groups working in DNA nanotechnology.

Modulation of the Cellular Uptake of DNA Origami through Control over Mass and Shape.

Designer nanoparticles with controlled shapes and sizes are increasingly popular vehicles for therapeutic delivery due to their enhanced cell-delivery performance. However, our ability to fashion nanoparticles has offered only limited control over these parameters. Structural DNA nanotechnology has an unparalleled ability to self-assemble three-dimensional nanostructures with near-atomic resolution features, and thus, it offers an attractive platform for the systematic exploration of the parameter space relevant to nanoparticle uptake by living cells. In this study, we examined the cell uptake of a panel of 11 distinct DNA-origami shapes, with the largest dimension ranging from 50-400 nm, in 3 different cell lines. We found that larger particles with a greater compactness were preferentially internalized compared with elongated, high-aspect-ratio particles. Uptake kinetics were also found to be more cell-type-dependent than shape-dependent, with specialized endocytosing dendritic cells failing to saturate over 12 h of study. The knowledge gained in the current study furthers our understanding of how particle shape affects cellular uptake and heralds the development of DNA nanotechnologies toward the improvement of current state-of-the-art cell-delivery vehicles.

Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation.

DNA nanostructures have evoked great interest as potential therapeutics and diagnostics due to ease and robustness of programming their shapes, site-specific functionalizations and responsive behaviours. However, their utility in biological fluids can be compromised through denaturation induced by physiological salt concentrations and degradation mediated by nucleases. Here we demonstrate that DNA nanostructures coated by oligolysines to 0.5:1 N:P (ratio of nitrogen in lysine to phosphorus in DNA), are stable in low salt and up to tenfold more resistant to DNase I digestion than when uncoated. Higher N:P ratios can lead to aggregation, but this can be circumvented by coating instead with an oligolysine-PEG copolymer, enabling up to a 1,000-fold protection against digestion by serum nucleases. Oligolysine-PEG-stabilized DNA nanostructures survive uptake into endosomal compartments and, in a mouse model, exhibit a modest increase in pharmacokinetic bioavailability. Thus, oligolysine-PEG is a one-step, structure-independent approach that provides low-cost and effective protection of DNA nanostructures for in vivo applications.

Molecular motion of donor-acceptor catenanes in water.

In this article, we use (1)H NMR spectroscopy to study the spontaneous molecular motion of donor-acceptor [2]catenanes in water. Our data supports the hypothesis that conformational motion dominantly occurs through a pirouetting mechanism, which involves less exposure of hydrophobic surfaces than in a rotation mechanism. Motion is controlled by the size of the catenane rings and the arrangement of the electron-deficient and electron-rich aromatic units.

Homochiral and meso figure eight knots and a Solomon link.

A homochiral naphthalenediimide-based building block forms in water a disulfide library of macrocycles containing topological isomers. We attempted to identify each of these isomers, and explored the mechanisms leading to their formation. The two most abundant species of the library were assigned as a topologically chiral Solomon link (60% of the library, as measured by high-performance liquid chromatography (HPLC)) and a topologically achiral figure eight knot (18% by HPLC), competing products with formally different geometries but remarkably similar 4-fold symmetries. In contrast, a racemic mixture of building blocks gives the near-quantitative formation of another new and more stable structure, assigned as a meso figure eight knot. Taken together, these results seem to uncover a correlation between the point chirality of the building block used and the topological chirality of the major structure formed. These and the earlier discovery of a trefoil knot also suggest that the number of rigid components in the building block may translate into corresponding knot symmetry and could set the basis of a new strategy for constructing complex topologies.

Discovery of an organic trefoil knot.

Molecular knots remain difficult to produce using the current synthetic methods of chemistry because of their topological complexity. We report here the near-quantitative self-assembly of a trefoil knot from a naphthalenediimide-based aqueous disulfide dynamic combinatorial library. The formation of the knot appears to be driven by the hydrophobic effect and leads to a structure in which the aromatic components are buried while the hydrophilic carboxylate groups remain exposed to the solvent. Moreover, the building block chirality constrains the topological conformation of the knot and results in its stereoselective synthesis. This work demonstrates that the hydrophobic effect provides a powerful strategy to direct the synthesis of entwined architectures.

Structural parameters governing the dynamic combinatorial synthesis of catenanes in water.

We report the first dynamic combinatorial synthesis in water of an all-acceptor [2]catenane and of different types of donor-acceptor [2] and [3]catenanes. Linking two electron-deficient motifs within one building block using a series of homologous alkyl chains provides efficient and selective access to a variety of catenanes and offers an unprecedented opportunity to explore the parameters that govern their synthesis in water. In this series, catenane assembly is controlled by a fine balance between kinetics and thermodynamics and subtle variations in the building block structure, such as the linker length and building block chirality. A remarkable and unexpected odd-even effect with respect to the number of atoms in the alkyl linker is reported.

Thermodynamics of supramolecular naphthalenediimide nanotube formation: the influence of solvents, side chains, and guest templates.

Amino-acid functionalized naphthalenediimides self-assemble into hydrogen-bonded supramolecular helical nanotubes via a noncooperative, isodesmic process; the self-assembly of ordered helical systems is usually realized through a cooperative process. This unexpected behavior was rationalized as a manifestation of entropy-enthalpy compensation. Fundamental insights into the thermodynamics governing this self-assembly were obtained through the fitting of the isodesmic model to (1)H NMR spectrometry and circular dichroism spectroscopy measurements. Furthermore, we have extended the application of this mathematical model, for the first time, to quantitatively estimate the effect of guests, solvents, and side chains on the stability of the supramolecular nanotube; most significantly, we demonstrate that C(60) acts as a template to stabilize the nanotube assembly and thereby substantially increase the degree of polymerization.

Supramolecular naphthalenediimide nanotubes.

Amino acid functionalized naphthalenediimides (NDIs) when dissolved in chloroform form a dynamic combinatorial library (DCL) in which the NDI building blocks are connected through reversible hydrogen bonds forming a versatile new supramolecular assembly in solution with intriguing host-guest properties. In chlorinated solvents the NDIs form supramolecular nanotubes which complex C(60), ion-pairs, and extended aromatic molecules. In the presence of C(70) a new hexameric receptor is formed at the expense of the nanotube; the equilibrium nanotube - hexameric receptor can be influenced by acid-base reactions. Achiral NDIs are incorporated in nanotubes formed by either dichiral or monochiral NDIs experiencing the "sergeants-and-soldiers" effect.

Microwave-assisted synthesis of naphthalenemonoimides and N-desymmetrized naphthalenediimides.

Naphthalenemonoimides and N-desymmetrized naphthalenediimides were synthesized using a stepwise microwave-assisted protocol. The steric and electronic properties of aliphatic amines determined the outcome of the reactions, while in the amino acid series their ability to solubilize the naphthalene dianhydride starting material was crucial. Molecular modeling was used to rationalize the observed selectivity.