DNA nanostructures constructed with multi-stranded motifs

Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds

Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Two-layer stacked multi-arm junction tiles and nanostructures assembled with small circular DNA molecules serving as scaffolds

One-layer multi-arm junction (mAJ) motifs have been investigated extensively for many kinds of planar 2D (two-dimension) lattices, surface-curved 3D (three-dimension) polyhedra, and complex 3D wireframe and tensegrity structures. Herein, we report the weaving strategy to achieve two-layer stacked multi-arm junction tiles (abbreviated as mAJ²) of 3AJ² and 4AJ², and several primary tessellation nanostructures of nanocages and 2D rhombus lattices carrying beautifully embossed 4-point stars. Challenges for perfect tessellation are also raised regarding the increase of motif complexity from 2D to 3D.

Addressable DNA nanotubes with repetitive components

Extended DNA nanostructures have already been constructed in a repetitive arrangement from millions of building blocks, many more than currently feasible with even the gold standard of addressable self-assembled structures. In order to construct addressable DNA nanostructures with more building blocks, it is desirable to arrange the addressable components repetitively. Accordingly, the overall size of the structure can be multiplied by the level of repetition in the addressable strands. In this study, we present a nanotube system that combines two seemingly conflicting features: addressability and repetitiveness. Based on an understanding of the tubulation resulting from the intrinsic curvature of the components, we produce DNA nanotubes with addressability available along the axial direction of the self-assembled tubes, which are also programmably repetitive along the lateral direction.

DNA nanostructures from double-C-shaped motifs with controllable twist and curvature

We demonstrate twist and curvature engineering in DNA nanostructures from the scaffold-free approach. The DNA 'LEGO' bricks adopted in this study are double-C-shaped motifs, and extended nanostructures are constructed to visualize the structural details of twist or curvature. By systematically deleting and inserting base pairs at certain domains of the component motifs, we are able to study various levels of the twist and curvature of the resulting nanostructures comprehensively.

A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding

The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.

Self-Assembly of Wireframe DNA Nanostructures from Junction Motifs

Wireframe frameworks have been investigated for the construction of complex nanostructures from a scaffolded DNA origami approach; however, a similar framework is yet to be fully explored in a scaffold-free "LEGO" approach. Herein, we describe a general design scheme to construct wireframe DNA nanostructures entirely from short synthetic strands. A typical edge of the resulting structures in this study is composed of two parallel duplexes with crossovers on both ends, and three, four, or five edges radiate out from a certain vertex. By using such a self-assembly scheme, we produced planar lattices and polyhedral objects.

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

DNA tile-based assembly provides a promising bottom-up avenue to create designer two-dimensional (2D) and three-dimensional (3D) crystalline structures that may host guest molecules or nanoparticles to achieve novel functionalities. Herein, we introduce a new kind of DNA tiles (named layered-crossover tiles) that each consists of two or four pairs of layered crossovers to bridge DNA helices in two neighboring layers with precisely predetermined relative orientations. By providing proper matching rules for the sticky ends at the terminals, these layered-crossover tiles are able to assemble into 2D periodic lattices with precisely controlled angles ranging from 20° to 80°. The layered-crossover tile can be slightly modified and used to successfully assemble 3D lattice with dimensions of several hundred micrometers with tunable angles as well. These layered-crossover tiles significantly expand the toolbox of DNA nanotechnology to construct materials through bottom-up approaches.