Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson–Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.     

An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom-up” Rational Design

A 3D array of organic semiconductors was assembled using a DNA scaffold. An octameric aniline molecule (“octaniline”) was incorporated into a DNA building block based on a dimeric tensegrity triangle. The construct self-assembled to form a 3D crystal. Reversible redox conversion between the pernigraniline and leucoemeraldine states of the octaniline is retained in the crystal. Protonic doping gave emeraldine salt at pH 5, corresponding to the conductive form of polyaniline. Redox cycling within the crystal was visualized by color changes and Raman microscopy. The ease of conversion between the octaniline states suggests that it is a viable electronic switch within a unique 3D structure.     

Functionalizing Designer DNA Crystals with a Triple‐Helical Veneer

DNA is a very useful molecule for the programmed self‐assembly of 2D and 3D nanoscale objects. 1 The design of these structures exploits Watson–Crick hybridization and strand exchange to stitch linear duplexes into finite assemblies. 2 – 4 The dimensions of these complexes can be increased by over five orders of magnitude through self‐assembly of cohesive single‐stranded segments (sticky ends). 5 , 6 Methods that exploit the sequence addressability of DNA nanostructures will enable the programmable positioning of components in 2D and 3D space, offering applications such as the organization of nanoelectronics, 7 the direction of biological cascades, 8 and the structure determination of periodically positioned molecules by X‐ray diffraction. 9 To this end we present a macroscopic 3D crystal based on the 3‐fold rotationally symmetric tensegrity triangle 3 , 6 that can be functionalized by a triplex‐forming oligonucleotide on each of its helical edges.     

DNA triangles and self-assembled hexagonal tilings

We have designed and constructed DNA complexes in the form of triangles. We have created hexagonal planar tilings from these triangles via self-assembly. Unlike previously reported structures self-assembled from DNA, our structures appear to involve bending of double helices. Bending helices may be a useful design option in the creation of self-assembled DNA structures. It has been suggested that DNA self-assembly may lead to novel materials and efficient computational devices.     

A DNA crystal designed to contain two molecules per asymmetric unit

We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal.     

Synthesis of DNA triangles with vertexes of bis(terpyridine)iron(II) complexes

The synthesis of the terpyridine derivative 1 tethered to a DNA oligonucleotide and its use for the preparation of two-way branched metal-organic modules capable of self-assembling into DNA triangles are described.     

Fabrication of Pascal-triangle Lattice of Proteins by Inducing Ligand Strategy

A protein Pascal triangle has been constructed as new type of supramolecular architecture by using the inducing ligand strategy that we previously developed for protein assemblies. Although mathematical studies on this famous geometry have a long history, no work on such Pascal triangles fabricated from native proteins has been reported so far due to their structural complexity. In this work, by carefully tuning the specific interactions between the native protein building block WGA and the inducing ligand R-SL , a 2D Pascal-triangle lattice with three types of triangular voids has been assembled. Moreover, a 3D crystal structure was obtained based on the 2D Pascal triangles. The distinctive carbohydrate binding sites of WGA and the intralayer as well as interlayer dimerization of RhB was the key to facilitate nanofabrication in solution. This strategy may be applied to prepare and explore various sophisticated assemblies based on native proteins.     

Fabrication of Pascal‐triangle Lattice of Proteins by Inducing Ligand Strategy

A protein Pascal triangle has been constructed as new type of supramolecular architecture by using the inducing ligand strategy that we previously developed for protein assemblies. Although mathematical studies on this famous geometry have a long history, no work on such Pascal triangles fabricated from native proteins has been reported so far due to their structural complexity. In this work, by carefully tuning the specific interactions between the native protein building block WGA and the inducing ligand R‐SL , a 2D Pascal‐triangle lattice with three types of triangular voids has been assembled. Moreover, a 3D crystal structure was obtained based on the 2D Pascal triangles. The distinctive carbohydrate binding sites of WGA and the intralayer as well as interlayer dimerization of RhB was the key to facilitate nanofabrication in solution. This strategy may be applied to prepare and explore various sophisticated assemblies based on native proteins.     

Double cohesion in structural DNA nanotechnology

Double cohesion has proved to be a useful tool to assemble robust 2D arrays of large tiles. Here we present a variety of examples showing the utility of this approach. We apply this principle to the 3 types of 2D lattice sections of arrays whose individual tiles are inherently 3 dimensional, because they contain three vectors that span 3-space. This application includes motifs which are based on the tensegrity triangle, the six-helix bundle motif and on three skewed triple crossover molecules. All of these designs have the potential to form 3 dimensional structures if all three directions of propagation are allowed. If one direction is blunted, 2D arrays form, and all 3 combinations are presented here. In addition, a large parallelogram array that was not attainable previously using single duplex cohesion was also constructed using double cohesion. For comparison, arrays which use another type of double cohesion, double paranemic (PX) cohesion are also presented. Double cohesion of sticky ends proved to be the more effective tool to assemble large motifs into arrays.     

3D Framework DNA Origami with Layered Crossovers

Designer DNA architectures with nanoscale geometric controls provide a programmable molecular toolbox for engineering complex nanodevices. Scaffolded DNA origami has dramatically improved our ability to design and construct DNA nanostructures with finite size and spatial addressability. Here we report a novel design strategy to engineer multilayered wireframe DNA structures by introducing crossover pairs that connect neighboring layers of DNA double helices. These layered crossovers (LX) allow the scaffold or helper strands to travel through different layers and can control the relative orientation of DNA helices in neighboring layers. Using this design strategy, we successfully constructed four versions of two‐layer parallelogram structures with well‐defined interlayer angles, a three‐layer structure with triangular cavities, and a 9‐ and 15‐layer square lattices. This strategy provides a general route to engineer 3D framework DNA nanostructures with controlled cavities and opportunities to design host–guest networks analogs to those produced with metal organic frameworks.     

Modular Reconfigurable DNA Origami: From Two-Dimensional to Three-Dimensional Structures

DNA origami enables the manipulation of objects at nanoscale, and demonstrates unprecedented versatility for fabricating both static and dynamic nanostructures. In this work, we introduce a new strategy for transferring modular reconfigurable DNA nanostructures from two-dimensional to three-dimensional. A 2D DNA sheet could be modularized into connected parts (e.g., two, three, and four parts in this work), which can be independently transformed between two conformations with a few DNA “trigger” strands. More interestingly, the transformation of the connected 2D modules can lead to the controlled, resettable structural conversion of a 2D sheet to a 3D architecture, due to the constraints induced by the connections between the 2D modules. This new approach can provide an efficient mean for constructing programmable, higher-order, and complex DNA objects, as well as sophisticated dynamic substrates for various applications.     

Hetero-assembly of gold nanoparticles on a DNA origami template

Hetero-assembling of spherical building blocks with well-defined spatial distribution holds great significance in developing chiral nanostructures. Herein, a strategy for hetero-assembling of gold nanoparticles(Au NPs) was demonstrated using rigid bifacial DNA origami as templates. By tuning the sizes and the fixed location of Au NPs on DNA origami, right-handed and left-handed Au NPs nanostructures were respectively constructed. Gel electrophoresis indicated the formation of the DNA origami-Au NPs complex and transmission electron microscopy(TEM) visually displayed the arrangement of Au NPs in these two chiral structures. The spatial configuration and 3D geometry of Au NPs were further illustrated by the stereographic TEM with tilting angles from ?30° to 30°. This strategy provides a universal approach to construct the asymmetrical 3D geometries, which may have potential applications in biomimicking and nanophotonics.     

Self-assembly of symmetric finite-size DNA nanoarrays

We report a novel and cost-effective strategy to self-assemble finite-size DNA nanoarrays. This strategy takes advantage of the geometric symmetry of the DNA nanostructures. In general, to construct a 2D array with a total of N tiles containing Cm symmetry, where m = 2, 3, 4, or 6, the number of unique tiles the fixed-size array requires is N/m, if N/m is an integral number, or Int(N/m) + 1, if N/m is an nonintegral number. We herein demonstrate two examples of fixed-size arrays with C2 and C4-fold symmetry.dagger     

Single‐Molecule Mechanochemical Sensing Using DNA Origami Nanostructures

While single‐molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single‐molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7‐tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet‐derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single‐molecule sensing with improved throughput.     

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

A highly loaded and integrated core–brush three-dimensional (3D) DNA nanostructure is constructed by programmatically assembling a locked DNA walking arm (DA) and hairpin substrate (HS) into a repetitive array along a well-designed DNA track generated by rolling circle amplification (RCA) and is applied as a 3D DNA nanomachine for rapid and sensitive intracellular microRNA (miRNA) imaging and sensing. Impressively, the homogeneous distribution of the DA and HS at a ratio of 1 : 3 on the DNA track provides a specific walking range for the DA to avoid invalid and random self-walking and notably improve the executive ability of the core–brush 3D DNA nanomachine, which easily solves the major technical challenges of traditional Au-based 3D DNA nanomachines: low loading capacity and low executive efficiency. As a proof of concept, the interaction of miRNA with the 3D DNA nanomachine could initiate the autonomous and progressive operation of the DA to cleave the HS for ultrasensitive ECL detection of target miRNA-21 with a detection limit as low as 3.57 aM and rapid imaging in living cells within 15 min. Therefore, the proposed core–brush 3D DNA nanomachine could not only provide convincing evidence for sensitive detection and rapid visual imaging of biomarkers with tiny change, but also assist researchers in investigating the formation mechanism of tumors, improving their recovery rates and reducing correlative complications. This strategy might enrich the method to design a new generation of 3D DNA nanomachine and promote the development of clinical diagnosis, targeted therapy and prognosis monitoring.

This study designed a highly loaded and integrated core–brush 3D DNA nanomachine for miRNA imaging and sensing, which easily solves the major technical challenges of traditional Au-based 3D nanomachines: low loading capacity and low executive efficiency.     

Recognition of hairpin DNA from coil DNA by electrospray mass spectrometry with annealing strategy

This research presented an annealing strategy to identify hairpin DNA from coil DNA with the same base composition but different arrangements using electrospray mass spectrometry(ESI-MS).A series of single-stranded DNA were annealed with their complementary sequences,respectively.All the five pairs of hairpin DNA and coil DNA were unambiguously distinguished by ESIMS with annealing strategy.This research offers a potential method to probe the DNA structure by comparing with mass spectral characteristics.     

Construction of pH-Triggered DNA Hydrogels Based on Hybridization Chain Reactions

As a novel type of bio-functional material,DNA hydrogels have attracted more and more attention due to their successful applications in 3D cell culturing and tissue engineering for the designable and programmable responsiveness.Herein,we have developed a pH-triggered DNA hydrogel based on a clamped hybridization chain reaction(C-HCR).In this system,a DNA switch was designed,which can release the initiator strand in a controllable way via the formation of the C-G-C4 triplex under the pH stimuli.While the pre-gelation solution is stable in neutral environment,the C-HCR will trigger the sol-gel transition as the pH decreased to 5.0.This strategy has endowed the DNA hydrogel with good controllability for triggering,which also shows potential in intellectual responsiveness to certain stimuli.     

A Reconfigurable DNA Accordion Rack

DNA nanostructure‐based mechanical systems that control the distance between elements of interest have demonstrated great potential for various applications, including nanoplasmonic systems, molecular reactors, and other nanotechnology platforms. However, previously reported systems could not collectively manipulate a 2D or 3D nanoscale network of elements to various forms in multiple stages. A reconfigurable DNA accordion rack structure is introduced that is a DNA beam lattice that changes its conformation with a small amount of short‐length DNA locks as the controlling input. The lattice shape of the 2D DNA accordion rack and the diameter and the height of the 3D DNA nanotubular structure made of the DNA accordion rack could be controlled. Furthermore, by sequentially repeating the detachment and the attachment of the different DNA locks using strand displacement, the shape reconfiguration was repeatedly carried out.     

Clamped Hybridization Chain Reactions for the Self‐Assembly of Patterned DNA Hydrogels

DNA hydrogels hold great potential for biological and biomedical applications owing to their programmable nature and macroscopic sizes. However, most previous studies involve spontaneous and homogenous gelation procedures in solution, which often lack precise control. A clamped hybridization chain reaction (C‐HCR)‐based strategy has been developed to guide DNA self‐assembly to form macroscopic hydrogels. Analogous to catalysts in chemical synthesis or seeds in crystal growth, we introduced DNA initiators to induce the gelation process, including crosslinked self‐assembly and clamped hybridization in three dimensions with spatial and temporal control. The formed hydrogels show superior mechanical properties. The use of printed, surface‐confined DNA initiators was also demonstrated for fabricating 2D hydrogel patterns without relying on external confinements. This simple method can be used to construct DNA hydrogels with defined geometry, composition, and order for various bioapplications.     

Electrochemical DNA Hybridization Detection Using DNA Cleavage

We report the new method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture probe DNA, thiolated single strand DNA labeled with electroactive ferrocene group, was immobilized on a gold electrode. After hybridization of target DNA of complementary and noncomplementary sequences, nonhybridized single strand DNA was cleaved using S1 nuclease. The difference of enzymatic cleavage on the modified gold electrode was characterized by cyclic voltammetry and differential pulse voltammetry. We successfully applied this method to the sequence‐selective discrimination between perfectly matched and mismatched target DNA including a single‐base mismatched target DNA. Our method does not require either hybridization indicators or other exogenous signaling molecules which most of the electrochemical hybridization detection systems require.