One‐Step Formation of “Chain‐Armor”‐Stabilized DNA Nanostructures

DNA‐based self‐assembled nanostructures are widely used to position organic and inorganic objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA‐based templates that are robust against degradation at elevated temperatures, low ion concentrations, adverse pH conditions, and DNases, we built 6‐helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3′‐ends and azides on their 5′‐ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so‐called DNA catenanes. Strikingly, the structures stayed topologically intact in pure water and even after precipitation from EtOH. The structures even withstood a temperature of 95 °C when all of the 24 strands were chemically interlocked.     

Self-assembly of Micrometer-long DNA Nanoribbons with Four Oligonucleotides

DNA nanostructures have found widespread applications in areas including nanoelectronics and biomedicine. However, traditional DNA origami needs a long single‐stranded virus DNA and hundreds of short DNA strands, which make this method complicated and money‐consuming. Here, we present a protocol for the assembly of DNA nanoribbons with only four oligonucleotides. DNA nanoribbons with different dimensions were successfully assembled with a 96‐base scafford strand and three short staples. These biotinylated nanoribbons could also be decorated with streptavidins. This approach suggests that there exist great design spaces for the creation of simple nucleic acid nanostructures which could facilitate their application in plasmonic or drug delivery.     

O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron

Tetrahedron DNA structures were formed by the assembly of three-way junction ( TWJ ) oligonucleotides containing O⁶-2′-deoxyguanosine-alkylene-O⁶-2′-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2′-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O⁶-alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.     

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.     

Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.     

基于纳米金胶标记DNA探针的电化学DNA传感器研究

以纳米金胶为标记物,将其标记于人工合成的5-端巯基修饰的寡聚核苷酸片段上,制成了具有电化学活性的金胶标记DNA电化学探针;在一定条件下,使其与固定在玻碳电极表面的靶序列进行杂交反应,利用ssDNA与其互补链杂交的高度序列选择性和极强的分子识别能力,以及纳米金胶的电化学活性,实现对特定序列DNA片段的电化学检测以及对DNA碱基突变的识别.     

DNA origami: the art of folding DNA

The advent of DNA origami technology greatly simplified the design and construction of nanometer-sized DNA objects. The self-assembly of a DNA-origami structure is a straightforward process in which a long single-stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm(2) and with a single "pixel" resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two- and three-dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.     

Topological Links between Duplex DNA and a Circular DNA Single Strand

DNA nanostructures of building blocks topologically linked at a precise position can be assembled from DNA duplexes and circularized oligonucleotides with the aid of peptide nucleic acids (PNAs). Shown schematically is a linked catenane yielding an earring topological DNA label.     

Information Coding in a Reconfigurable DNA Origami Domino Array

DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti‐counterfeiting approach based on conformational transformation‐mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.     

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.     

Reconfigurable Plasmonic Nanostructures Controlled by DNA Origami

Precise surface functionalization and reconfigurable capability of nanomaterials are essential to construct complex nanostructures with specific functions.Here we show tire assembly of a reconfigurable plasmonic nanostructure,which executes both conformational and plasmonic changes in response to DNA strands.In this work,different sized gold nanoparticles(AuNPs)were arranged site-specifically on the surface of a DNA origami clamp nanostructure.The opening and closing of the DNA origami clamp could be precisely controlled by a series of strand emplacement reactions.Therefore,the patterns of these AuNPs could be switched between two different configura-tions.The observed plasmon band shift indicates the change of the plasmonic interactions among the assembled AuNPs.Our study achieves the construction of reconfigurable nanomaterials with tunable plasmonic interactions,and will enrich the toolbox of DNA-based functional nanomachinery.     

Ferrocenyl‐Modified DNA: Synthesis,Characterization and Integration with Semiconductor Electrodes

The ferrocenyl‐nucleoside, 5‐ethynylferrocenyl‐2′‐deoxycytidine ( 1 ) has been prepared by Pd‐catalyzed cross‐coupling between ethynylferrocene and 5‐iodo‐2′‐deoxycytidine and incorporated into oligonucleotides by using automated solid‐phase synthesis at both silica supports (CPG) and modified single‐crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl‐nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl‐modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12‐mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid‐phase methods were also used to synthesise 12‐mer ferrocenyl‐containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface‐bound ferrocenyl‐DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene–phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO₄, a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation‐induced changes in ferrocene–phosphate distances.     

Complex Reconfiguration of DNA Nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold‐mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural‐reconfiguration method that utilizes the modularly interconnected architecture of single‐stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two‐dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three‐dimensional DNA cuboid.     

Computer‐Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes

The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two‐dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.     

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.     

Binary Assembly of Au Nanoparticles with Controllable Two‐dimensional Architecture Directed by Phosphate Backbone Modified Oligonucleotide

A three complementary strand oligonucleotide system was employed to assemble two different‐sized, 15 and 25 nm, Au nanoparticles into binary two‐dimensional (2D) structures. First, two non‐complementary strands of phosphate backbone modified oligonucleotides (PM oligo‐DNA) were loaded on the surface of the 15 and 25 nm Au nanoparticles, respectively. Upon the addition of the third linker DNA, which was half complementary to each of the modified DNA, the Au nanoparticles would be assembled to binary 2D aggregates. The number of the 15 nm Au nanoparticles around a 25 nm Au naoparticle can be readily controlled by the length of the DNA helix used.     

Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low‐Energy Electrons (0.5–9 eV)

Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low‐energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross‐section for oligonucleotides modified with 8‐bromoadenine (^8BrA). These results were evaluated against DEA measurements with isolated ^8BrA in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.     

Application of the avidin–biotin interaction to immobilize DNA in the development of electrochemical impedance genosensors

Impedance spectroscopy is a rapidly developing technique for the transduction of biosensing events at the surface of an electrode. The immobilization of biomaterial as DNA strands on the electrode surface alters the capacitance and the interfacial electron transfer resistance of the conductive electrodes. The impedimetric technique is an effective method of probing modifications to these interfacial properties, thus allowing the differentiation of hybridization events. In this work, an avidin bulk-modified graphite–epoxy biocomposite (Av-GEB) was employed to immobilize biotinylated oligonucleotides as well as double-stranded DNA onto the electrode surface. Impedance spectra were recorded to detect the change in the interfacial electron transfer resistance (R _et) of the redox marker ferrocyanide/ferricyanide at a polarization potential of +0.17 V. The sensitivity of the technique and the good reproducibility of the results obtained with it confirm the validity of this method based on a universal affinity biocomposite platform coupled with the impedimetric technique.     

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single‐molecule imaging of triple helix formation in DNA nanostructures. The binding of the single‐molecule third strand to double‐stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson–Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high‐speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.