Universal pH‐Responsive and Metal‐Ion‐Free Self‐Assembly of DNA Nanostructures

pH‐responsiveness has been widely pursued in dynamic DNA nanotechnology, owing to its potential in biosensing, controlled release, and nanomachinery. pH‐triggering systems mostly depend on specific designs of DNA sequences. However, sequence‐independent regulation could provide a more general tool to achieve pH‐responsive DNA assembly, which has yet to be developed. Herein, we propose a mechanism for dynamic DNA assembly by utilizing ethylenediamine (EN) as a reversibly chargeable (via protonation) molecule to overcome electrostatic repulsions. This strategy provides a universal pH‐responsivity for DNA assembly since the regulation originates from externally co‐existing EN rather than specific DNA sequences. Furthermore, it endows structural DNA nanotechnology with the benefits of a metal‐ion‐free environment including nuclease resistance. The concept could in principle be expanded to other organic molecules which may bring unique controls to dynamic DNA assembly.     

A Signal‐Passing DNA‐Strand‐Exchange Mechanism for Active Self‐Assembly of DNA Nanostructures

DNA nanostructured tiles play an active role in their own self‐assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self‐assembly of tiles and enables local communication during the self‐assembly process. This localized signal‐passing mechanism provides a new element of control for autonomous self‐assembly of DNA nanostructures.     

DNA Computing Systems Activated by Electrochemically‐triggered DNA Release from a Polymer‐brush‐modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA‐based Identity, AND and XOR logic gates. Single‐stranded DNA molecules were loaded on the mixed poly(N ,N ‐dimethylaminoethyl methacrylate) (PDMAEMA)/poly(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAEMA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.     

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

Probing Biomolecular Interactions at Conductive and Semiconductive Surfaces by Impedance Spectroscopy: Routes to Impedimetric Immunosensors,DNA‐Sensors,and Enzyme Biosensors

Impedance spectroscopy is a rapidly developing electrochemical technique for the characterization of biomaterial‐functionalized electrodes and biocatalytic transformations at electrode surfaces, and specifically for the transduction of biosensing events at electrodes or field‐effect transistor devices. The immobilization of biomaterials, e.g., enzymes, antigens/antibodies or DNA on electrodes or semiconductor surfaces alters the capacitance and interfacial electron transfer resistance of the conductive or semiconductive electrodes. Impedance spectroscopy allows analysis of interfacial changes originating from biorecognition events at electrode surfaces. Kinetics and mechanisms of electron transfer processes corresponding to biocatalytic reactions occurring at modified electrodes can be also derived from Faradaic impedance spectroscopy. Different immunosensors that use impedance measurements for the transduction of antigen‐antibody complex formation on electronic transducers were developed. Similarly, DNA biosensors using impedance measurements as readout signals were developed. Amplified detection of the analyte DNA using Faradaic impedance spectroscopy was accomplished by the coupling of functionalized liposomes or by the association of biocatalytic conjugates to the sensing interface providing biocatalyzed precipitation of an insoluble product on the electrodes. The amplified detections of viral DNA and single‐base mismatches in DNA were accomplished by similar methods. The changes of interfacial features of gate surfaces of field‐effect transistors (FET) upon the formation of antigen‐antibody complexes or assembly of protein arrays were probed by impedance measurements and specifically by transconductance measurements. Impedance spectroscopy was also applied to characterize enzyme‐based biosensors. The reconstitution of apo‐enzymes on cofactor‐functionalized electrodes and the formation of cofactor‐enzyme affinity complexes on electrodes were probed by Faradaic impedance spectroscopy. Also biocatalyzed reactions occurring on electrode surfaces were analyzed by impedance spectroscopy. The theoretical background of the different methods and their practical applications in analytical procedures were outlined in this article.     

Reciprocal Self‐Assembly of Peptide–DNA Conjugates into a Programmable Sub‐10‐nm Supramolecular Deoxyribonucleoprotein

To overcome the limitations of molecular assemblies, the development of novel supramolecular building blocks and self‐assembly modes is essential to create more sophisticated, complex, and controllable aggregates. The self‐assembly of peptide–DNA conjugates (PDCs), in which two orthogonal self‐assembly modes, that is, β‐sheet formation and Watson–Crick base pairing, are covalently combined in one supramolecular system, is reported. Despite extensive research, most self‐assembly studies have focused on using only one type of building block, which restricts structural and functional diversity compared to multicomponent systems. Multicomponent systems, however, suffer from poor control of self‐assembly behaviors. Covalently conjugated PDC building blocks are shown to assemble into well‐defined and controllable nanostructures. This controllability likely results from the decrease in entropy associated with the restriction of the molecular degrees of freedom by the covalent constraints. Using this strategy, the possibility to thermodynamically program nano‐assemblies to exert gene regulation activity with low cytotoxicity is demonstrated.     

Determination of DNA Hypermethylation Using Anti‐cancer Drug‐Temozolomide

An electrochemical drug‐DNA biosensor was developed for the detection of interaction between the anti‐cancer drug, Temozolomide (TMZ), and DNA sequences by using Differential Pulse Voltammetry at the graphite electrode surfaces. TMZ is a pro‐drug and an alkylating agent that crosses the blood‐brain barrier, so it is mainly used for brain cancers treatment. In this study, we aim to develop a‐proof‐of‐concept study to investigate the effect of TMZ on formerly methylated DNA sequences since TMZ shows its anti‐cancer activity by methylating the DNA. Interaction between TMZ and DNA causes localized distortion of DNA away from an idealized B‐form, resulting in a wider major groove and greater steric accessibility of functional groups in the base of the groove. According to the results, TMZ behaves as a ‘hybridization indicator’ because of its different electrochemical behavior to different strands of DNA. After interaction with TMZ, hybrid (double stranded DNA‐dsDNA) signals decreased dramatically whereas probe (single stranded DNA‐ssDNA) and control signals remain almost unchanged. The signal differences enabled us to distinguish ssDNA and dsDNA without using a label or tag. It is the first study to demonstrate the interaction between the TMZ and dsDNA created from probe and target. We use specific oligonucleotides sequences instead of using long dsDNA sequences.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission

The design of turn‐on dyes with optical signals sensitive to the formation of supramolecular structures provides fascinating and underexplored opportunities for G‐quadruplex (G4) DNA detection and characterization. Here, we show a new switching mechanism that relies on the recognition‐driven disaggregation (on‐signal) of an ultrabright coumarin‐quinazoline conjugate. The synthesized probe selectively lights‐up parallel G4 DNA structures via the disassembly of its supramolecular state, demonstrating outputs that are easily integrable into a label‐free molecular logic system. Finally, our molecule preferentially stains the G4‐rich nucleoli of cancer cells.     

Gold‐Nanoparticle‐Mediated Jigsaw‐Puzzle‐like Assembly of Supersized Plasmonic DNA Origami

DNA origami has rapidly emerged as a powerful and programmable method to construct functional nanostructures. However, the size limitation of approximately 100 nm in classic DNA origami hampers its plasmonic applications. Herein, we report a jigsaw‐puzzle‐like assembly strategy mediated by gold nanoparticles (AuNPs) to break the size limitation of DNA origami. We demonstrated that oligonucleotide‐functionalized AuNPs function as universal joint units for the one‐pot assembly of parent DNA origami of triangular shape to form sub‐microscale super‐origami nanostructures. AuNPs anchored at predefined positions of the super‐origami exhibited strong interparticle plasmonic coupling. This AuNP‐mediated strategy offers new opportunities to drive macroscopic self‐assembly and to fabricate well‐defined nanophotonic materials and devices.     

Directed Self‐Assembly of DNA Tiles into Complex Nanocages

Tile‐based self‐assembly is a powerful method in DNA nanotechnology and has produced a wide range of well‐defined nanostructures. But the resulting structures are relatively simple. Increasing the structural complexity and the scope of the accessible structures is an outstanding challenge in molecular self‐assembly. A strategy to partially address this problem by introducing flexibility into assembling DNA tiles and employing directing agents to control the self‐assembly process is presented. To demonstrate this strategy, a range of DNA nanocages have been rationally designed and constructed. Many of them can not be assembled otherwise. All of the resulting structures have been thoroughly characterized by gel electrophoresis and cryogenic electron microscopy. This strategy greatly expands the scope of accessible DNA nanostructures and would facilitate technological applications such as nanoguest encapsulation, drug delivery, and nanoparticle organization.     

Dual‐Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires

The combination of oligonucleotides and synthetic supramolecular systems allows for novel and long‐needed modes of regulation of the self‐assembly of both molecular elements. Discotic molecules were conjugated with short oligonucleotides and their assembly into responsive supramolecular wires studied. The self‐assembly of the discotic molecules provides additional stability for DNA‐duplex formation owing to a cooperative effect. The appended oligonucleotides allow for positional control of the discotic elements within the supramolecular wire. The programmed assembly of these hybrid architectures can be modulated through the DNA, for example, by changing the number of base pairs or salt concentration, and through the discotic platform by the addition of discotic elements without oligonucleotide handles. These hybrid supramolecular‐DNA structures allow for advanced levels of control over 1D dynamic platforms with responsive regulatory elements at the interface with biological systems.     

An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells

Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six‐letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six‐letter DNA library to selectively bind liver cancer cells; and 2) in a six‐letter self‐assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer‐nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer‐targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.     

Self‐Assembly of Complex DNA Tessellations by Using Low‐Symmetry Multi‐arm DNA Tiles

Modular DNA tile‐based self‐assembly is a versatile way to engineer basic tessellation patterns on the nanometer scale, but it remains challenging to achieve high levels of structural complexity. We introduce a set of general design principles to create intricate DNA tessellations by employing multi‐arm DNA motifs with low symmetry. We achieved two novel Archimedean tiling patterns, (4.8.8) and (3.6.3.6), and one pattern with higher‐order structures beyond the complexity observed in Archimedean tiling. Our success in assembling complicated DNA tessellations demonstrates the broad design space of DNA structural motifs, enriching the toolbox of DNA tile‐based self‐assembly and expanding the complexity boundaries of DNA tile‐based tessellation.     

Theoretical perspective on properties of DNA‐functionalized surfaces

The molecular recognition properties of DNA gave rise to many novel materials and applications such as DNA biosensors, DNA‐functionalized colloidal materials, DNA origami and DNA‐based directed surface assembly. The DNA‐functionalized surfaces are used in biosensors and for programmed self‐assembly of biological, organic and inorganic moieties into novel materials. However, surface density, length, and linker design of the surface functionalized DNAs significantly influence the properties of DNA‐driven assemblies and materials. This perspective discusses the understanding of structure and dynamics of DNA immobilized on the surfaces from the theoretical point of view including recent progress in analytical theories, atomistic simulations, and coarse‐grained models. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1563–1568, 2011     

Crystallization of DNA‐Capped Gold Nanoparticles in High‐Concentration,Divalent Salt Environments

The multiparametric nature of nanoparticle self‐assembly makes it challenging to circumvent the instabilities that lead to aggregation and achieve crystallization under extreme conditions. By using non‐base‐pairing DNA as a model ligand instead of the typical base‐pairing design for programmability, long‐range 2D DNA–gold nanoparticle crystals can be obtained at extremely high salt concentrations and in a divalent salt environment. The interparticle spacings in these 2D nanoparticle crystals can be engineered and further tuned based on an empirical model incorporating the parameters of ligand length and ionic strength.     

Reconfigurable T‐junction DNA Origami

DNA self‐assembly allows the construction of nanometre‐scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single‐stranded loops embedded in a double‐stranded DNA template and is programmed by a set of double‐stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T‐junctions formed by hybridization of single‐stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T‐junction origami motifs and that assembly can be performed at room temperature.     

Crystallization of DNA‐Capped Gold Nanoparticles in High‐Concentration,Divalent Salt Environments

The multiparametric nature of nanoparticle self‐assembly makes it challenging to circumvent the instabilities that lead to aggregation and achieve crystallization under extreme conditions. By using non‐base‐pairing DNA as a model ligand instead of the typical base‐pairing design for programmability, long‐range 2D DNA–gold nanoparticle crystals can be obtained at extremely high salt concentrations and in a divalent salt environment. The interparticle spacings in these 2D nanoparticle crystals can be engineered and further tuned based on an empirical model incorporating the parameters of ligand length and ionic strength.     

Flow‐Enabled Self‐Assembly of Large‐Scale Aligned Nanowires

One‐dimensional nanowires enable the realization of optical and electronic nanodevices that may find applications in energy conversion and storage systems. Herein, large‐scale aligned DNA nanowires were crafted by flow‐enabled self‐assembly (FESA). The highly oriented and continuous DNA nanowires were then capitalized on either as a template to form metallic nanowires by exposing DNA nanowires that had been preloaded with metal salts to an oxygen plasma or as a scaffold to direct the positioning and alignment of metal nanoparticles and nanorods. The FESA strategy is simple and easy to implement and thus a promising new method for the low‐cost synthesis of large‐scale one‐dimensional nanostructures for nanodevices.     

Programmed Self‐Assembly of a Quadruplex DNA Nanowire

The ability to produce, reproducibly and systematically, well‐defined quadruplex DNA nanowires through controlled rational design is poorly understood despite potential utility in structural nanotechnology. The programmed hierarchical self‐assembly of a long four‐stranded DNA nanowire through cohesive self‐assembly of GpC and CpG “sticky” ends is reported. The encoding of bases within the quadruplex stem allows for an uninterrupted π‐stacking system with rectilinear propagation for hundreds of nanometers in length. The wire is mechanically stable and features superior nuclease resistance to double‐stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic investigation of well‐defined DNA nanostructures for uses in optoelectronic and electronic devices as well as other structural nanotechnology applications.