Ion‐Responsive Hemin–G‐Quadruplexes for Switchable DNAzyme and Enzyme Functions

Programmed nucleic acid sequences undergo K⁺ ion‐induced self‐assembly into G‐quadruplexes and separation of the supramolecular structures by the elimination of K⁺ ions by crown ether or cryptand ion‐receptors. This process allows the switchable formation and dissociation of the respective G‐quadruplexes. The different G‐quadruplex structures bind hemin, and the resulting hemin–G‐quadruplex structures reveal horseradish peroxidase DNAzyme catalytic activities. The following K⁺ ion/receptor switchable systems are described: 1) The K⁺‐induced self‐assembly of the Mg²⁺‐dependent DNAzyme subunits into a catalytic nanostructure using the assembly of G‐quadruplexes as bridging unit. 2) The K⁺‐induced stabilization of the anti‐thrombin G‐quadruplex nanostructure that inhibits the hydrolytic functions of thrombin. 3) The K⁺‐induced opening of DNA tweezers through the stabilization of G‐quadruplexes on the “tweezers’ arms" and the release of a strand bridging the tweezers into a closed structure. In all of the systems reversible, switchable, functions are demonstrated. For all systems two different signals are used to follow the switchable functions (fluorescence and the catalytic functions of the derived hemin–G‐quadruplex DNAzyme).     

DNA Switches: From Principles to Applications

The base sequence of nucleic acid encodes structural and functional properties into the biopolymer. Structural information includes the formation of duplexes, G‐quadruplexes, i‐motif, and cooperatively stabilized assemblies. Functional information encoded in the base sequence involves the strand‐displacement process, the recognition properties by aptamers, and the catalytic functions of DNAzymes. This Review addresses the implementation of the information encoded in nucleic acids to develop DNA switches. A DNA switch is a supramolecular nucleic acid assembly that undergoes cyclic, switchable, transitions between two distinct states in the presence of appropriate triggers and counter triggers, such as pH value, metal ions/ligands, photonic and electrical stimuli. Applications of switchable DNA systems to tailor switchable DNA hydrogels, for the controlled drug‐release and for the activation of switchable enzyme cascades, are described, and future perspectives of the systems are addressed.     

Switchable Enzyme/DNAzyme Cascades by the Reconfiguration of DNA Nanostructures

Mimicking cellular transformations and signal transduction pathways by means of biocatalytic cascades proceeding in organized media is a scientific challenge. We describe two DNA machines that enable the “ON/OFF” switchable activation and deactivation of three‐component biocatalytic cascades. One system consists of a reconfigurable DNA tweezers‐type structure, whereas in the second system the catalytic cascade proceeds on a switchable DNA clamp scaffold. The three‐component catalytic cascades consist of β‐galactosidase (β‐Gal), glucose oxidase (GOx), and the K⁺‐ion‐stabilized hemin‐G‐quadruplex horseradish peroxidase (HRP)‐mimicking DNAzyme. The hemin‐G‐quadruplex‐bridged closed structure of the tweezers or clamp allows the biocatalytic cascades to operate (switched “ON′′), whereas separation of the hemin‐G‐quadruplex by means of 18‐crown‐6‐ether opens the tweezers/clamp structures, thus blocking the catalytic cascade (switched ”OFF“). This study is complemented by two‐component, switchable biocatalytic cascades composed of GOx and hemin‐G‐quadruplex assembled on hairpin‐bridged DNA tweezers or clamp nanostructures.     

Chemical Regulation of DNA i‐Motifs for Nanobiotechnology and Therapeutics

DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four‐stranded intercalated DNA structures called i‐motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i‐motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i‐motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long‐lasting debate regarding the stability of i‐motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i‐motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i‐motif‐targeted regulation of gene expression, telomere maintenance, and therapeutic applications.     

Non‐B DNA Structures Show Diverse Conformations and Complex Transition Kinetics Comparable to RNA or Proteins—A Perspective from Mechanical Unfolding and Refolding Experiments

With the firm demonstration of the in vivo presence and biological functions of many non‐B DNA structures, it is of great significance to understand their physiological roles from the perspective of structural conformation, stability, and transition kinetics. Although relatively simple in primary sequences compared to proteins, non‐B DNA species show rather versatile conformations and dynamic transitions. As the most‐studied non‐B DNA species, the G‐quadruplex displays a myriad of conformations that can interconvert between each other in different solutions. These features impose challenges for ensemble‐average techniques, such as X‐ray crystallography, NMR spectroscopy, and circular dichroism (CD), but leave room for single‐molecular approaches to illustrate the structure, stability, and transition kinetics of individual non‐B DNA species in a solution mixture. Deconvolution of the mixture can be further facilitated by statistical data treatment, such as iPoDNano (i ntegrated po pulation d econvolution with nano meter resolution), which resolves populations with subnanometer size differences. This Personal Account summarizes current mechanical unfolding and refolding methods to interrogate single non‐B DNA species, with an emphasis on DNA G‐quadruplexes and i‐motifs. These single‐molecule studies start to demonstrate that structures and transitions in non‐B DNA species can approach the complexity of those in RNA or proteins, which provides solid justification for the biological functions carried out by non‐B DNA species.     

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich “toolbox” of structures used to develop DNA‐based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH‐induced, switchable assembly and dissociation of triplex‐DNA‐bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH‐responsive systems and materials are described. Examples include semiconductor‐loaded DNA‐stabilized microcapsules, DNA‐functionalized dye‐loaded metal–organic frameworks (MOFs), and the pH‐induced release of the loads. Furthermore, the design of stimuli‐responsive DNA‐based hydrogels undergoing reversible pH‐induced hydrogel‐to‐solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape‐memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.     

An Adamantane‐Based Building Block for DNA Networks

DNA governs the storage and transfer of genetic information through generations in all living systems with the exception of some viruses. Its physicochemical nature and the Watson–Crick base pairing properties allow molecular constructions at nanometer length, thereby enabling the design of desired structural motifs, which can self‐assemble to form large supramolecular arrays and scaffolds. The tailor‐made DNAs have been an interesting material for such designed nanoscale constructions. However, the synthesis of specific structures with a desired molecular function is still in its infancy and therefore has to be further explored. To add a new dimension to this approach, we have synthesized a rigid three‐way branched adamantane motif, which is capable of forming highly stable DNA networks. The moiety generated could serve as a useful building block for DNA‐based nanoconstructions.     

Cell‐Surface Engineering by a Conjugation‐and‐Release Approach Based on the Formation and Cleavage of Oxime Linkages upon Mild Electrochemical Oxidation and Reduction

We report a strategy to rewire cell surfaces for the dynamic control of ligand composition on cell membranes and the modulation of cell–cell interactions to generate three‐dimensional (3D) tissue structures applied to stem‐cell differentiation, cell‐surface tailoring, and tissue engineering. We tailored cell surfaces with bioorthogonal chemical groups on the basis of a liposome‐fusion and ‐delivery method to create dynamic, electroactive, and switchable cell‐tissue assemblies through chemistry involving chemoselective conjugation and release. Each step to modify the cell surface: activation, conjugation, release, and regeneration, can be monitored and modulated by noninvasive, label‐free analytical techniques. We demonstrate the utility of this methodology by the conjugation and release of small molecules to and from cell surfaces and by the generation of 3D coculture spheroids and multilayered cell tissues that can be programmed to undergo assembly and disassembly on demand.     

Recognizing Hybrid/Mixed G-quadruplex in Human Telomeres by Using a Cyanine Dye Supramolecule with Confocal Laser Scanning Microscopy

Single‐stranded telomeric DNA tends to form a four‐base‐paired planar structure termed G‐quadruplex. Although kinds of G‐quadruplex structures in vitro have been documented in the presence of potassium or sodium, recognition of these DNA motifs (both in vitro and in vivo) is still an important issue in understanding the biological function of the G‐quadruplex structures in telomeres as well as developing anticancer agents. Herein we address this important question through the distinctive properties of a supramolecular system of cyanine dye 3,3′‐di(3‐sulfopropyl)‐4,5,4′,5′‐dibenzo‐9‐methyl‐thiacarbocyanine triethylammonium salt (MTC) upon binding to different DNA motifs. Interaction of MTC with hybrid/mixed G‐quadruplex results in a set of unique spectrophotometric signatures which are completely different from those arising from binding to other DNA motifs. Furthermore, such feature could be extended to map the locations of DNAs on interface. Linear duplex and mixed G‐quadruplex in human telomeres assembled on Au film and stained by MTC were directly recognized by confocal laser scanning microscopy (CLSM). All results suggested that MTC supramolecular system may be a good probe of specific G‐quadruplex structure.     

Monomer–Dimer Equilibrium for the 5′–5′ Stacking of Propeller‐Type Parallel‐Stranded G‐Quadruplexes: NMR Structural Study

Guanine‐rich sequence motifs, which contain tracts of three consecutive guanines connected by single non‐guanine nucleotides, are abundant in the human genome and can form a robust G‐quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5′–5′ stacked dimeric propeller‐type G‐quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer–dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high‐definition structure of a simple monomeric G‐quadruplex containing three single‐residue loops, which could serve as a reference for propeller‐type G‐quadruplex structures in solution.     

Spatial Structuring of a Supramolecular Hydrogel by using a Visible‐Light Triggered Catalyst

Spatial control over the self‐assembly of synthetic molecular fibers through the use of light‐switchable catalysts can lead to the controlled formation of micropatterns made up of hydrogel structures. A photochromic switch, capable of reversibly releasing a proton upon irradiation, can act as a catalyst for in situ chemical bond formation between otherwise soluble building blocks, thereby leading to fiber formation and gelation in water. The use of a photoswitchable catalyst allows control over the distribution as well as the mechanical properties of the hydrogel material. By using homemade photomasks, spatially structured hydrogels were formed starting from bulk solutions of small molecule gelator precursors through light‐triggered local catalyst activation.     

Rational Design of pH‐Responsive DNA Motifs with General Sequence Compatibility

Reconfigurable molecular events are key to molecular machines. In response to external cues, molecular machines rearrange/change their structures to perform certain functions. Such machines exist in nature, for example cell surface receptors, and have been artificially engineered. To be able to build sophisticated and efficient molecular machines for an increasing range of applications, constant efforts have been devoted to developing new mechanisms of controllable structural reconfiguration. Herein, we report a general design principle for pH‐responsive DNA motifs for general DNA sequences (not limited to triplex or i‐motif forming sequences). We have thoroughly characterized such DNA motifs by polyacrylamide gel electrophoresis (PAGE) and fluorescence spectroscopy and demonstrated their applications in dynamic DNA nanotechnology. We expect that it will greatly facilitate the development of DNA nanomachines, biosensing/bioimaging, drug delivery, etc.     

Light‐Induced Reversible Reconfiguration of DNA‐Based Constitutional Dynamic Networks: Application to Switchable Catalysis

The light‐induced reversible and cyclic reconfiguration of constitutional dynamic networks, consisting of supramolecular nucleic acid structures as constituents and a photoisomerizable trans/cis‐azobenzene‐functionalized nucleic acid as the trigger is demonstrated. In addition, the cyclic photochemical reconfiguration of the constitutional dynamic networks guides the switchable on/off operation of an emerging hemin/G‐quadruplex DNAzyme.     

Self‐Assembled Monolayers with Dynamicity Stemming from (Bio)Chemical Conversions: From Construction to Application

Surfaces with “dynamicity” whereby surface properties can be modulated by an external stimulus on user demand have been actively exploited for the past decade. These switchable surfaces with dynamic properties are widely used for a number of applications such as micro/nanoarrays, biomolecule immobilization, basic cell studies, and tissue engineering on a variety of materials. This minireview highlights the dynamic control of surface properties on self‐assembled monolayers and focuses on dynamicity that stems from (bio)chemical conversions achieved by electrical potentials, photoillumination, chemical reagents, enzymes, and pH.     

Modified Electrodes with Switchable Selectivity for Cationic and Anionic Redox Species

The modified electrode functionalized with a mixed‐polymer brush composed of poly(2‐vinylpyridine) and polyacrylic acid tethered to the surface demonstrated switchable interfacial properties discriminating negatively and positively charged redox species. The switchable electrochemical process was characterized by differential pulse voltammetry and Faradaic impedance spectroscopy. The electrochemical system was discussed as a model of an electrochemical multiplexer with two chemical redox inputs, the pH input operating as the selecting signal and one electronic output signal readable by the impedance spectroscopy in the form of the interfacial resistance. The modified electrode represents a novel component for integration with biocatalytic and biocomputing systems aiming at biochemically and electronically controlled actuators.     

Targeting Non‐B‐Form DNA in Living Cells

Under certain conditions, repetitive DNA motifs have the potential to adopt non‐B‐form DNA structures, such as hairpins, triplexes, Z‐DNA, quadruplexes, and i‐motifs. Some non‐B‐form DNAs have been proposed to cause mutations and, consequently, participate in several biologically important processes, including regulation, evolution, and human disease. Advancement in the knowledge of specific interactions between molecules and non‐B‐form DNAs at the molecular level in living cells is important for understanding their biological functions. In this review, we describe the latest studies on molecules that target non‐B‐form DNAs in vivo, with a focus on Z‐DNA, G‐quadruplexes, triplexes, i‐motifs, and hairpins.     

Fabrication of Defined Polydopamine Nanostructures by DNA Origami‐Templated Polymerization

A versatile, bottom‐up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage‐mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase‐mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as “supramolecular glue” for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami‐controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template.     

Anion Responsive Imidazolium‐Based Polymers

Stimuli responsiveness in polymer design is providing basis for diversely new and advanced materials that exhibit switchable porosity in membranes and coatings, switchable particle formation and thermodynamically stable nanoparticle dispersions, polymers that provide directed mechanical stress in response to intensive fields, and switchable compatibility of nanomaterials in changing environments. The incorporation of ionic liquid monomers has resulted in many new polymers based on the imidazolium group. These polymers exhibit all of the above‐articulated material properties. Some insight into how these anion responsive polymers function has become empirically available. Much opportunity remains for extending our understanding as well as for designing more refined stimuli‐responsive materials.     

Assembly of Bacteriophage into Functional Materials

For the last decade, the fabrication of ordered structures of phage has been of great interest as a means of utilizing the outstanding biochemical properties of phage in developing useful materials. Combined with other organic/inorganic substances, it has been demonstrated that phage is a superior building block for fabricating various functional devices, such as the electrode in lithium‐ion batteries, photovoltaic cells, sensors, and cell‐culture supports. Although previous research has expanded the utility of phage when combined with genetic engineering, most improvements in device functionality have relied upon increases in efficiency owing to the compact, more densely packable unit size of phage rather than on the unique properties of the ordered nanostructures themselves. Recently, self‐templating methods, which control both thermodynamic and kinetic factors during the deposition process, have opened up new routes to exploiting the ordered structural properties of hierarchically organized phage architectures. In addition, ordered phage films have exhibited unexpected functional properties, such as structural color and optical filtering. Structural colors or optical filtering from phage films can be used for optical phage‐based sensors, which combine the structural properties of phage with target‐specific binding motifs on the phage‐coat proteins. This self‐templating method may contribute not only to practical applications, but also provide insight into the fundamental study of biomacromolecule assembly in in vivo systems under complicated and dynamic conditions.