Light-driven DNA nanomachine with a photoresponsive molecular engine

Dynamic Gold Nanostructures Based on DNA Self Assembly

The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.

Light Responsive DNA Nanomaterials and Their Biomedical Applications

DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.

A Visible-Light Regulated ATP Transport in Retinal-Modified Pillar[6]arene Layer-by-Layer Self-Assembled Sub-Nanochannel

Natural light-responsive rhodopsins play a critical role in visual conversion, signal transduction, energy transmission, etc., which has aroused extensive interest in the past decade. Inspired by these gorgeous works of living beings, scientists have constructed various biomimetic light-responsive nanochannels to mimic the behaviors of rhodopsins. However, it is still challenging to build stimuli-responsive sub-nanochannels only regulated by visible light as the rhodopsins are always at the sub-nanometer level and regulated by visible light. Pillar[6]arenes have an open cavity of 6.7 Å, which can selectively recognize small organic molecules. They can be connected to ions of ammonium or carboxylate groups on the rims. Therefore, we designed and synthesized the amino and carboxyl-derived side chains of pillar[6]arenes with opposite charges. The sub-nanochannels were constructed through the electrostatic interaction of layer-by-layer self-assembled amino and carboxyl-derived pillar[6]arenes. Then, the natural chromophore of the retinal with visible light-responsive performance was modified on the upper edge of the sub-nanochannel to realize the visible light switched on and off. Finally, we successfully constructed a visible light-responsive sub-nanochannel, providing a novel method for regulating the selective transport of energy-donating molecules of ATP.

Site-Selective Photo-Crosslinking of Stilbene Pairs in a DNA Duplex Mediated by Ruthenium Photocatalyst

We herein report a method for site-selective photo-crosslinking of a DNA duplex. A stilbene pair was introduced into a DNA duplex and a ruthenium complex was conjugated with a triplex-forming oligonucleotide. We demonstrated that [2+2] photocycloaddition of the stilbene pair occurred upon irradiation with visible light when the ruthenium complex was in close proximity due to triplex formation. No reaction occurred when the ruthenium complex was not in proximity to the stilbene pair. The wavelength of visible light used was of lower energy than the wavelength of UV light necessary for direct excitation of stilbene. Quantum chemical calculation indicated that ruthenium complex catalyzed the photocycloaddition via triplet-triplet energy transfer. Site selectivity of this photo-crosslinking system was evaluated using a DNA duplex bearing two stilbene pairs as a substrate; we showed that the site of crosslinking was precisely regulated by the sequence of the oligonucleotide linked to the ruthenium complex. Since this method does not require orthogonal photoresponsive molecules, it will be useful in construction of complex photoresponsive DNA circuits, nanodevices and biological tools.

A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower

Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.

Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme

Single-stranded RNA folds into a variety of secondary and higher-order structures. Distributions and dynamics of multiple RNA conformations are responsible for the biological function of RNA. We here developed a photoswitchable molecular glue for RNA, which could reversibly control the association of two unpaired RNA regions in response to light stimuli. The photoswitchable molecular glue, NCTA, is an RNA-binding ligand possessing a photoisomerizable azobenzene moiety. Z-NCTA is an active ligand for the target RNA containing 5'-WGG-3'/5'-WGG-3' (W = U or A) site and stabilizes its hybridized state, while its isomer E-NCTA is not. Photoreversible isomerization of NCTA enabled control of the secondary and tertiary structure of the target RNA. The RNA-cleaving activity of hammerhead ribozyme, where appropriate RNA folding is necessary, could be reversibly regulated by photoirradiation in cells treated with NCTA, demonstrating precise photocontrol of RNA structure and function by the photoswitchable molecular glue.

Transient Dynamic Operation of G-Quadruplex-Gated Glucose Oxidase-Loaded ZIF-90 Metal-Organic Framework Nanoparticle Bioreactors

Glucose oxidase-loaded ZIF-90 metal-organic framework nanoparticles conjugated to hemin-G-quadruplexes act as functional bioreactor hybrids operating transient dissipative biocatalytic cascaded transformations consisting of the glucose-driven H2O2-mediated oxidation of Amplex-Red to resorufin or the glucose-driven generation of chemiluminescence by the H2O2-mediated oxidation of luminol. One system involves the fueled activation of a reaction module leading to the temporal formation and depletion of the bioreactor conjugate operating the nickase-guided transient biocatalytic cascades. The second system demonstrates the fueled activation of a reaction module yielding a bioreactor conjugate operating the exonuclease III-dictated transient operation of the two biocatalytic cascades. The temporal operations of the bioreactor circuits are accompanied by kinetic models and computational simulations enabling us to predict the dynamic behavior of the systems subjected to different auxiliary conditions.

Probing Near-infrared Absorbance of E and Z Diazene Isomers via Antiaromaticity

The photoswitching behaviors of heteroaryl azos and azobenzenes have attracted considerable interest due to their applications from material science to pharmacology. However, the use of UV light limits their application, especially in biomedicine and photopharmacology. In this work, using several aromaticity descriptors, including anisotropy of the induced current density analysis and nucleus-independent chemical shifts, we systematically investigate the relationship between anti-aromaticity and the absorption of a series of heterocyclic azos. We have demonstrated that the antiaromatic heterocycles substituted with diazenes enable the significant red shifts of the n → π* and π → π* transition bands of E and Z isomers via density functional theory calculations. Moreover, introducing substituents into heterocycles could further tune the absorption. Finally, the λmax of the first transition bands of the E (ca. 1026 nm) and Z isomers (ca. 1167 nm) of azos is achieved in the near-infrared region.

Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery

Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.

Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases

Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH-A base pair and a metal-mediated UOH-GdIII-UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH-A and UOH-GdIII-UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.

Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications

Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.

Cascaded, Feedback-Driven, and Spatially Localized Emergence of Constitutional Dynamic Networks Driven by Enzyme-Free Catalytic DNA Circuits

The enzyme-free catalytic hairpin assembly (CHA) process is introduced as a functional reaction module for guided, high-throughput, emergence, and evolution of constitutional dynamic networks, CDNs, from a set of nucleic acids. The process is applied to assemble networks of variable complexities, functionalities, and spatial confinement, and the systems provide possible mechanistic pathways for the evolution of dynamic networks under prebiotic conditions. Subjecting a set of four or six structurally engineered hairpins to a promoter P₁ leads to the CHA-guided emergence of a [2 × 2] CDN or the evolution of a [3 × 3] CDN, respectively. Reacting of a set of branched three-arm DNA-hairpin-functionalized junctions to the promoter strand activates the CHA-induced emergence of a three-dimensional (3D) CDN framework emulating native gene regulatory networks. In addition, activation of a two-layer CHA cascade circuit or a cross-catalytic CHA circuit and cascaded driving feedback-driven evolution of CDNs are demonstrated. Also, subjecting a four-hairpin-modified DNA tetrahedron nanostructure to an auxiliary promoter strand simulates the evolution of a dynamically equilibrated DNA tetrahedron-based CDN that undergoes secondary fueled dynamic reconfiguration. Finally, the effective permeation of DNA tetrahedron structures into cells is utilized to integrate the four-hairpin-functionalized tetrahedron reaction module into cells. The spatially localized miRNA-triggered CHA evolution and reconfiguration of CDNs allowed the logic-gated imaging of intracellular RNAs. Beyond the bioanalytical applications of the systems, the study introduces possible mechanistic pathways for the evolution of functional networks under prebiotic conditions.

Programming DNA Reaction Networks Using Allosteric DNA Hairpins

The construction of DNA reaction networks with complex functions using various methods has been an important research topic in recent years. Whether the DNA reaction network can perform complex tasks and be recycled directly affects the performance of the reaction network. Therefore, it is very important to design and implement a DNA reaction network capable of multiple tasks and reversible regulation. In this paper, the hairpin allosteric method was used to complete the assembly task of different functional nucleic acids. In addition, information conversion of the network was realized. In this network, multiple hairpins were assembled into nucleic acid structures with different functions to achieve different output information through the cyclic use of trigger strands. A method of single-input dual-output information conversion was proposed. Finally, the network with signal amplification and reversible regulation was constructed. In this study, the reversible regulation of different functional nucleic acids in the same network was realized, which shows the potential of this network in terms of programmability and provides new ideas for constructing complex and multifunctional DNA reaction networks.

Ratiometrically homogeneous electrochemical biosensor based on the signal amplified strategy of dual DNA nanomachines for microRNA analysis

Precise and sensitive microRNA (miRNA) analysis is very significant for early disease diagnosis. In this work, a dual DNA nanomachines-based homogeneous electrochemical biosensor was constructed for the sensitively ratiometric detection of miRNA by a nicking enzyme (Nt.AlwI)-assisted cycling signal amplification strategy. The Co-based metal organic frameworks (Co-MOFs) and toluidine blue (TB) were employed as signal probes and internal reference probes, respectively. The introduction of internal reference probes can actually calibrate the interferent factors of the analytical system to improve the stability in detection procedure. In addition, with the help of the magnetic separation technique, the homogeneous electrochemical biosensor provides a more simpler way for the development of immobilization-free electrochemical miRNA biosensors, avoiding the complex modification procedure of traditional electrochemical biosensing interfaces. Consequently, taking advantages of this proposed dual DNA nanomachines-based homogeneous electrochemical biosensor, the highly sensitive and selective detection of miRNA-141 as model could be accomplished in ranging from 1 fM to 10 nM with detection limit of 0.46 fM. This strategy exhited good sensitivity and stability to integrate the nicking enzyme-powered dual DNA nanomachines with the ratiometric electrochemical output modes, which open new opportunities for the sensitive and reliable diagnosis of miRNA-related diseases.

Controlling DNA nanodevices with light-switchable buffers

Control over synthetic DNA-based nanodevices can be achieved with a variety of physical and chemical stimuli. Actuation with light, however, is as advantageous as difficult to implement without modifying DNA strands with photo-switchable groups. Herein, we show that DNA nanodevices can be controlled using visible light in photo-switchable aqueous buffer solutions in a reversible and highly programmable fashion. The strategy presented here is non-invasive and allows the remote control with visible light of complex operations of DNA-based nanodevices such as the reversible release/loading of cargo molecules.

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.

Two-Dimensional Excitonic Networks Directed by DNA Templates as an Efficient Model Light-Harvesting and Energy Transfer System

Photosynthetic organisms organize discrete light-harvesting complexes into large-scale networks to facilitate efficient light collection and utilization. Inspired by nature, herein, synthetic DNA templates were used to direct the formation of dye aggregates with a cyanine dye, K21, into discrete branched photonic complexes, and two-dimensional (2D) excitonic networks. The DNA templates ranged from four-arm DNA tiles, ≈10 nm in each arm, to 2D wireframe DNA origami nanostructures with different geometries and varying dimensions up to 100×100 nm. These DNA-templated dye aggregates presented strongly coupled spectral features and delocalized exciton characteristics, enabling efficient photon collection and energy transfer. Compared to the discrete branched photonic systems templated on individual DNA tiles, the interconnected excitonic networks showed approximately a 2-fold increase in energy transfer efficiency. This bottom-up assembly strategy paves the way to create 2D excitonic systems with complex geometries and engineered energy pathways.

Excited-State-Selective Ultrafast Relaxation Dynamics and Photoisomerization of trans-4,4'-Azopyridine

Excited-state dynamics of trans-4,4'-azopyridine in ethanol is studied using femtosecond transient absorption with 30 fs temporal resolution. Exciting the system at three different wavelengths, 460 and 290 (275) nm, to access the S₁ nπ* and S₂ ππ* electronic states, respectively, reveals a 195 cm^-1 vibrational coherence, which suggests that the same mode is active in both nπ* and ππ* relaxation channels. Following S₁-excitation, relaxation proceeds via a nonrotational pathway, where a fraction of the nπ* population is trapped in a planar minimum (lifetime, 2.1 ps), while the remaining population travels further to a second shallow minimum (lifetime, 300 fs) prior to decay into the ground state. Population of the S₂ state leads to 30 fs nonrotational relaxation with a concurrent buildup of nπ* population and nearly simultaneous formation of hot ground-state species. An increase in the cis-isomer quantum yield upon ππ* versus nπ* excitation is observed, which is opposite to trans-azobenzene.

Molecular doping of nucleic acids into light emitting crystals driven by multisite-intermolecular interaction

We reveal the fundamental understanding of molecular doping of DNAs into organic semiconducting tris (8-hydroxyquinoline) aluminum (Alq₃) crystals by varying types and numbers of purines and pyrimidines constituting DNA. Electrostatic, hydrogen bonding, and π-π stacking interactions between Alq₃ and DNAs are the major factors affecting the molecular doping. Longer DNAs induce a higher degree of doping due to electrostatic interactions between phosphate backbone and Alq₃. Among four bases, single thymine bases induce the multisite interactions of π-π stacking and hydrogen bonding with single Alq₃, occurring within a probability of 4.37%. In contrast, single adenine bases form multisite interactions, within lower probability (1.93%), with two-neighboring Alq₃. These multisite interactions facilitate the molecular doping into Alq₃ particles compared to cytosines or guanines only forming π-π stacking. Thus, photoluminescence and optical waveguide phenomena of crystals were successfully tailored. This discovery should deepen our fundamental understanding of incorporating DNAs into organic semiconducting crystals.

Controllable DNA hybridization by host-guest complexation-mediated ligand invasion

Dynamic regulation of nucleic acid hybridization is fundamental for switchable nanostructures and controllable functionalities of nucleic acids in both material developments and biological regulations. In this work, we report a ligand-invasion pathway to regulate DNA hybridization based on host-guest interactions. We propose a concept of recognition handle as the ligand binding site to disrupt Watson-Crick base pairs and induce the direct dissociation of DNA duplex structures. Taking cucurbit[7]uril as the invading ligand and its guest molecules that are integrated into the nucleobase as recognition handles, we successfully achieve orthogonal and reversible manipulation of DNA duplex dissociation and recovery. Moreover, we further apply this approach of ligand-controlled nucleic acid hybridization for functional regulations of both the RNA-cleaving DNAzyme in test tubes and the antisense oligonucleotide in living cells. This ligand-invasion strategy establishes a general pathway toward dynamic control of nucleic acid structures and functionalities by supramolecular interactions.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

Light-responsive nanochannels based on the supramolecular host–guest system

The light-responsive nanochannel of rhodopsin gained wider research interest from its crucial roles in light-induced biological functions, such as visual signal transduction and energy conversion, though its poor stability and susceptibility to inactivation in vitro have limited its exploration. However, the fabrication of artificial nanochannels with the properties of physical stability, controllable structure, and easy functional modification becomes a biomimetic system to study the stimulus-responsive gating properties. Typically, light-responsive molecules of azobenzene (Azo), retinal, and spiropyran were introduced into nanochannels as photo-switches, which can change the inner surface wettability of nanochannels under the influence of light; this ultimately results in the photoresponsive nature of biomimetic nanochannels. Furthermore, the fine-tuning of their stimulus-responsive properties can be achieved through the introduction of host–guest systems generally combined with a non-covalent bond, and the assembling process is reversible. These host–guest systems have been introduced into the nanochannels to form different functions. Based on the host–guest system of light-responsive reversible interaction, it can not only change the internal surface properties of the nanochannel and control the recognition and transmission behaviors but also realize the controlled release of a specific host or guest molecules in the nanochannel. At present, macrocyclic host molecules have been introduced into nanochannels including pillararenes, cyclodextrin (CD), and metal–organic frameworks (MOFs). They are introduced into the nanochannel through chemical modification or host–guest assemble methods. Based on the changes in the light-responsive structure of azobenzene, spiropyran, retinal, and others with macrocycle host molecules, the surface charge and hydrophilic and hydrophobic properties of the nanochannel were changed to regulate the ionic and molecular transport. In this study, the development of photoresponsive host and guest-assembled nanochannel systems from design to application is reviewed, and the research prospects and problems of this photo-responsive nanochannel membrane are presented.

DNA-POINT: DNA Patterning of Optical Imprint for Nanomaterials Topography

Engineering well-defined scale-spanning structures through transfer of diverse biomolecules and materials to a surface is of tremendous interest in life sciences research yet remains profoundly challenging. Here, we report a novel method, termed as DNA patterning of optical imprint for nanomaterials topography (DNA-POINT), for rapid photopatterning of large area, geometrically complex surfaces via light-responsive DNA. Our method employs top-down multiphoton-driven patterning of azobenzene-modified DNA strands, offering precise position control of molecules and nanoparticles along the axial plane and a template for bottom-up self-assembly of multiple layers of different chemical composition along the vertical plane. We demonstrate the surface patterning of plasmonic gold nanoparticles, fluorophore-labeled oligonucleotides, and multiple layers consisting of molecule-nanoparticle hybrid patterns into preconceived shapes without compromising on the functionality of the biomolecules. Furthermore, we exhibit scanning mode operation of DNA-POINT, thereby paving the way for maskless and cleanroom-free fast fabrication of biochips for high-throughput diagnostics and biosensing applications.

Linear and Nonlinear Optical Properties of Azobenzene Derivatives Modified with an (Amino)naphthalene Moiety

The design of two-photon absorbing azobenzene (AB) derivatives has received much attention; however, the two-photon absorption (2PA) properties of bis-conjugated azobenzene systems are relatively less explored. Here, we present the synthesis of six azobenzene derivatives and three bis-azobenzenes substituted (or not) at para position(s) with one or two amino group(s). Their linear and nonlinear absorption properties are studied experimentally and theoretically. The switching behavior and thermal stability of the Z-isomer are studied for unsubstituted mono- (1a, 2a) and bis-azobenzene (3a) compounds, showing that when the length of the π system increases, the half-life of the Z-isomer decreases. Moreover, along with the increase of π-conjugation, the photochromic characteristics are impaired and the photostationary state (PSS) related to E-Z photoisomerization is composed of 89% of the Z-isomer for 2a and 26% of the Z-isomer for 3a. Importantly, the 2PA cross-section increases almost five-fold on extending the π-conjugation (2a vs 3a) and by about one order of magnitude when comparing two systems: the unsubstituted π-electron one (2a, 3a) with D-π-D (2c, 3c). This work clarifies the contribution of π-conjugation and substituent effects to the linear and nonlinear optical properties of mono- and bis-azobenzene compounds based on the experimental and theoretical approaches.

Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models

Dynamic, transient, out-of-equilibrium networks guide cellular genetic, metabolic or signaling processes. Designing synthetic networks emulating natural processes imposes important challenges including the ordered connectivity of transient reaction modules, engineering of the appropriate balance between production and depletion of reaction constituents, and coupling of the reaction modules with emerging chemical functions dictated by the networks. Here we introduce the assembly of three coupled reaction modules executing a cascaded dynamic process leading to the transient formation and depletion of three different Mg²⁺-ion-dependent DNAzymes. The transient operation of the DNAzyme in one layer triggers the dynamic activation of the DNAzyme in the subsequent layer, leading to a three-layer transient catalytic cascade. The kinetics of the transient cascade is computationally simulated. The cascaded network is coupled to a polymerization/nicking DNA machinery guiding transient synthesis of three coded strands acting as “gene models”, and to the rolling circle polymerization machinery leading to the transient synthesis of fluorescent Zn(II)-PPIX/G-quadruplex chains or hemin/G-quadruplex catalytic wires.

A reaction network executing a cascaded transient formation and depletion of three different catalytic strands is introduced. The system is coupled to the secondary temporal synthesis of different coded strands as gene models.

Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides

Labelling of oligonucleotides with dyes, targeting ligands, and other moieties has become ever more essential in life-sciences. Conventionally, modifications are introduced to oligonucleotides during solid phase synthesis by special phosphoramidites functionalised with a chemical handle or the desired functional group. In this work, we present a facile and inexpensive method to introduce modifications to oligonucleotides without the need for special phosphoramidites. Sulfonyl azides are applied to react with one or more selected phosphite intermediates during solid phase synthesis. We have prepared 11 sulfonyl azides with different chemical handles such as amine, azide, alkyne, and thiol, and we have further introduced functionalities such as pyrene, other dyes, photo-switchable azobenzenes, and a steroid. The method is compatible with current phosphoramidite-based automated oligonucleotide synthesis and serves as a simple alternative to the unstable and expensive special phosphoramidites currently used for conjugation to oligonucleotides.

Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids

The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.

Lipid bilayer-assisted dynamic self-assembly of hexagonal DNA origami blocks into monolayer crystalline structures with designed geometries

The DNA origami technique is used to construct custom-shaped nanostructures that can be used as components of two-dimensional crystalline structures with user-defined structural patterns. Here, we designed an Mg²⁺-responsive hexagonal 3D DNA origami block with self-shape-complementary ruggedness on the sides. Hexagonal DNA origami blocks were electrostatically adsorbed onto a fluidic lipid bilayer membrane surface to ensure lateral diffusion. A subsequent increase in the Mg²⁺ concentration in the surrounding environment induced the self-assembly of the origami blocks into lattices with prescribed geometries based on a self-complementary shape fit. High-speed atomic force microscopy (HS-AFM) images revealed dynamic events involved in the self-assembly process, including edge reorganization, defect splitting, diffusion, and filling, which provide a glimpse into how the lattice structures are self-improved.

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Lipid bilayer-assisted self-assembly of 3D DNA origami blocks was achieved

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Time-lapse AFM imaging of the self-assembly processes was performed

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Different assembly patterns were achieved from a single DNA origami design

DNA Hairpins and Dumbbell-Wheel Transitions Amplified Walking Nanomachine for Ultrasensitive Nucleic Acid Detection

Nucleic acids, including circulating tumor DNA (ctDNA), microRNA, and virus DNA/RNA, have been widely applied as potential disease biomarkers for early clinical diagnosis. In this study, we present a concept of DNA nanostructures transitions for the construction of DNA bipedal walking nanomachine, which integrates dual signal amplification for direct nucleic acid assay. DNA hairpins transition is developed to facilitate the generation of multiple target sequences; meanwhile, the subsequent DNA dumbbell-wheel transition is controlled to achieve the bipedal walker, which cleaves multiple tracks around electrode surface. Through combination of strand displacement reaction and digestion cycles, DNA monolayer at the electrode interface could be engineered and target-induced signal variation is realized. In addition, pH-assisted detachable intermolecular DNA triplex design is utilized for the regeneration of electrochemical biosensor. The high consistency between this work and standard quantitative polymerase chain reaction is validated. Moreover, the feasibilities of this biosensor to detect ctDNA and SARS-CoV-2 RNA in clinical samples are demonstrated with satisfactory accuracy and reliability. Therefore, the proposed approach has great potential applications for nucleic acid based clinical diagnostics.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.

Capsule-like DNA Hydrogels with Patterns Formed by Lateral Phase Separation of DNA Nanostructures

Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems.

Multipurpose made colorimetric materials for amines, pH change and metal ion detection

Sensors are routinely developed for specific applications, but multipurpose sensors are challenging, due to stability and poor functional design. We report organic materials that operate in solution and gas phase. They show a strong response behaviour to at least three types of environmental changes: pH, amine and metal ion binding/detection. We have confirmed and validated our findings using various analytical and computational methods. We found that the changes in polarity of the solvent and pH not only red shift the tail of the absorption spectra, but also extend the peak optical absorption of these structures by up to 100 nm, with consequential effects on the optical gap and colour changes of the materials. Acid–base response has been studied by spectrophotometric titrations with trifluoroacetic acid (TFA) and triethyl amine (TEA). The experiments show excellent reversibility with greater sensitivity to base than acid for all compounds. Analysis into metal sensing using Zn(ii) and Cu(ii) ions as analytes show that the materials can successfully bind the cations forming stable complexes. Moreover, a strong suppression of signal with copper gives an operative modality to detect the copper ion as low as 2.5 × 10⁻⁶ M. The formation of the metal complexes was also confirmed by growing crystals using a slow diffusion method; subsequent single crystal X-ray analysis reveals the ratio of ligand to metal to be 2 to 1. To test sensitivity towards various amine vapours, paper-based sensors have been fabricated. The sensors show a detection capability at 1 ppm of amine concentration. We have employed CIE L*a*b* colour space as the evaluation method, this provides numeric comparison of the samples from different series and allows comparison of small colour differences, which are generally undetectable by the human-eye. It shows that the CIE L*a*b* method can assess both sensitivity to a particular class of analytes and a specificity response to individual amines in this subclass offering an inexpensive and versatile methodology.

Multi-responsive colorimetric sensors based on the hydrazone motif, which are perfectly suited for chemo sensing applications have been developed.

Recent advances in constructing high-order DNA structures

Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.

Photoresponsive DNA materials and their applications

Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.

Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties

DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...

Aggregation-Induced Emission Luminogens with Photoresponsive Behaviors for Biomedical Applications

Fluorescent biomedical materials can visualize subcellular structures and therapy processes in vivo. The aggregation-induced emission (AIE) phenomenon helps suppress the quenching effect in the aggregated state suffered by conventional fluorescent materials, thereby contributing to design strategies for fluorescent biomedical materials. Photoresponsive biomedical materials have attracted attention because of the inherent advantages of light; i.e., remote control, high spatial and temporal resolution, and environmentally friendly characteristics, and their combination with AIE facilitates development of fluorescent molecules with efficient photochemical reactions upon light irradiation. In this review, organic compounds with AIE features for biomedical applications and design strategies for photoresponsive AIE luminogens (AIEgens) are first summarized briefly. Applications are then reviewed, with the employment of photoresponsive and AIE-active molecules for photoactivation imaging, super-resolution imaging, light-induced drug delivery, photodynamic therapy with photochromic behavior, and bacterial targeting and killing being discussed at length. Finally, the future outlook for AIEgens is considered with the aim of stimulating innovative work for further development of this field.

Aggregation-induced emission (AIE)-guided dynamic assembly for disease imaging and therapy

The phenomenon of aggregation-induced emission (AIE) is inseparable from molecular aggregation and self-assembly. Therefore, the combination of AIE and supramolecular self-assembly is well-matched. AIE-guided dynamic assembly (AGDA) could effectively respond to the endogenous stimuli (such as pH, enzymes, redox molecules) and exogenous stimuli (temperature, light, ultrasound) in the disease microenvironment, so as to achieve specific imaging and diagnosis of the disease lesions. Moreover, AGDA also dynamically adjust the intramolecular motions of AIE molecules, thereby adjusting the energy dissipation pathways and realizing the switch between photodynamic therapy and photothermal therapy for superior therapeutic effects. In this review, we aim to give an overview of the constructing strategies, stimuli-responsive imaging, regulation of intramolecular motion of AGDA in recent years, which is expected to grasp the research status and striving directions of AGDA for imaging and therapy.

Synthesis and Functionality Study of Photoswitchable Hydrazone Oligodeoxynucleotides

This article provides a detailed procedure for the chemical synthesis and characterization of photoswitchable hydrazone phosphoramidite and its incorporation into oligodeoxynucleotides. The synthesis starts with commercially available deoxyuridine, followed by conversion of the 4-oxo into a 4-chloro moiety via Appel reaction to install the key hydrazone group in the absence of base. The hydrazone phosphoramidite building block is compatible with the conventional amidite chemistry protocols for solid-phase synthesis of oligodeoxynucleotides. Our method expands the current nucleotide pool by adding a novel, functional DNA building block that is suitable for a broad spectrum of applications, including the regulation of DNA-enzyme interactions and DNA synthesis by irradiation with cell-friendly blue light. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of photoswitchable hydrazone phosphoramidite Basic Protocol 2: Synthesis and purification of oligodeoxynucleotides containing the hydrazone photoswitch Basic Protocol 3: Primer extension assay for functionality studies of hydrazone cytidine.

Photoinduced azobenzene-modified DNA dehybridization: insights into local and cooperativity effects from a molecular dynamics study

Photoresponsive azobenzene-modified DNA (RNA) has become a very fruitful material for nanotechnology due to the capability of switching on and off hybridization (i.e., duplex formation) in smart nanostructures. This nanomaterial exploits the well-known azobenzene trans/cis photo-isomerization. In fact, it has been found that DNA tethered with trans-azobenzene shows normal nucleic acid recognition and hybridization, while the cis form destabilizes the duplex configuration, eventually leading to DNA unzipping. However, while the working principle of the light-triggered DNA dehybridization is apparent, specific details of this mechanism still remain elusive to experiments. Previous in silico studies successfully addressed some aspects (e.g., local structural effects, thermal stability, and early events of azobenzene photoisomerization) of this challenging molecular process characterized by timescales spanning several orders of magnitude, from picoseconds (i.e., azobenzene photoisomerization) to micro- and milli-seconds (i.e., complete strand detachment). In this work, inspired by a recent report by Asanuma and coworkers, we focus on the local and cooperativity effects played by multiple azobenzene units on a 10-mer azobenzene-modified DNA duplex. Using molecular dynamics (MD) simulations, we investigated nine systems equipped with a variable number (from 1 to 7) of photoswitch units and different configurations, focusing our analysis on the initial events (from few ps to hundreds of ns) characterizing DNA destabilization upon trans-to-cis isomerization, such as hydrogen bonding breakage and base pair misalignment. Results highlight, on one hand, the local effects of single azobenzene units on DNA duplex structure and, on the other hand, the cooperative role that multiple photoswitches show in enhancing and accelerating DNA dehybridization following trans-to-cis conversion, in agreement with previously reported data and observations.

Photoresponsive Control of G-Quadruplex DNA Systems

G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.

Photo-Controllable Phase Transition of Arylazopyrazole-Conjugated Oligonucleotides

Phase transition is a promising aspect of DNA as biopolymers. Anionic DNA oligonucleotides easily form complexes with cationic polypeptides such as polylysine, and duplex formation significantly influences their complexation and resulting microcompartments. In this study, phase transition of microcompartments containing DNA and polylysine was systematically induced by modulating duplex formation of arylazopyrazole-conjugated oligonucleotides with light. We demonstrated that UV irradiation destabilized DNA duplex and generated isotropic coacervates, while duplex stabilization by visible light irradiation caused the formation of liquid crystalline coacervates. This photocontrol of phase transition was highly repeatable, and similar changes were observed even after ten cycles of light irradiation. Our approach would provide a robust control layer to the development of tailor-made microcompartments.

Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy

RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.