Modelling Photosynthesis with ZnII -Protoporphyrin All-DNA G-Quadruplex/Aptamer Scaffolds

Photodynamic Therapy Synergizes CD47 Blockade Strategy for Enhanced Antitumor Therapy

The antitumor strategies based on innate immunity activation have become favored by researchers in recent years. In particular, strategies targeting antiphagocytic signaling blockade to enhance phagocytosis have been widely reported. For example, the addition of prophagocytic signals such as calreticulin could make the strategy significantly more effective. In this study, an antitumor strategy that combines photodynamic therapy (PDT) with CD47 blockade has been reported. This approach promotes the maturation of dendritic cells and the presentation of tumor antigens by PDT-mediated tumor immunogenic cell death, as well as the enhancement of cytotoxic T lymphocyte infiltration in tumor areas and the phagocytic activity of phagocytes. Furthermore, the downregulation and blockage of CD47 protein could further promote phagocytic activity, strengthen the innate immune system, and ultimately elevate the antitumor efficacy and inhibit tumor metastasis.

Amplification of an Electrochemiluminescence-Emissive Aptamer into DNA Nanotags for Sensitive Fecal Calprotectin Determination

The precision additive manufacturing and tessellated multitasking out of the structural DNA nanotechnology enable a configurable expression of densified electrochemiluminescent (ECL) complexes, which would streamline the bioconjugation while multiplying signals. Herein, a completely DNA-scaffold ECL "polyploid" was replicated out via the living course of rolling circle amplification. The amplicon carried the aptameric sequences of ZnPPIX/TSPP porphyrin as photoreactive centers that rallied at periodical intervals of the persistent extension into a close-packed nanoflower, ZnPDFI/II. Both microscopies and electrophoresis proved the robust nesting of guests at their deployed gene loci, while multispectral comparisons among cofactor substituents pinpointed the pivotal roles of singlet seclusion and Zn2+-chelation for the sake of intensive ECL irradiation. The adversity-resilient hydrogel texture made lipoidal filmogens as porphyrinic ECL prerequisites to be of no need at all, thus not only simplifying assay flows but also inspiring an in situ labeling plan. Upon bioprocessing optimization, an enriched probe ZnPDFIII was further derived that interpolated the binding motif related to calprotectin as validated by molecular docking and affinity titration. With it being a strongly indicative marker of inflammatory bowel disease (IBD), a competitive ECL aptasensing strategy was contrived, managing a signal-on and sensitive detection in mild conditions with a subnanogram-per-milliliter limit of detection by 2 orders of magnitude lower than the standard method as well as a comparable accuracy in clinical stool sample testing. Distinct from those conventional chemophysical rebuilding routes, this de novo biosynthetic fusion demonstrated a promising alternative toward ECL-source bioengineering, which may intrigue vibrant explorations of other ECL-shedding fabrics and, accordingly, a new bioanalytic mode downstream.

Photo- and Redox-Regulated Transmembrane Ion Transporters

Synthetic supramolecular ion transporters find applications as potential therapeutics and as tools for engineering functional membranes. Stimuli-responsive systems enable external control over transport, which is necessary for targeted activation. The Minireview provides an overview of current approaches to developing stimuli-responsive ion transport systems, including channels and mobile carriers, that can be controlled using photo or redox inputs.

Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription

Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.

Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes

A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.

Switchable and dynamic G-quadruplexes and their applications

G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO₂ nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.

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.

Fabrication of bifunctional G-quadruplex-hemin DNAzymes for colorimetric detection of apurinic/apyrimidinic endonuclease 1 and microRNA-21

G-quadruplex-based complexes have been widely used in various analytical methods due to their outstanding capabilities of generating colorimetric, fluorescent or electrochemical signals. However, since loop sequences in traditional G-quadruplex structures are quite short, it is difficult to establish biosensors solely using G-quadruplex-based complexes. Herein, we attempted to lengthen the loop sequences of G-quadruplex structures and found that G-quadruplex-hemin DNAzymes (G-DNAzymes) with long loops (even 30 nucleotides) maintain high peroxidase activity. In addition, the peroxidase activity is not affected by the hybridization of the long loop with its complementary counterpart. Consequently, G-DNAzyme can be endowed with an additional function by taking the long loop as a recognition element, which may facilitate the construction of diverse colorimetric biosensors. Furthermore, by designing an apurinic/apyrimidinic site or a complementary sequence of microRNA-21 (miRNA-21) in long loops, bifunctional G-DNAzymes can be split in the presence of apurinic/apyrimidinic endonuclease 1 (APE1) or miRNA-21, decreasing their peroxidase activities. Accordingly, APE1 and miRNA-21 are quantified using 3,3',5,5'-tetramethylbenzidine as a chromophore. Using the G-DNAzyme, APE1 can be detected in a linear range from 2.5 to 22.5 U mL^-1 with a LOD of 1.8 U mL^-1. It is to be noted that benefitting from duplex-specific nuclease-induced signal amplification, the linear range of the miRNA-21 biosensor is broadened to 5 orders of magnitude, while the limit of detection is as low as 73 fM. This work demonstrates that G-DNAzymes with long loops can both generate signals and recognize targets, providing an alternative strategy to design G-quadruplex-based analytical methods.

Bioinspired Artificial Photosynthetic Systems

Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.

An ion transport switch based on light-responsive conformation-dependent G-quadruplex transmembrane channels

A light-responsive ion transport switch has been developed based on conformation-dependent azobenzene-incorporated lipophilic G-quadruplex channels, which provides a new smart approach for the selective transport of K⁺ ions across the lipid membrane.

Mimicking Functions of Native Enzymes or Photosynthetic Reaction Centers by Nucleoapzymes and Photonucleoapzymes

The covalent linkage of catalytic units to aptamer sequence-specific nucleic acids exhibiting selective binding affinities for substrates leads to functional scaffolds mimicking native enzymes, nucleoapzymes. The binding of the substrates to the aptamer and their structural orientation with respect to the catalytic units duplicate the functions of the active center of enzymes. The possibility of linking the catalytic sites directly, or through spacer units, to the 5'-end, 3'-end, and middle positions of the aptamers allows the design of nucleoapzyme libraries, revealing structure-functions diversities, and these can be modeled by molecular dynamics simulations. Catalytic sites integrated into nucleoapzymes include DNAzymes, transition metal complexes, and organic ligands. Catalytic transformations driven by nucleoapzymes are exemplified by the oxidation of dopamine or l-arginine, hydroxylation of tyrosine to l-DOPA, hydrolysis of ATP, and cholic acid-modified esters. The covalent linkage of photosensitizers to the tyrosinamide aptamer leads to a photonucleoapzyme scaffold that binds the N-methyl-N'-(3-aminopropane)-4,4'-bipyridinium-functionalized tyrosinamide to the aptamer. By linking the photosensitizer directly, or through a spacer bridge to the 5'-end or 3'-end of the aptamer, we demonstrate a library of supramolecular photosensitizer/electron acceptor photonucleoapzymes mimicking the functions of photosystem I in the photosynthetic apparatus. The photonucleoapzymes catalyze the photoinduced generation of NADPH, in the presence of ferredoxin-NADP+-reductase (FNR), or the photoinduced H2 evolution catalyzed by Pt nanoparticles. The future prospects of nucleoapzymes and photonucleoapzymes are discussed.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.