Programmed dissociation of dimer and trimer origami structures by aptamer-ligand complexes

Cyclic transitions of DNA origami dimers driven by thermal cycling

It is widely observed that life activities are regulated through conformational transitions of biological macromolecules, which inspires the construction of environmental responsive nanomachines in recent years. Here we present a thermal responsive DNA origami dimers system, whose conformations can be cyclically switched by thermal cycling. In our strategy, origami dimers are assembled at high temperatures and disassembled at low temperatures, which is different from the conventional strategy of breaking nanostructures using high temperatures. The advantage of this strategy is that the dimers system can be repeatedly operated without significant performance degradation, compared to traditional strategies such as conformational transitions via i-motif and G-quadruplexes, whose performance degrades with sample dilution due to repeated addition of trigger solutions. The cyclic conformational transitions of the dimers system are verified by fluorescence curves and AFM images. This research offered a new way to construct cyclic transformational nanodevices, such as reusable nanomedicine delivery systems or nanorobots with long service lifetimes.

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.

DNA Kirigami Driven by Polymerase-Triggered Strand Displacement

The precursors of functional biomolecules in living cells are synthesized in a bottom-up manner and subsequently activated by modification into a delicate structure with near-atomic precision. DNA origami technology provides a promising way to mimic the synthesis of precursors, although mimicking the modification process is a challenge. Herein, a DNA paper-cutting (DNA kirigami) method to trim origami into designer nanostructures is proposed, where the modification is implemented by a polymerase-triggered DNA strand displacement reaction. Six geometric shapes are created by cutting rectangular DNA origami. Gel electrophoresis and atomic force microscopy results demonstrate the feasibility and capability of the DNA paper-cutting method. The proposed DNA paper-cutting strategy can enrich the toolbox for dynamically transforming DNA origami and has potential applications in biomimetics. .

Self-assembled DNA origami-based duplexed aptasensors combined with centrifugal filters for efficient and rechargeable ATP detection

DNA origami technology has great potential for biosensor applications. Here, we described the construction of a self-assembled DNA origami biosensor for the precise localization of fluorescent aptamers. Due to the molecular weight difference between DNA origami and aptamer, centrifugal filters were used to quantitatively detect adenosine triphosphate (ATP). The ATP-specific aptamer labeled with fluorescence reporter 6-carboxyfluorescein FAM (FAM-aptamer) was selected as the recognition element and signal probe. ATP duplexed aptamers bound to triangular DNA origami by base-complementary pairing, resulting in high fluorescence signals on the origami arrays. The competitive binding of ATP toward the FAM-aptamer triggered the release of FAM-aptamer-ATP complexes from the surface of the origami array, resulting in weakened fluorescence signals. For ATP quantification, 100 kD centrifugal filters were employed, followed by measurement of the fluorescence signal trapped on the origami arrays of the filter device. The successful synthesis of origami-aptamer arrays was characterized by atomic force microscopy, laser confocal microscopy, and electrophoresis. Fluorescence measurements exhibited an excellent linear relationship with logarithms of ATP concentrations within 0.1-100 ng mL^-1, with a detection limit of 0.29 ng mL^-1. By replacing aptamers and complementary strands, we demonstrated the potential of this method for 17β-estradiol detection. Considering that the detection mechanism is based on the hybridization and displacement of DNA strands, the detection system had the potential for recharging. Our study provides new insights into applying DNA origami technology in small molecule detection.

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.

Disassembly of DNA origami dimers controlled by programmable polymerase primers

The disassembly of DNA origami dimers with programmable primers, driven by polymerase-triggered strand displacement.

A novel strategy for programmable DNA tile self-assembly with a DNAzyme-mediated DNA cross circuit

The proposed strategy promotes the controllability and modularization of trigger elements, realizes programmable molecular self-assembly, and has broad applications for the construction of DNA nanodevices.

Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

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.

Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems

Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.

Incorporation of a metal-mediated base pair into an ATP aptamer - using silver(I) ions to modulate aptamer function

For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials

Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.

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

All-DNA scaffolds act as templates for the organization of photosystem I model systems. A series of DNA templates composed of Zn^II -protoporphyrin IX (Zn^II PPIX)-functionalized G-quadruplex conjugated to the 3'- or 5'-end of the tyrosinamide (TA) aptamer and Zn^II PPIX/G-quadruplex linked to the 3'- and 5'-ends of the TA aptamer through a four-thymidine bridge. Effective photoinduced electron transfer (ET) from Zn^II PPIX/G-quadruplex to bipyridinium-functionalized tyrosinamide, TA-MV²⁺ , bound to the TA aptamer units is demonstrated. The effectiveness of the primary ET quenching of Zn^II PPIX/G-quadruplex by TA-MV²⁺ controls the efficiency of the generation of TA-MV^+. . The photosystem-controlled formation of TA-MV^+. by the different photosystems dictates the secondary activation of the ET cascade corresponding to the ferredoxin-NADP⁺ reductase (FNR)-catalysed reduction of NADP⁺ to NADPH by TA-MV^+. , and the sequestered alcohol dehydrogenase catalysed reduction of acetophenone to 1-phenylethanol by NADPH.

Aptamer-Functionalized DNA Nanostructures for Biological Applications

DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.

Nucleoapzymes: catalyst-aptamer conjugates as enzyme-mimicking structures

The conjugation of catalytic sites to sequence-specific, ligand-binding nucleic acid aptamers yields functional catalytic ensembles mimicking the catalytic/binding properties of native enzymes. These catalyst-aptamer conjugates termed 'nucleoapzymes' reveal structural diversity, and thus, vary in their catalytic activity, due to the different modes of conjugation of the catalytic units to the nucleic acid aptamer scaffold. The concept of nucleoapzymes is introduced with the assembly of a set of catalysts consisting of the hemin/G-quadruplex DNAzyme (hGQ) conjugated to the dopamine aptamer. The nucleoapzymes catalyze the oxidation of dopamine by H2O2 to yield aminochrome. The catalytic processes are controlled by the structures of the nucleoapzymes, and chiroselective oxidation of l-DOPA and d-DOPA by the nucleoapzymes is demonstrated. In addition, the conjugation of a Fe(III)-terpyridine complex to the dopamine aptamer and of a bis-Zn(II)-pyridyl-salen-type complex to the ATP-aptamer yields hybrid nucleoapzymes (conjugates where the catalytic site is not a biomolecule) that catalyze the oxidation of dopamine to aminochrome by H2O2 and the hydrolysis of ATP to ADP, respectively. Variable, structure-controlled catalytic activities of the different nucleoapzymes are demonstrated. Molecular dynamic simulations are applied to rationalize the structure-catalytic function relationships of the different nucleoapzymes. The challenges and perspectives of the research field are discussed.

Active generation of nanoholes in DNA origami scaffolds for programmed catalysis in nanocavities

DNA origami tiles provide nanostructures for the spatial and temporal control of functional loads on the scaffolds. Here we introduce the active generation of nanoholes in the origami scaffolds using DNAzymes or light as triggers and present the programmed and switchable catalysis in the resulting nanocavities. We engineer “window” domains locked into the origami scaffolds by substrates of the Zn²⁺-ion- or Pb²⁺-ion-dependent DNAzymes. Using Zn²⁺ ions and/or Pb²⁺ ions, the programmed unlocking of the “window” domains is demonstrated. The tailored functionalization of the origami scaffolds allows the programmed operation of catalytic processes in the confined nanocavities. Also, the “window” domain is integrated into the origami scaffold using photoisomerizable azobenzene-modified locks. The cyclic photoisomerization of the locks between the cis and trans states leads to a reversible opening and closure of the nanoholes and to the cyclic light-induced switching of catalytic processes in the nanocavities.

DNA origami provide scaffolds for spatial and temporal control of catalytic functions in confined nanocavities. Here the authors engineer nanoholes in DNA origami scaffolds.

Control of the stepwise assembly-disassembly of DNA origami nanoclusters by pH stimuli-responsive DNA triplexes

We present the pH-triggered reversible assembly of DNA origami clusters in a stepwise fashion. The structure formation and dissociation are controlled by a series of consecutive pH-stimulation processes that rely on the triplex-to-duplex transition of DNA triplexes in different pH conditions. This multilevel dynamic assembly strategy brings more structural complexity and provides the possibility of developing intelligent materials for engineering applications.

Artificial Photosynthesis with Electron Acceptor/Photosensitizer-Aptamer Conjugates

Sequence-specific aptamers act as functional scaffolds for the assembly of photosynthetic model systems. The Ru(II)-tris-bipyridine photosensitizer is conjugated by different binding modes to the antityrosinamide aptamer to yield a set of photosensitizer-aptamer binding scaffolds. The N-methyl-N'-(3-aminopropane)-4,4'-bipyridinium electron acceptor, MV²⁺, is covalently linked to tyrosinamide, TA, to yield the conjugate TA-MV²⁺. The tyrosinamide unit in TA-MV²⁺ acts as a ligand for anchoring TA-MV²⁺ to the Ru(II)-tris-bipyridine-aptamer scaffold, generating the diversity of photosensitizer-aptamer/electron acceptor supramolecular conjugates. Effective electron transfer quenching in the photosynthetic model systems is demonstrated, and the quenching efficiencies are controlled by the structural features of the conjugates. The redox species generated by the photosensitizer-aptamer/electron acceptor supramolecular systems mediate the ferredoxin-NADP⁺ reductase, FNR, catalyzed synthesis of NADPH, and the Pt-nanoparticle-catalyzed evolution of hydrogen (H₂). The novelty of the study rests on the unprecedented use of aptamer scaffolds as functional units for organizing photosynthetic model systems.

Triggering nucleic acid nanostructure assembly by conditional kissing interactions

Nucleic acids are biomolecules of amazing versatility. Beyond their function for information storage they can be used for building nano-objects. We took advantage of loop–loop or kissing interactions between hairpin building blocks displaying complementary loops for driving the assembly of nucleic acid nano-architectures. It is of interest to make the interaction between elementary units dependent on an external trigger, thus allowing the control of the scaffold formation. To this end we exploited the binding properties of structure-switching aptamers (aptaswitch). Aptaswitches are stem–loop structured oligonucleotides that engage a kissing complex with an RNA hairpin in response to ligand-induced aptaswitch folding. We demonstrated the potential of this approach by conditionally assembling oligonucleotide nanorods in response to the addition of adenosine.

Triggered Reversible Reconfiguration of G-Quadruplex-Bridged "Domino"-Type Origami Dimers: Application of the Systems for Programmed Catalysis

The reversible and switchable reconfiguration of the two-origami-dimer mixture AB plus CD into the dimer mixture DA plus BC and back using the triggered formation of K⁺-ion-stabilized G-quadruplexes and subsequent treatment with 18-crown-6-ether is presented. The reconfiguration processes are followed by atomic force microscopy imaging of the dimer structures that include tiles marked with 0, 1, 2, and 3 4× hairpin labels. By the functionalization of AB and CD dimers with the Mg²⁺-ion-dependent DNAzyme subunits, the AB plus CD mixture leads to the cleavage of the fluorophore- and quencher-modified substrate of the DNAzyme and to the activation of the fluorescence of the fluorophore (fluorescein)-modified fragment product. The K⁺-ion-induced isomerization of the mixture of AB plus CD into the mixture DA plus BC separates the Mg²⁺-ion-dependent DNAzyme subunits and concomitantly reconfigures the K⁺-ion-stabilized G-quadruplex associated with the two dimers. After the binding of hemin to the G-quadruplexes, the hemin/G-quadruplex DNAzyme is generated, leading to the catalyzed oxidation of Amplex Red by H₂O₂ to yield the fluorescent resorufin product. By the cyclic treatment of the AB plus CD mixture with K⁺ ions to yield the DA plus BC mixture and the subsequent recovery of the AB plus CD mixture by subjecting the DA plus BC mixture to 18-crown-6-ether, the fluorescence output signals of the system are switched on and off between the fluorescence of fluorescein and resorufin, respectively.

Functional and Biomimetic DNA Nanostructures on Lipid Membranes

Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by  external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.

DNA-Responsive SiO2 Nanoparticles, Metal-Organic Frameworks, and Microcapsules for Controlled Drug Release

Recent advances addressing the development of stimuli-responsive nucleic acid (DNA)-functionalized micro/nanocarriers for the controlled release of drugs are presented. The DNA associated with the drug-loaded carriers acts as capping units that lock the drugs in the carriers. In the presence of appropriate triggers, the capping units are unlocked, resulting in the release of the drugs. Three types of DNA-modified carriers are discussed, including mesoporous SiO₂ nanoparticles (MP SiO₂ NPs), metal-organic framework nanoparticles (NMOFs) and micro/nanocapsules. The triggers to unlock the DNA gating units include pH, the dissociation of K⁺-stabilized G-quadruplexes in the presence of crown ethers, the catalytic dissociation of the capping units by enzymes or DNAzymes, the dissociation of capping units by the formation of aptamer-ligand complexes (particularly ligands acting as biomarkers for different diseases), and the use of light for the photochemical unlocking of the DNA gates. Different issues related to the targeting of the different drug-loaded carriers to cancer cells, the switchable ON/OFF release of the drug loads, and the selective cytotoxicity of the drug-loaded carriers toward cancer cells are discussed. Finally, the future perspectives of the stimuli-responsive DNA-based, drug-loaded micro/nanocarriers for future nanomedicine and, in particular, the development of autonomous sense-and-treat systems are addressed.

DNA Aptamers for the Functionalisation of DNA Origami Nanostructures

DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed.

Metal-ion responsive reversible assembly of DNA origami dimers: G-quadruplex induced intermolecular interaction

We present a novel metal-ion stimulated organization of DNA origami nanostructures by employing G-quadruplexes as stimuli-responsive bridges. The reversible assembly process of DNA origami was the result of conformational changes between the G-quadruplex and its single-strand state induced by monovalent cations. This study might stimulate a new design of responsive DNA-based intelligent nanomaterials.

An aptamer-enabled DNA nanobox for protein sensing

DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. While DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase. The protein acts as the key which enables box opening. We observe highly specific protein-mediated box opening by both transmission electron microscopy and fluorescence. Aptamer-enabled DNA boxes have significant potential for enabling direct responses to proteins and other biomolecules in nanoscale diagnostics, drug delivery and sensing devices.