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With the advent of fluorescence superresolution microscopy, nano-sized structures can be imaged with a previously unprecedented accuracy. Therefore, it is rapidly gaining importance as an analytical tool in the life sciences and beyond. However, the images obtained so far lack an absolute scale in terms of fluorophore numbers. Here, we use, for the first time, a detailed statistical model of the temporal imaging process which relies on a hidden Markov model operating on two timescales. This allows us to extract this information from the raw data without additional calibration measurements. We show this on the basis of added data from experiments on single Alexa 647 molecules as well as GSDIM/dSTORM measurements on DNA origami structures with a known number of labeling positions. [ABSTRACT FROM AUTHOR]

The chemically synthesizable quantum emitters such as quantum dots (QDs), fluorescent nanodiamonds (FNDs), and organic fluorescent dyes can be integrated with an easy-to-craft quantum nanophotonic device, which would be readily developed by non-lithographic solution process. As a representative example, the solution dipping or casting of such soft quantum emitters on a flat metal layer and subsequent drop-casting of plasmonic nanoparticles can afford the quantum emitter-coupled plasmonic nanocavity (referred to as a nanoparticle-on-mirror (NPoM) cavity), allowing us for exploiting various quantum mechanical behaviors of light–matter interactions such as quantum electrodynamics (QED), strong coupling (e.g., Rabi splitting), and quantum mirage. This versatile, yet effective soft quantum nanophotonics would be further benefitted from a deterministic control over the positions and orientations of each individual quantum emitter, particularly at the molecule level of resolution. In this review, we will argue that DNA nanotechnology can provide a gold vista toward this end. A collective set of exotic characteristics of DNA molecules, including Watson-Crick complementarity and helical morphology, enables reliable grabbing of quantum emitters at the on-demand position and steering of their directors at the single molecular level. More critically, the recent advances in large-scale integration of DNA origami have pushed the reliance on the distinctly well-formed single device to the regime of the ultra-scale device arrays, which is critical for promoting the practically immediate applications of such soft quantum nanophotonics. [ABSTRACT FROM AUTHOR]

The tumor suppressor BRCA2 participates in DNA double-strand break repair by RAD51-dependent homologous recombination and protects stressed DNA replication forks from nucleolytic attack. We demonstrate that the C-terminal Recombinase Binding (CTRB) region of BRCA2, encoded by gene exon 27, harbors a DNA binding activity. CTRB alone stimulates the DNA strand exchange activity of RAD51 and permits the utilization of RPA-coated ssDNA by RAD51 for strand exchange. Moreover, CTRB functionally synergizes with the Oligonucleotide Binding fold containing DNA binding domain and BRC4 repeat of BRCA2 in RPA-RAD51 exchange on ssDNA. Importantly, we show that the DNA binding and RAD51 interaction attributes of the CTRB are crucial for homologous recombination and protection of replication forks against MRE11-mediated attrition. Our findings shed light on the role of the CTRB region in genome repair, reveal remarkable functional plasticity of BRCA2, and help explain why deletion of Brca2 exon 27 impacts upon embryonic lethality. Exon 27 of the tumor suppressor BRCA2 encodes a portion of the protein crucial for DNA repair, genome maintenance, and tumor suppression. Here the authors show that this domain binds DNA and the RAD51 recombinase to enhance the assembly of RAD51-DNA complexes. [ABSTRACT FROM AUTHOR]

Viral genomes can be compressed into a near‐spherical nanochamber to form infectious particles. In order to mimic the virus morphology and packaging behavior, we invented a programmable icosahedral DNA nanoframe with enhanced rigidity and encapsulated the phiX174 bacteriophage genome. The packaging efficiency could be modulated through specific anchoring strands adjustment, and the trapped phage genome remained accessible for enzymatic operations. Moreover, the packed complex could infect Escherichia coli (E. coli) cells through bacterial uptake to produce plaques. This rigid icosahedral DNA architecture demonstrated a versatile platform to develop virus mimetic particles for convenient functional nucleic acid entrapment, manipulation and delivery. [ABSTRACT FROM AUTHOR]

A rectangle DNA origami nanostructure equipped with doxorubicin-derived prodrugs targeting a tumor cell-specific enzyme (NQO1) is constructed. Combining the high prodrug payload of DNA origami and NQO1-activated chemotherapy, this nanosystem presents therapeutic selectivity for NQO1-overexpressing MCF-7 cells over healthy L02 cells, offering a potent strategy for precision cancer therapy. [ABSTRACT FROM AUTHOR]

Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This study investigates the folding pattern design and deployment behavior of origami-based foldable conical structures. The geometric analysis is performed to design the six fold line pattern to obtain foldable conical structures. A single-story origami cone, modeled with pin-jointed framework, is selected for the analytical investigation. The axial strains, nodal forces, relative rotation of the fold polygons, and the strain energy during the deployment are obtained analytically. Moreover, the influence of design parameters ( m and α 1 ) on the deployment behavior of a single story cone is investigated. The results indicate that several fold configurations exhibit a bistable behavior during the motion, and these bistable configurations undergo lesser deformations than other singly stable fold configurations. Then, the folding and deployment process is simulated numerically using FE software to verify the accuracy of the analytical approach. The numerical results are completely consistent with the analytical results. The existence of bistability is verified using the variation of elastic strain energy during the motion. An analytical approach to obtain the bistability points for any conical folding pattern is presented and verified using numerical simulations. The influence of design parameters, materials, and scaling on the bistability point is also investigated. The results show that the bistability is solely a geometrical phenomenon, and scaling does not change the deformation behavior of the cone. Finally, the deployment dynamics of both singly stable and bistable multistory conical structures are discussed, with their potential applications. [ABSTRACT FROM AUTHOR]

Purpose: Paper aims to preparation of new acid disperse dyes based on thiadiazol derivatives and evaluation of their use as antimicrobial colorants in digital transfer-printing ink formulations for printing onto polyester fabric substrates. Design/methodology/approach: New disperse dyes based on 1,3,4 - thiadiazol derivative (dyes 1–3) were prepared and evaluated by different analysis then formulated as colored materials in the ink formulations. The viscosity, dynamic surface tension and particle size distribution of the prepared inks were measured. The printed polyester fabric substrates were tested using a variety of tests, including light fastness, washing, alkali perspiration and Crock fastness, as well as depth of penetration. Density-functional theory (DFT) calculations were carried out at the Becke3-Lee-Yang-parr (B3LYP) level using the 6–311** basis set, and the biological activity of the prepared disperse dyes was investigated. Findings: The obtained results of the physical of the prepared ink revealed that thiadiazol disperse ink is a promising ink formulation for polyester printing and agrees with the quality of the printed polyester fabric. The optimization geometry for molecular structures agreed with the analysis of these compounds. The HOMO/LUMO and energy gap of the studied system were discussed. The molecular docking analysis showed strong interaction with DNA Gyrase and demonstrated to us the high ability of these inks to act as antimicrobial agents. Practical implications: The prepared inks containing the prepared thiadiazol disperse dye were high-performance and suitable for this type of printing technique, according to the results. The prepared inks resist the growth of microorganisms and thus increase the ink's storage stability. Originality/value: The prepared disperse dyes based on 1,3,4 - thiadiazol derivative (dyes 1–3) can be a promising colorant in different applications, like some types of paint formulations and as a colorant in printing of different fabric substrates. [ABSTRACT FROM AUTHOR]

A working hypothesis issues from patterns of methylation in the 5′-UTR of the DAT1 gene. We considered relationships between pairs of CpGs, of which one on the main-gene strand and another on the complementary opposite strand (COS). We elaborated on data from ADHD children: we calculated all possible combinations of probabilities (estimated by multiplying two raw values of methylation) in pairs of CpGs from either strand. We analyzed all correlations between any given pair and all other pairs. For pairs correlating with M6-M6COS, some pairs had cytosines positioning to the reciprocal right (e.g., M3-M2COS and M6-M5COS), other pairs had cytosines positioning to the reciprocal left (e.g., M2-M3COS; M5-M6COS). Significant pair-to-pair correlations emerged between main-strand and COS CpG pairs. Through graphic representations, we hypothesized that DNA folded to looping conformations: the C1GG C2GG C3GG and C5G C6G motifs would become close enough to allow cytosines 1-2-3 to interact with cytosines 5-6 (on both strands). Data further suggest a sliding, with left- and right-ward oscillations of DNA strands. While thorough empirical verification is needed, we hypothesize simultaneous methylation of main-strand and COS DNA ("methylation dynamics") to serve as a promising biomarker. [ABSTRACT FROM AUTHOR]

Enzymes, as elements with catalytic functions, can be rationally designed and multiple assembled to form a composite catalytic system and achieve cascade catalytic functions. Enzyme cascade catalysis could produce various chemical products with high conversion rate in short time. With the development of DNA nanotechnology, assembling enzymes to different nucleic acid-based scaffolds in different spatial organizations could effectively improve the catalytic efficiency of enzymes. Herein, we review the construction and application of nucleic acid-based scaffold systems from the perspective of template assembly in three dimensions. The challenges and future outlooks in the development of enzyme cascades are also discussed. Key points: • The principles and construction of various nucleic acid scaffolds are summarized • The application of nucleic acid scaffolds in enzyme cascade catalysis is discussed [ABSTRACT FROM AUTHOR]

DNA sequence alterations within DNA repeat domains inexplicably enhance the stability and delay the expansion of interrupted repeat domains. Here we propose mechanisms that rationalise such unanticipated outcomes. Specifically, we describe how interruption of a DNA repeat domain restricts the ensemble space available to dynamic, slip out, repeat bulge loops by introducing energetic barriers to loop migration. We explain how such barriers arise because some possible loop isomers result in energetically costly mismatches in the duplex portion of the repeat domain. We propose that the reduced ensemble space is the causative feature for the observed delay in repeat DNA expansion. We further posit that the observed loss of the interrupting repeat in some expanded DNAs reflects the transient occupation of loop isomer positions that result in a mismatch in the duplex stem due to 'leakiness' in the energy barrier. We propose that if the lifetime of such a low probability event allows for recognition by the mismatch repair system, then 'repair' of the repeat interruption can occur; thereby rationalising the absence of the interruption in the final expanded DNA 'product.' Our proposed mechanistic pathways provide reasoned explanations for what have been described as 'puzzling' observations, while also yielding insights into a biomedically important set of coupled genotypic phenomena that map the linkage between DNA origami thermodynamics and phenotypic disease states. [ABSTRACT FROM AUTHOR]

Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large 'origami' structures with thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures – the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We present an efficient and readily applicable strategy for the covalent ligation of proteins to DNA origami by using the SpyCatcher–SpyTag (SC–ST) connector system. This approach showed orthogonality with other covalent connectors and has been used exemplarily for the immobilization and study of stereoselective ketoreductases to gain insight into the spatial arrangement of enzymes on DNA nanostructures. [ABSTRACT FROM AUTHOR]

We here show a reconfigurable DNA/plasmonic nanodevice with a precisely tunable and DNA-free interparticle gap. The nanodevice comprises two DNA boxes for the size-selective incorporation of nanoparticles in a face-to-face orientation and an underlying switchable DNA platform for the controlled and reversible adjustment of the interparticle distance. [ABSTRACT FROM AUTHOR]

Controlled dielectric breakdown (CDB) is gaining popularity for fabricating solid‐state nanopores in situ with size control in a simple, low‐cost, and scalable way. This technique could be used for a broad type of applications in the field of nucleic acid analysis and even for protein studies. In this work, we studied the entry and transport of double‐stranded DNAs using a solid‐state nanopore fabricated by CDB as a function of applied voltage for two different DNA lengths. We showed that the blockade rate increases exponentially with voltage up to 120 mV. The energy barrier depends on the chain length, and the dwell times decrease with applied voltage up to 120 mV. Moreover, no matter the chain length, it is possible to differentiate two families of blockade amplitudes, high and low ones, due to DNA folding. [ABSTRACT FROM AUTHOR]

The development of DNA delivery techniques is critical to promote the wider use of deoxyribonucleic acids as cellular transporters. The present study aimed to develop a type of DNA nanoparticle (citZ-box) to automatically load and release cargo. The restriction enzyme can cleave citZ-boxes at pro-designed sites, and the enhanced green fluorescent protein gene (eGFP) can be delivered into the B. subtilis protoplasts by them. The process of eGFP expression is recorded using a confocal microscope over 4 h. Here, multiscaffold and multimodular designs are used for citZ-box assembly with a DAEDALUS module, DX_cage_design and rem (edge_length, 21), to ensure the structure was predicted as B-type DNA. Finally the citZ-box is estimated to be a 50.7 nm cube. The 3D structure of the citZ-box particle is detected to be approximately 50.3 ± 0.3 nm. DNA nanoparticles prepared as citZ-boxes have great potential as drug carriers with automatic loading and releasing abilities. The DNA origami design algorithm DAEDALUS is modified to design a nanoscale cube with a two-step assembly protocol, assembling 9 modules from three DNA scaffolds and the complementary staples, combined to form the DNA origami cube. [ABSTRACT FROM AUTHOR]

The nonlinearities inherent in the mechanics of origami make it a rich design space for multistable structures and mechanical metamaterials. Here, we investigate the multistability of a classic origami base: the symmetric eightfold waterbomb. We prove that the waterbomb is bistable for certain crease properties, and derive bounds on, and closed-form approximations of, its stable states. We introduce a simplified form of the waterbomb kinematics and present a design procedure for tuning the depth and the symmetry/asymmetry of its energy wells. By incorporating the concept of pretensioned torsional springs, we also demonstrate the existence of tristable cases for the waterbomb fold pattern. We then apply the analysis of a single waterbomb to study quasione-dimensional arrays of waterbombs, where we discover a conserved geometric-kinematic quantity in which the number of popped-up and poppeddown vertices is determined uniquely through analysis of the origami structure's boundaries. This culminates with a discussion of how the quasi-onedimensional array may be designed to achieve stable states with various degeneracies, kinematics and gaps between energy levels. Collectively, this work presents an alternative approach for characterizing origami multistability properties and reveals an origami design motif that has potential applications in physically reconfigurable structures, mechanical energy absorption and metamaterials. [ABSTRACT FROM AUTHOR]

Eukaryotic cells that swim by the beating of nanoscale elastic filaments (flagella) present a promising locomotion paradigm for man‐made analogues essential for next‐generation in‐vivo treatments and for the study of collective phenomena at the low Reynolds number limit. However, artificial analogues have been limited to many microns in size due to the engineering challenges of fabricating actable flexible filaments at the nanoscale—thereby narrowing the application scope. Here, made‐to‐order nanoscale filaments designed on the molecular level are fabricated using the DNA‐origami technique. It is found that magnetic beads anisotropically covered with such bundles move in a ballistic fashion when wagged back and forth under an external magnetic field. Furthermore, by comparing bead dynamics at a range of bundle coverages and driving frequencies, compelling evidence is amassed to suggest that this ballistic motion is imparted by the beating of the DNA origami filaments as synthetic flagella. This proof‐of‐concept work opens up avenues for further made‐for‐purpose appendages designed using DNA self‐assembly and with it ever more complex locomotion on the nano and microscale. [ABSTRACT FROM AUTHOR]

Nanocellulose hydrogels have been shown to be excellent platforms for sustained delivery of drug molecules. In this study, we examine the suitability of anionic nanocellulose hydrogels for the sustained release of various nanoparticles. Systems releasing nanoparticles could produce applications especially for therapeutic nanocarriers, whose life-times in vivo might be limited. Micelles, liposomes and DNA origami nanostructures were incorporated into the nanocellulose hydrogels, and their release rates were measured. Two different hydrogel qualities (with 1% and 2% mass of fiber content) were used for each nanoparticle formulation. We showed that the drug release rates depend on nanoparticle size, shape, and charge. Smaller particles with neutral charge were released faster from 1% hydrogels than from 2% hydrogels. Nanoparticles with cationic labeling were retained in both hydrogels, whereas for the neutral nanoparticles, we were able to determine the cut-off size for released particles for both hydrogels. Rod-shaped DNA origami were released rapidly even though their length was above the cut-off size of spherical particles, indicating that their smaller radial dimension facilitates their fast release. Based on our results, anionic nanocellulose hydrogels are versatile platforms for the sustained release of the chosen model nanoparticles (liposomes, micelles, and DNA origami). Alternatively, for the tightly bound nanoparticles, this could lead to nanoparticle reservoirs within hydrogels, which could act as immobilized drug release systems. [ABSTRACT FROM AUTHOR]

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions. [ABSTRACT FROM AUTHOR]

Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman’s laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched junction molecules that will self-assemble into target structures without unwanted substructures forming. We use graph theory, which is a natural design tool for self-assembling DNA complexes, to address this problem. After determining that finding optimal design strategies for this method is generally NP-complete, we provide pragmatic solutions in the form of programs for special settings and provably optimal solutions for natural assembly targets such as platonic solids, regular lattices, and nanotubes. These examples also illustrate the range of design challenges. [ABSTRACT FROM AUTHOR]

Aflatoxin B 1 (AFB 1) is a highly toxic mycotoxin that readily contaminates major food crops. This study presents a novel ratiometric electrochemical paper-based aptasensor for AFB 1 detection that utilizes a structure-switching aptamer. The sensor detects AFB 1 by folding the DNA aptamer, reducing the electron transfer efficiency between the methylene blue (MB) molecules attached to the DNA and the electrode surface. An inner reference element modified with ferrocene (Fc) is co-assembled on the electrode surface of the paper-based biosensor to enhance the accuracy of AFB 1 detection. In the presence of target AFB 1 , a folded target–aptamer complex is formed, distancing the MB molecules from the electrode and generating a low current signal in a differential pulse voltammetry mode. The ratio of oxidation currents for MB and Fc serves as the metric for monitoring AFB 1 levels. The detection range spans from 20.0 to 1000.0 ng mL−1, with a limit of detection of 7.6 ng mL−1. The paper-based aptasensor exhibits excellent specificity and stability. Additionally, its high reliability and applicability are validated by the strong correlation observed between the sensor results and the results obtained using UPLC−MS/MS analysis of real samples. This study offers a low-cost, readily available approach for portable detection of foodborne hazards. • A paper-based ratiometric electrochemical sensor for portable detection of AFB 1. • The sensor assembly procedure is very simple, only contains two key steps. • This sensor exhibits a desirable response range and lower limit of detection. • The aptasensor is suitable for the detection AFB 1 contamination in real samples. • This study offers a low-cost, readily available approach for portable detection. [ABSTRACT FROM AUTHOR]

Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios. • Tetrahedral DNA nanostructures (TDNs) can significantly amplify the fluorescent signals in expansion microscopy (ExM). • No anchoring agent in TDN-ExM was required to retain the fluorescence signal on the hydrogel, so samples with better uniformity were obtained. • TDN-ExM integrates seamlessly with other super-resolution techniques, enhancing overall resolution. [ABSTRACT FROM AUTHOR]

DNA Origami NanostructuresIn article number 2400094, Adrian Keller and co‐workers explore the effect of photo‐generated reactive oxygen species (ROS) on the stability of DNA origami nanostructures in different ionic environments. Low ionic strength is found to result in more severe ROS‐induced damage. Part of the damage obtained under such conditions is reversible and can be repaired by the post‐exposure addition of Mg2+ ions..By Lukas Rabbe; Jaime Andres Garcia‐Diosa; Guido Grundmeier and Adrian KellerReported by Author; Author; Author; Author [Extracted from the article]

In this study, the complexities of intracellular processes have been analyzed, including DNA folding, alternative splicing, mitochondrial function, and enzyme transport in lysosomes. Based on a previously proposed hypothesis (Levinthal's generalized paradox), a conclusion is made that all abovementioned processes cannot be realized with sufficient accuracy and in a realistic timeframe within the framework of classical physics. It is unclear why the cell functions at all. For the cell to function, its internal environment must be highly structured. In this regard, the cell shares similarities with computational devices (computers). In this study, quantum models of interactions between biologically important molecules were constructed, taking into account the long-range effects. One significant aspect of these models is the special role of the phase of the wavefunction, which serves as a controlling parameter. Experiments have been proposed that may confirm or refute these models. [ABSTRACT FROM AUTHOR]

[Display omitted] • An "off–on" fluorescence nanobiosensor based on MoS 2 nanosheets and CdTe QDs was designed to detect Ag+. • The nanobiosensor towards Ag+ indicated excellent sensitivity and anti-interference. • The limit of detection is as low as 1.1 nM. • The constructed biosensor can realize Ag+ detection in different real samples. Silver ion (Ag+) is a significant metal pollutant known for its potential toxicity to aquatic life and human health. Long-term exposure to toxic heavy metals will do great harm to humans and animals. Therefore, it is urgent to develop an efficient method for detecting Ag+. Herein, we have developed a simple, sensitive, highly selective and cost-effective fluorescence "off-on" mode nanosensor based on environmentally friendly and biocompatible materials for sensitive detection of Ag+ in aqueous environments. In this sensing strategy, Ag+ can specifically interact with the cytosine-cytosine (C-C) mismatch in single-stranded DNA, where Ag+ induces the folding of single-stranded DNA to form hairpin structures and stable metal-mediated cytosine-Ag+-cytosine (C-Ag+-C) base pairs via coordinate bonds. Massive changes to the molecular volume and fluorescence signal are brought about by the development of the C-Ag+-C complex. To reach our objective, CdTe quantum dots (CdTe QDs) with low toxicity and strong signal were prepared as fluorophores for detecting Ag+ target. Using the inner filter effect (IFE) between hydrophilic CdTe QDs and MoS 2 nanosheets to achieve the fluorescence quenching of the CdTe QDs, and the subsequent fluorescence turn-on process is due to the formation of C-Ag+-C complex, which makes its probe fluorophore far away from the surface of MoS 2 nanosheets, thus realizing fluorescence "off-on" sensing strategy. The proposed nanosensor can distinguish Ag+ from other interfering ions with high sensitivity and selectivity. The nanosensor proposed here possesses a quick response time of 8 min and an ultra-low detection limit of 1.1 nM. [ABSTRACT FROM AUTHOR]

DNA-origami nanostructures have shown promising applications in single molecule localization microscopy. They have become a reference standard for benchmarking and for developing new techniques for nanoscopy. Here, we present a pipeline for quantifying the quality of these nano-structures when imaging multiple instances of them using DNA-PAINT technique. We show on several experimental datasets that these structures can have deformations and that the designed binding sites are not equally accessible for the labelled imager strands during the image acquisition process. These limitations result in non-uniform activation of the sites over the origami pattern when fusing the instances into a single reconstruction. [Display omitted] • Uneven distribution of localization events over DNA origami structure. • Binding sites on the edge of structures were localized less often than central. • Reliable activation counts per DNA strand can be made via particle fusion. [ABSTRACT FROM AUTHOR]

Most multiplexed photoelectrochemical (PEC) sensors require additional instrumentation and cumbersome electrode modification and surface partitioning, which limits their portability and instrument miniaturization. Herein, a pH-responsive programmable triple DNA nanomachine was developed for constructing a reconfigurable multiplex PEC sensing platform. By programming the base sequence, T-A·T-riched triple DNA was designed to construct integrated nano-controlled release machine (INCRM) for simultaneous recognition of multiple targets. The INCRM enables to recognize two targets in one step, and sequentially separate the signal labels by pH adjustment. The detached signal label catalyzes glucose to produce gluconic acid, causing the C-riched DNA fold into a triple structure on the electrode surface. As a result, one target can be detected relying on the enhanced photocurrent due to accelerated electron transfer between the CdS QD labeled at the end of C-riched DNA and the electrode. The triplex DNA dissociation in pH 7.4 buffer reconfigures the electrode interface, which can be continued to detect another target. The feasibility of the multiplexed sensor is verified by the detection of extensively coexisting antibiotics enrofloxacin (ENR) and ciprofloxacin (CIP). Under the optimal conditions, wide linear range (10 fg/mL ∼ 1 μg/mL) and low detection limit (3.27 fg/mL and 9.60 fg/mL) were obtained. The pH-regulated programmable triplex DNA nanomachine-based sensing platform overcomes the technical difficulties of conventional multiplexed PEC assay, which may open the way for miniaturization of multiplexed PEC sensors. [ABSTRACT FROM AUTHOR]

Double-stranded DNA translocates through sufficiently large nanopores either in a linear single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be controlled by changing the electrolyte concentration, pH, and polyethylene glycol content of the measurement buffer. At pH 8 in 1M LiCl or 0.35M KCl, single-file translocations make up more than 90% of the total. We attribute the effect to the onset of electro-osmotic flow from the pore at low ionic strength. Our hypothesis on the critical role of flows is supported by the preferred orientation of entry of a strand that has been folded into a multi-helix structure at one end. Control over DNA folding is critical for nanopore sensing approaches that use modifications along a DNA strand and the associated secondary current drops to encode information. [ABSTRACT FROM AUTHOR]

We built and characterised a macroscopic self-assembly reactor that agitates magnetic, centimeter- sized particles with a turbulent water flow. By scaling up the self-assembly processes to the centimeter-scale, the characteristic time constants also drastically increase. This makes the system a physical simulator of microscopic self-assembly, where the interaction of inserted particles is easily observable. Trajectory analysis of single particles reveals their velocity to be a Maxwell-Boltzmann distribution and it shows that their average squared displacement over time can be modelled by a confined random walk model, demonstrating a high level of similarity to the Brownian motion. The interaction of two particles has been modelled and verified experimentally by observing the distance between two particles over time. The disturbing energy (analogue to temperature) that was obtained experimentally increases with sphere size and differs by an order of magnitude between single-sphere and two-sphere systems (approximately 80 µJ versus 6.5 µJ, respectively). [ABSTRACT FROM AUTHOR]

Dynamic regulation of DNA origami nanostructures is important for the fabrication of intelligent DNA nanodevices. Toehold-mediated strand displacement is a common regulation strategy, which utilizes trigger strands to assemble and disassemble nanostructures. Such trigger strands are required to be completely complementary to the corresponding substrate strands, which strictly demands orthogonality and accuracy of the sequence design. Herein, we present a disassembly strategy of DNA origami dimers based on polymerase-triggered strand displacement, where the polymerase primers, as the trigger strands, were only partially complementary to the toehold region of the substrate strands. To demonstrate the programmability of trigger strands, we utilized primers with different sequence combination patterns to disassemble DNA origami dimers. The statistical summary of AFM images and fluorescence curves proved the feasibility of the new strategy. The utilization of polymerase-triggered strand displacement on the disassembly of DNA origami structures enriches the toolbox for the dynamic regulation of DNA nanostructures. [ABSTRACT FROM AUTHOR]

The article presents a study on a strategy developed to simultaneously cocrystallize multitype DNA origami frames (DOF) in a programmable manner to synthesize types of nanoparticle superlattices based on binding nanoparticles to DOFs. Topics discussed include the octahedral DOFs used to construct three-dimensional DNA platforms, the advantages of the multiple-unit systems over single-unit systems, and a way to diversify the synthesis of the crystals using the strategy.

Hierarchical, chiral hybrid superstructures of chromophores and nanoparticles are expected to give rise to intriguing unveiled chiroptical responses originating from the complex chiral interactions among the components. Herein, DNA origami cavity that could self‐assemble into one‐dimensional (1D) DNA tubes was employed as a scaffold to accurately organize metal nanoparticles and chromophores. The chiral interactions were studied at the level of individual hybrid particles and their 1D hybrid superstructures. Complex chirality mechanisms involving global structural chirality, plasmon‐induced circular dichroism (PICD) and exciton‐coupled circular dichroism (ECCD) were disentangled. The multiplexed CD spectrum superposition revealed the chirality evolution at different length scales. These results can offer a model for boosting the theoretical understanding of classical‐quantum hybrid systems, and would inspire the future design of optically‐active substances across length scales. [ABSTRACT FROM AUTHOR]

Block copolymer‐based polymersomes are important building blocks for the bottom‐up design of protocells and are considered advantageous over liposomes due to their higher mechanical stability and chemical versatility. Endowing both types of vesicles with capabilities for transmembrane transport is important for creating nanoreactor functionality and has been achieved by insertion of protein nanopores, even into comparably thick polymersome membranes. Still, the design space for protein nanopores is limited and higher flexibility might be accessible by de novo design of DNA nanopores, which have thus far been limited largely to liposome systems. Here, we introduce the successful insertion of two different 3D DNA origami nanopores into PMOXA‐b‐PDMS‐b‐PMOXA polymersomes, and confirm pore formation by dye influx studies and microscopy. This research thus opens the further design space of this versatile class of large DNA origami nanopores for polymersome‐based functional protocells. [ABSTRACT FROM AUTHOR]

DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed "HSV1 pockets" to agglomerated "HSV1 sleeves". "Pockets" were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity. [ABSTRACT FROM AUTHOR]

Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks. [ABSTRACT FROM AUTHOR]

The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs. Author summary: To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na+ and Mg2+) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops. [ABSTRACT FROM AUTHOR]

G-rich telomeric DNA plays a major role in the stabilization of chromosomes and can fold into a plethora of different G-quadruplex structures in the presence of mono- and divalent cations. The reversed human telomeric DNA sequence (5′-(GGG ATT)4; RevHumTel) was previously shown to have interesting properties that can be exploited for chemical sensing and as a chemical switch in DNA nanotechnology. Here, we analyze the specific G-quadruplex structures formed by RevHumTel in the presence of K+, Na+, Mg2+ and Ca2+ cations using circular dichroism spectroscopy (CDS) and Förster resonance energy transfer (FRET) based on fluorescence lifetimes. CDS is able to reveal strand and loop orientations, whereas FRET gives information about the distances between the 5′-end and the 3′-end, and also, the number of G-quadruplex species formed. Based on this combined information we derived specific G-quadruplex structures formed from RevHumTel, i.e., a chair-type and a hybrid-type G-quadruplex structure formed in presence of K+, whereas Na+ induces the formation of up to three different G-quadruplexes (a basket-type, a propeller-type and a hybrid-type structure). In the presence of Mg2+ and Ca2+ two different parallel G-quadruplexes are formed (one of which is a propeller-type structure). This study will support the fundamental understanding of the G-quadruplex formation in different environments and a rational design of G-quadruplex-based applications in sensing and nanotechnology. [ABSTRACT FROM AUTHOR]

DNA nanotechnology has provided credible approaches for assembly of three‐dimensional (3D) lattices with complex patterns. However, the symmetries are strictly dependent on their initial configurations and difficult to alter via non‐thermal treatments. While switchable nucleic acid structures have been employed to construct deformable DNA motifs, it remains challenging to arrange them anisotropically in 3D lattices to trigger directed collective shape transition and dynamic symmetry conversion. In this work, we used octahedral DNA origami frames to synthesize four DNA origami lattices by placing the pH‐reactive i‐motif sequences in the desired dimensions. Thereinto, lattices with an anisotropic design can switch between simple cubic (SC) and simple tetragonal (ST) upon pH change. Small angle X‐ray scattering (SAXS) results reveal the feasibility of obtaining 3D lattices with sensitive responses to external stimuli, expanding the way to obtain low‐symmetry lattices. [ABSTRACT FROM AUTHOR]

This review paper gives overview of the present status and further development in nanorobotics. Nanobots are very tiny machines designed to perform a specific task whose components are at or close to the scale of a nanometer. As consequence of nanotechnology, new technique consisting of device coming into market among these nanobots fields opportunity in cure of human illness. This bots are made of a single strand of DNA folded into desired shape. Bots will have two states - an "off" position, where the clamshells are closed tightly to bypass healthy cell without any damage and an "on" position, where clamshell opens up to expose cancerous cell from human body. In this paper included about method of working, composition, types, challenges in development and properties of nanobots. [ABSTRACT FROM AUTHOR]

The tool kit for label‐free single‐molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore‐based technologies. Currently, various sources of nanopores, including biological, fabricated solid‐state, hybrid and recently de novo chemically synthesized ion‐like channels have put in use for rapid single‐molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami‐based devices, enables the assembly of complex and dynamic 3‐dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid‐state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid‐based systems or coupled with other solid‐state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA‐based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications. [ABSTRACT FROM AUTHOR]

DNA origami has been widely used to construct nanophotonic structures due to its unparallel capability in assembling photonic nanomaterials with nanometer precision. Nevertheless, the majority of fabricated fluorescence‐based nanophotonic systems so far operate in the ultraviolet‐visible (UV‐Vis) region, which are accompanied by limitations of shallow penetration and potential light damage. Herein, we constructed a reconfigurable nanophotonic heterostructure by integrating an upconversion nanoparticle (UCNP) and a gold nanorod (AuNR) on a DNA origami switch (DOS) template. With the unique anti‐Stokes luminescence of UCNP whose excitation wavelength is mostly located in the near‐infrared (NIR) region, the obtained reconfigurable nanophotonic system can be excited by 980 laser light and generates visible light emission. In our nanophotonic system, the DNA origami template serves as a switch to reversibly tune the optical properties of UCNP. The construction of this nanophotonic heterostructure expands the toolbox of DNA origami‐based nanophotonic systems that may hold great potential in optical biosensing and imaging. [ABSTRACT FROM AUTHOR]

With the great advancement of experimental tools, a tremendous amount of biomolecular data has been generated and accumulated in various databases. The high dimensionality, structural complexity, the nonlinearity, and entanglements of biomolecular data, ranging from DNA knots, RNA secondary structures, protein folding configurations, chromosomes, DNA origami, molecular assembly, to others at the macromolecular level, pose a severe challenge in their analysis and characterization. In the past few decades, mathematical concepts, models, algorithms, and tools from algebraic topology, combinatorial topology, computational topology, and topological data analysis, have demonstrated great power and begun to play an essential role in tackling the biomolecular data challenge. In this work, we introduce biomolecular topology, which concerns the topological problems and models originated from the biomolecular systems. More specifically, the biomolecular topology encompasses topological structures, properties and relations that are emerged from biomolecular structures, dynamics, interactions, and functions. We discuss the various types of biomolecular topology from structures (of proteins, DNAs, and RNAs), protein folding, and protein assembly. A brief discussion of databanks (and databases), theoretical models, and computational algorithms, is presented. Further, we systematically review related topological models, including graphs, simplicial complexes, persistent homology, persistent Laplacians, de Rham—Hodge theory, Yau—Hausdorff distance, and the topology-based machine learning models. [ABSTRACT FROM AUTHOR]

The use of DNA nanotechnology is rapidly growing due to the unprecedented programmability of geometric, mechanical, and dynamic properties. This technology has led to an impressive library of nanoscale structures and devices that are useful across physics, chemistry, and engineering. A challenge for materials researchers and engineers is to reliably expand DNA technology to larger scales, much like natural biomolecular materials assemble nanoscale components into functional filaments, capsules, and more. This review explores the expansion of structural DNA nanotechnology to the micrometer scale and beyond, covering strategies for hierarchical assembly of DNA nanostructures using (1) DNA base pairing, (2) base stacking interactions, and (3) DNA-peptide conjugates while highlighting examples of how these supramolecular assemblies are being used as functional materials. [ABSTRACT FROM AUTHOR]

This design research aims to propose a HyFlex strategy for students and participants in the workplace using massive open online course (MOOC) flipped between the two settings, an active in-classroom to an action learning in the workplace. The research methods were designed into two major parts, where the first part was a design stage which included the review and design process, while the second part involved case studies. The learning design is analogous to an origami paper folding system that processes the diversified questioning of real-world problems and recursively reflects the thought, action, and solutions to the problems. The case studies showed a statistically significant increase in participants' creative problem-solving at the 0.5 level. [ABSTRACT FROM AUTHOR]

Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami's internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols. DNA origami can be coated in a layer of silica to improve chemical and thermal stability however; it is unclear if this is a surface or interpenetrating layer. Here, the authors use in situ small-angle X-ray scattering to study silica deposition and observe internal silica formation resulting in DNA origami condensation and structure shrinkage. [ABSTRACT FROM AUTHOR]

The bending and twisting of DNA origami structures are important features for controlling the physical properties of DNA nanodevices. It has not been fully explored yet how to finely tune the bending and twisting of curved DNA structures. Traditional tuning of the curved DNA structures was limited to controlling the in-plane-bending angle through varying the numbers of base pairs of deletions and insertions. Here, we developed two tuning strategies of curved DNA origami structures from in silico and in vitro aspects. In silico, the out-of-plane bending and twisting angles of curved structures were introduced, and were tuned through varying the patterns of base pair deletions and insertions. In vitro, a chemical adduct (ethidium bromide) was applied to dynamically tune a curved spiral. The 3D structural conformations, like chirality, of the curved DNA structures were finely tuned through these two strategies. The simulation and TEM results demonstrated that the patterns of base pair insertions and deletions and chemical adducts could effectively tune the bending and twisting of curved DNA origami structures. These strategies expand the programmable accuracy of curved DNA origami structures and have potential in building efficient dynamic functional nanodevices. [ABSTRACT FROM AUTHOR]