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Nucleic acids are considered as promising materials for developing exquisite nanostructures from one to three dimensions. The advances of DNA nanotechnology facilitate ingenious design of DNA nanostructures with diverse shapes and sizes. Especially, the algebraic topological framework nucleic acids (ATFNAs) are functional DNA nanostructures that engineer guest molecules (e. g., nucleic acids, proteins, small molecules, and nanoparticles) stoichiometrically and spatially. The intrinsic precise properties and tailorable functionalities of ATFNAs hold great promise for biological applications, such as cell recognition and immunotherapy. This Perspective highlights the concept and development of precisely assembled ATFNAs, and outlines the new frontiers and opportunities for exploiting the structural advantages of ATFNAs for biological applications. [ABSTRACT FROM AUTHOR]

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics. [ABSTRACT FROM AUTHOR]

There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, “art-like” DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. [ABSTRACT FROM AUTHOR]

CRISPR/Cas system is to be a powerful tool to construct the nucleic acid diagnostic platform. Specific recognition and cleavage of CRISPR/Cas systems enable selective recognition of analytes and physicochemical signal translation of biorecognition events. Given the diversity of Cas effectors, we outline various types of Cas effectors and their associated single‐guide RNA (sgRNA), protospacer adjacent motif (PAM) sequence, or protospacer flanking sequence (PFS), as well as the characteristics of the CRISPR/Cas complex in nucleic acid detection. In light of this, we discuss the coupling of CRISPR/Cas systems to various biosensing strategies (e.g., amplification strategy, electronic methods, or optical methods) and point‐of‐care testing (POCT) (e.g., paper‐based lateral flow assays, field‐effect transistor, microfluidics devices, and solid‐state nanopore sensors) that could enable the specificity and sensitivity of the diagnostic platform for biosensing applications. Additionally, we also discuss the new frontiers and the challenges to be addressed in this field. [ABSTRACT FROM AUTHOR]

Efficient biocatalytic cascade reactions play a crucial role in guiding intricate, specific and selective intracellular transformation processes. However, the catalytic activity of the enzyme cascade reaction in bulk solution was greatly impacted by the spatial morphology and inter‐enzyme distance. The programmability and addressability nature of framework nucleic acid (FNA) allows to be used as scaffold for immobilization and to direct the spatial arrangement of enzyme cascade molecules. Here, we used tetrahedral DNA framework (TDF) as nanorulers to assemble two enzymes for constructing a double‐enzyme complex, which significantly enhance the catalytic efficiency of sarcosine oxidase (SOx)/horseradish peroxidase (HRP) cascade system. We synthesized four types of TDF nanorulers capable of programming the lateral distance between enzymes from 5.67 nm to 12.33 nm. Enzymes were chemical modified by ssDNA while preserving most catalytic activity. Polyacrylamide gel electrophoresis (PAGE), transmission electron microscopy (TEM) and atomic force microscopy (AFM) were used to verify the formation of double‐enzyme complex. Four types of double‐enzyme complexes with different enzyme distance were constructed, in which TDF26(SOx+HRP) exhibited the highest relative enzyme cascade catalytic activity, ~3.11‐fold of free‐state enzyme. Importantly, all the double‐enzyme complexes demonstrate a substantial improvement in enzyme cascade catalytic activity compared to free enzymes. [ABSTRACT FROM AUTHOR]

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized. [ABSTRACT FROM AUTHOR]

The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer‐associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection‐ of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker‐based biosensors are discussed. [ABSTRACT FROM AUTHOR]

Encapsulating individual mammalian cells with biomimetic materials holds potential in ex vivo cell culture and engineering. However, current methodologies often present tradeoffs between homogeneity, stability, and cell compatibility. Here, inspired by bacteria that use proteins stably anchored on their outer membranes to nucleate biofilm growth, we develop a single‐cell encapsulation strategy by using a DNA framework structure as a nucleator (DFN) to initiate the growth of DNA hydrogels under cell‐friendly conditions. We find that among the tested structures, the tetrahedral DFN can evenly and stably reside on cell membranes, effectively initiating hybridization chain reactions which generate homogeneously dense yet flexible single‐cell encapsulation for diverse cell lines. The encapsulation persists for up to 72 hours in a serum‐containing cell culture environment, representing a ~70‐fold improvement compared to encapsulations mediated by single‐stranded DNA nucleators. The metabolism and proliferation of the encapsulated cells are suppressed, but can be restored to the original efficiencies upon release, suggesting the superior cell compatibility of the encapsulation. We also find that compared to naked cells, the encapsulated cells exhibit a lower autophagy level after undergoing mechanical stress, suggesting the protective effect of the DNA encapsulation. This method may provide a new tool for ex vivo cell engineering. [ABSTRACT FROM AUTHOR]

Encapsulating individual mammalian cells with biomimetic materials holds potential in ex vivo cell culture and engineering. However, current methodologies often present tradeoffs between homogeneity, stability, and cell compatibility. Here, inspired by bacteria that use proteins stably anchored on their outer membranes to nucleate biofilm growth, we develop a single‐cell encapsulation strategy by using a DNA framework structure as a nucleator (DFN) to initiate the growth of DNA hydrogels under cell‐friendly conditions. We find that among the tested structures, the tetrahedral DFN can evenly and stably reside on cell membranes, effectively initiating hybridization chain reactions which generate homogeneously dense yet flexible single‐cell encapsulation for diverse cell lines. The encapsulation persists for up to 72 hours in a serum‐containing cell culture environment, representing a ~70‐fold improvement compared to encapsulations mediated by single‐stranded DNA nucleators. The metabolism and proliferation of the encapsulated cells are suppressed, but can be restored to the original efficiencies upon release, suggesting the superior cell compatibility of the encapsulation. We also find that compared to naked cells, the encapsulated cells exhibit a lower autophagy level after undergoing mechanical stress, suggesting the protective effect of the DNA encapsulation. This method may provide a new tool for ex vivo cell engineering. [ABSTRACT FROM AUTHOR]

Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop‐initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one‐stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost‐effective detection of low‐abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS‐CoV‐2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point‐of‐care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics. [ABSTRACT FROM AUTHOR]

Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop‐initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one‐stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost‐effective detection of low‐abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS‐CoV‐2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point‐of‐care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics. [ABSTRACT FROM AUTHOR]

The precise arrangement of single entity is a crucial objective of nanoscience and holds great promise in various fields such as biology and material science. In this work, we develop a "DNA framework‐mediated geometric renormalization" (DFMGR) strategy to reassemble gold nanoparticles into specific geometric shapes on a 2‐dimensional (2D) fluidic membrane interface. Cholesterol‐modified AuNPs are randomly anchored on the supported lipid bilayer (SLB) via the cholesterol‐lipid interaction. We demonstrate that AuNPs are laterally mobile on SLB and could be further rearranged into a specific geometric shape by DNA framework containing algebraically topological DNA arms. Using scanning electron microscope (SEM) imaging approach, simple geometric shapes, such as points assembled by monomers, line segments assembled by dimers, triangles assembled by trimers are visually presented. Interestingly, we found that the statistic angle (58.77°) and side length (12.21 nm) of triangles obtained from SEM images were both agreed well with the theoretical angle of 60° and side length of 12.58 nm. And the relative error of the angle calculated was as low as 0.33 %. These results indicated that the DFMGR strategy showed precise regulation ability for the AuNPs renormalization. We believe that DNA framework‐mediated geometric renormalization strategy would be a powerful means for regulating ligand‐receptor interactions in biosystems and for nanoparticle assembling in material science. [ABSTRACT FROM AUTHOR]

Single entities detection reveals heterogeneity and random processes hidden in ensemble measurements. Obtaining accurate single‐entity information is challenging. The electrochemical analysis is at high spatial resolution and high temporal resolution to analyze single entities and measure the fast kinetics process. In this minireview, we will focus on the electrochemical strategies for single multiscale entities. [ABSTRACT FROM AUTHOR]

Membrane curvature reflects physical forces operating on the lipid membrane, which plays important roles in cellular processes. Here, we design a mechanosensitive DNA (MSD) nanomachine that mimics natural mechanosensitive PIEZO channels to convert the membrane tension changes of lipid vesicles with different sizes into fluorescence signals in real time. The MSD nanomachine consists of an archetypical six‐helix‐bundle DNA nanopore, cholesterol‐based membrane anchors, and a solvatochromic fluorophore, spiropyran (SP). We find that the DNA nanopore effectively amplifies subtle variations of the membrane tension, which effectively induces the isomerization of weakly emissive SP into highly emissive merocyanine isomers for visualizing membrane tension changes. By measuring the membrane tension via the fluorescence of MSD nanomachine, we establish the correlation between the membrane tension and the curvature that follows the Young‐Laplace equation. This DNA nanotechnology‐enabled strategy opens new routes to studying membrane mechanics in physiological and pathological settings. [ABSTRACT FROM AUTHOR]

Membrane curvature reflects physical forces operating on the lipid membrane, which plays important roles in cellular processes. Here, we design a mechanosensitive DNA (MSD) nanomachine that mimics natural mechanosensitive PIEZO channels to convert the membrane tension changes of lipid vesicles with different sizes into fluorescence signals in real time. The MSD nanomachine consists of an archetypical six‐helix‐bundle DNA nanopore, cholesterol‐based membrane anchors, and a solvatochromic fluorophore, spiropyran (SP). We find that the DNA nanopore effectively amplifies subtle variations of the membrane tension, which effectively induces the isomerization of weakly emissive SP into highly emissive merocyanine isomers for visualizing membrane tension changes. By measuring the membrane tension via the fluorescence of MSD nanomachine, we establish the correlation between the membrane tension and the curvature that follows the Young‐Laplace equation. This DNA nanotechnology‐enabled strategy opens new routes to studying membrane mechanics in physiological and pathological settings. [ABSTRACT FROM AUTHOR]

The trans‐cleavage property of CRISPR‐Cas12a system makes it an excellent tool for disease diagnosis. Nevertheless, most methods based on CRISPR‐Cas system still require pre‐amplification of the target to achieve the desired detection sensitivity. Here we generate Framework‐Hotspot reporters (FHRs) with different local densities to investigate their effect on trans‐cleavage activity of Cas12a. We find that the cleavage efficiency increases and the cleavage rate accelerates with increasing reporter density. We further construct a modular sensing platform with CRISPR‐Cas12a‐based target recognition and FHR‐based signal transduction. Encouragingly, this modular platform enables sensitive (100 fM) and rapid (<15 min) detection of pathogen nucleic acids without pre‐amplification, as well as detection of tumor protein markers in clinical samples. The design provides a facile strategy for enhanced trans cleavage of Cas12a, which accelerates and broadens its applications in biosensing. [ABSTRACT FROM AUTHOR]

The trans‐cleavage property of CRISPR‐Cas12a system makes it an excellent tool for disease diagnosis. Nevertheless, most methods based on CRISPR‐Cas system still require pre‐amplification of the target to achieve the desired detection sensitivity. Here we generate Framework‐Hotspot reporters (FHRs) with different local densities to investigate their effect on trans‐cleavage activity of Cas12a. We find that the cleavage efficiency increases and the cleavage rate accelerates with increasing reporter density. We further construct a modular sensing platform with CRISPR‐Cas12a‐based target recognition and FHR‐based signal transduction. Encouragingly, this modular platform enables sensitive (100 fM) and rapid (<15 min) detection of pathogen nucleic acids without pre‐amplification, as well as detection of tumor protein markers in clinical samples. The design provides a facile strategy for enhanced trans cleavage of Cas12a, which accelerates and broadens its applications in biosensing. [ABSTRACT FROM AUTHOR]

The detection of biomarkers using sensitive and selective analytical devices is critically important for the early stage diagnosis and treatment of diseases. The synergy between the high specificity of nucleic acid recognition units and the great sensitivity of electrochemical signal transductions has already shown promise for the development of efficient biosensing platforms. Yet nucleic-acid based electrochemical biosensors often rely on target amplification strategies (e.g., polymerase chain reactions) to detect analytes at clinically relevant concentration ranges. The complexity and time-consuming nature of these amplification methods impede moving nucleic acid-based electrochemical biosensors from laboratory-based to point-of-care test settings. Fortunately, advancements in nanotechnology have provided growing evidence that the recruitment of nanoscaled materials and structures can enhance the biosensing performance (particularly in terms of sensitivity and response time) to the level suitable for use in point-of-care diagnostic tools. This Review highlights the significant progress in the field of nucleic acid-based electrochemical nanobiosensing with the focus on the works published during the last five years. [ABSTRACT FROM AUTHOR]

Dynamic interactions of enzymes, including programmable configuration and cycling of enzymes, play important roles in the regulation of cellular metabolism. Here, we constructed a super DNA‐enzymes molecule (SDEM) that comprises at least two cascade enzymes and multiple linked DNA strands to control and detect metabolism. We found that the programmable SDEM, which comprises glucose oxidase (GOx) and horseradish peroxidase (HRP), has a 20‐fold lower detection limit and a 1.6‐fold higher reaction rate than free enzymes. An SDEM can be assembled and disassembled using a hairpin structure and a displacement DNA strand to complete multiple cycles. An entropically driven catalytic assembly (catassembly) enables different SDEMs to switch from an SDEM with GOx and HRP cascades to an SDEM with sarcosine oxidase (SOX) and HRP cascades in over six orders of magnitude less time than without the catassembly to detect different metabolisms (GO and sarcosine) on demand. [ABSTRACT FROM AUTHOR]

Dynamic interactions of enzymes, including programmable configuration and cycling of enzymes, play important roles in the regulation of cellular metabolism. Here, we constructed a super DNA‐enzymes molecule (SDEM) that comprises at least two cascade enzymes and multiple linked DNA strands to control and detect metabolism. We found that the programmable SDEM, which comprises glucose oxidase (GOx) and horseradish peroxidase (HRP), has a 20‐fold lower detection limit and a 1.6‐fold higher reaction rate than free enzymes. An SDEM can be assembled and disassembled using a hairpin structure and a displacement DNA strand to complete multiple cycles. An entropically driven catalytic assembly (catassembly) enables different SDEMs to switch from an SDEM with GOx and HRP cascades to an SDEM with sarcosine oxidase (SOX) and HRP cascades in over six orders of magnitude less time than without the catassembly to detect different metabolisms (GO and sarcosine) on demand. [ABSTRACT FROM AUTHOR]

Early screening and diagnosis are the most effective ways to prevent the occurrence and progression of cancers, thus many biosensing strategies have been developed to achieve economic, rapid, and effective detection of various cancer biomarkers. Recently, functional peptides have been gaining increasing attention in cancer-related biosensing due to their advantageous features of a simple structure, ease of synthesis and modification, high stability, and good biorecognition, self-assembly and antifouling capabilities. Functional peptides can not only act as recognition ligands or enzyme substrates for the selective identification of different cancer biomarkers but also function as interfacial materials or self-assembly units to improve the biosensing performances. In this review, we summarize the recent advances in functional peptide-based biosensing of cancer biomarkers according to the used techniques and the roles of peptides. Particular attention is focused on the use of electrochemical and optical techniques, both of which are the most commonly used techniques in the field of biosensing. The challenges and promising prospects of functional peptide-based biosensors in clinical diagnosis are also discussed. [ABSTRACT FROM AUTHOR]

Enzyme clustering is widely used in many organisms to increase the catalytic efficiency of cascade reactions. Inspired by nature, organizing enzymes within a cascade reaction also draws much attention in both basic research and industrial processes. An important step for organizing enzymes precisely in vitro is enzyme modification. However, modifying enzymes without sacrificing their activity remains challenging until now. For example, labeling enzymes with DNA, one of the well-established enzyme modification methods, has been shown to significantly reduce the enzymatic activity. Herein we report an enzyme conjugation method that can rescue the reduction of enzymatic activity caused by DNA labeling. We demonstrate that immobilizing DNA-modified enzymes on the vertex of TDNs (tetrahedral DNA nanostructures) enhances the enzymatic activity compared with their unmodified counterparts. Using this strategy, we have further developed an ultra-sensitive and high-throughput electrochemical biosensor for sarcosine detection, which holds great promise for prostate cancer screening. [ABSTRACT FROM AUTHOR]

Controlling the deposition and diffusion of adsorbed atoms (adatoms) on the surface of a solid material is vital for engineering the shape and function of nanocrystals. Here, we report the use of single‐stranded DNA (oligo‐adenine, oligo‐A) to encode the wettability of gold seeds by homogeneous gold adatoms to synthesize highly tunable plasmonic nanostructures. We find that the oligo‐A attachment transforms the nanocrystal growth mode from the classical Frank‐van der Merwe to the Volmer‐Weber island growth. Finely tuning the oligo‐A density can continuously change the gold‐gold contact angle (θ) from 35.1±3.6° to 125.3±8.0°. We further demonstrate the versatility of this strategy for engineering nanoparticles with different curvature and dimensions. With this unconventional growth mode, we synthesize a sub‐nanometer plasmonic cavity with a geometrical singularity when θ>90°. Superfocusing of light in this nanocavity produces a near‐infrared intraparticle plasmonic coupling, which paves the way to surface engineering of single‐particle plasmonic devices. [ABSTRACT FROM AUTHOR]

Controlling the deposition and diffusion of adsorbed atoms (adatoms) on the surface of a solid material is vital for engineering the shape and function of nanocrystals. Here, we report the use of single‐stranded DNA (oligo‐adenine, oligo‐A) to encode the wettability of gold seeds by homogeneous gold adatoms to synthesize highly tunable plasmonic nanostructures. We find that the oligo‐A attachment transforms the nanocrystal growth mode from the classical Frank‐van der Merwe to the Volmer‐Weber island growth. Finely tuning the oligo‐A density can continuously change the gold‐gold contact angle (θ) from 35.1±3.6° to 125.3±8.0°. We further demonstrate the versatility of this strategy for engineering nanoparticles with different curvature and dimensions. With this unconventional growth mode, we synthesize a sub‐nanometer plasmonic cavity with a geometrical singularity when θ>90°. Superfocusing of light in this nanocavity produces a near‐infrared intraparticle plasmonic coupling, which paves the way to surface engineering of single‐particle plasmonic devices. [ABSTRACT FROM AUTHOR]

Sensitive and accurate analysis of specific subpopulations in circulating extracellular vesicles (EVs) can provide a wealth of information for cancer diagnosis and management. Thus, we propose herein a new electrochemical biosensing method based on a proximity labeling-assisted click conjugation strategy. The method's core design is use of antibody-guided proximity labeling to equip target EVs with a large amount of alkyne groups, so that azide-tagged silver nanoparticles can be accurately loaded onto target EV surfaces, via click conjugation, to generate significant electrochemical responses. Adopting CD44-positive EVs as the model, the electrochemical method was demonstrated by analyzing target EVs across a wide linear range (103–109 particles/mL) with acceptable sensitivity and specificity. Satisfactory utility in clinical blood samples, and versatility with human epidermal growth factor receptor-2-positive EVs as alternative targets, were also shown. This method may thus provide a novel approach to specific subgroup analyses of circulating EVs, and is expected to offer reliable guidance for cancer diagnoses and management strategies. [ABSTRACT FROM AUTHOR]

DNA nanomachines with artificial intelligence have attracted great interest, which may open a new era of precision medicine. However, their in vivo behavior, including early diagnosis and therapeutic effect are limited by their targeting efficiency. Here, a tetrahedral DNA framework (TDF)‐based nanodevice for in vivo near‐infrared (NIR) diagnosis of early‐stage AKI is developed. This nanodevice comprises three functional modules: a size‐tunable TDF nanostructure as kidney‐targeting vehicle, a binding module for the biomarker kidney injury molecule‐1 (Kim‐1), and a NIR signaling module. The cooperation of these modules allows the nanodevice to be selectively accumulated in injured kidney tissues with high Kim‐1 level, generating strong NIR fluorescence; whereas the nanodevice with the proper size can be rapidly cleared in healthy kidneys to minimize the background. By using this nanodevice, the early diagnosis of AKI onset is demonstrated at least 6 h ahead of Kim‐1 urinalysis, or 12 h ahead of blood detection. It is envisioned that this TDF‐based nanodevice may have implications for the early diagnosis of AKI and other kidney diseases. [ABSTRACT FROM AUTHOR]

Multivalent interactions of biomolecules play pivotal roles in physiological and pathological settings. Whereas the directionality of the interactions is crucial, the state‐of‐the‐art synthetic multivalent ligand–receptor systems generally lack programmable approaches for orthogonal directionality. Here, we report the design of programmable atom‐like nanoparticles (aptPANs) to direct multivalent aptamer–receptor binding on the cell interface. The positions of the aptamer motifs can be prescribed on tetrahedral DNA frameworks to realize atom‐like orthogonal valence and direction, enabling the construction of multivalent molecules with fixed aptamer copy numbers but different directionality. These directional‐yet‐flexible aptPAN molecules exhibit the adaptability to the receptor distribution on cell surfaces. We demonstrate the high‐affinity tumor cell binding with a linear aptPAN oligomer (≈13‐fold improved compared to free aptamers), which leads to ≈50 % suppression of cell growth. [ABSTRACT FROM AUTHOR]

Multivalent interactions of biomolecules play pivotal roles in physiological and pathological settings. Whereas the directionality of the interactions is crucial, the state‐of‐the‐art synthetic multivalent ligand–receptor systems generally lack programmable approaches for orthogonal directionality. Here, we report the design of programmable atom‐like nanoparticles (aptPANs) to direct multivalent aptamer–receptor binding on the cell interface. The positions of the aptamer motifs can be prescribed on tetrahedral DNA frameworks to realize atom‐like orthogonal valence and direction, enabling the construction of multivalent molecules with fixed aptamer copy numbers but different directionality. These directional‐yet‐flexible aptPAN molecules exhibit the adaptability to the receptor distribution on cell surfaces. We demonstrate the high‐affinity tumor cell binding with a linear aptPAN oligomer (≈13‐fold improved compared to free aptamers), which leads to ≈50 % suppression of cell growth. [ABSTRACT FROM AUTHOR]

A DNA origami nanocaliper is employed as a shape-resolved nanomechanical device, with pH-responsive triplex DNA integrated into the two arms. The shape transition of the nanocaliper results in a subtle difference depending on the local pH that is visible via TEM imaging, demonstrating the potential of these nanocalipers to act as a universal platform for pH sensing at the nanoscale. [ABSTRACT FROM AUTHOR]

Advances in bioimaging technologies have led to unprecedented findings of novel biological processes at the nanoscale. However, there remains an ever-lasting demand for the improvement of spatiotemporal resolution, multiplexity, and smart responsiveness of bioimaging in living systems. In recent decades, self-assembled DNA nanostructures with highly programmable shape, nanometer addressability, and structural responsiveness have shown great promise in developing nanoscale probes and labels for high-performance bioimaging. Here, we briefly review the recent progress in structural DNA nanotechnology and the development of DNA frameworks, and summarize the bioimaging strategies empowered by DNA nanotechnology. We highlight the advantages of DNA nanostructures in overcoming the bottlenecks in bioimaging and discuss the challenges and opportunities in this field. [ABSTRACT FROM AUTHOR]

The response sensitivity of a molecular sensor is determined by the folding cooperativity of its responsive module. Using an H+-responsive dimeric DNA i-motif as a model, we demonstrate the enhancement of its folding cooperativity through preorganization by a DNA framework, and with it we fabricate robust intracellular pH sensors with high response sensitivity. [ABSTRACT FROM AUTHOR]

Variation of DNA conformation is important in regulating gene expression and mediating drug‐DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label‐free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i‐motifs, G‐quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label‐free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells. [ABSTRACT FROM AUTHOR]

Variation of DNA conformation is important in regulating gene expression and mediating drug‐DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label‐free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i‐motifs, G‐quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label‐free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells. [ABSTRACT FROM AUTHOR]

Molecular recognition in cell biological process is characterized with specific locks‐and‐keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically‐engineered ligand systems enable the exploration of the binding strength between ligand‐receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10‐fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands. [ABSTRACT FROM AUTHOR]

Molecular recognition in cell biological process is characterized with specific locks‐and‐keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically‐engineered ligand systems enable the exploration of the binding strength between ligand‐receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10‐fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands. [ABSTRACT FROM AUTHOR]

Aligning carbon nanotubes (CNTs) is a key challenge for fabricating CNT‐based electronic devices. Herein, we report a spherical nucleic acid (SNA) mediated approach for the highly precise alignment of CNTs at prescribed sites on DNA origami. We find that the cooperative DNA hybridization occurring at the interface of SNA and DNA‐coated CNTs leads to an approximately five‐fold improvement of the positioning efficiency. By combining this with the intrinsic positioning addressability of DNA origami, CNTs can be aligned in parallel with an extremely small angular variation of within 10°. Moreover, we demonstrate that the parallel alignment of CNTs prevents incorrect logic functionality originating from stray conducting paths formed by misaligned CNTs. This SNA‐mediated method thus holds great potential for fabricating scalable CNT arrays for nanoelectronics. [ABSTRACT FROM AUTHOR]

Aligning carbon nanotubes (CNTs) is a key challenge for fabricating CNT‐based electronic devices. Herein, we report a spherical nucleic acid (SNA) mediated approach for the highly precise alignment of CNTs at prescribed sites on DNA origami. We find that the cooperative DNA hybridization occurring at the interface of SNA and DNA‐coated CNTs leads to an approximately five‐fold improvement of the positioning efficiency. By combining this with the intrinsic positioning addressability of DNA origami, CNTs can be aligned in parallel with an extremely small angular variation of within 10°. Moreover, we demonstrate that the parallel alignment of CNTs prevents incorrect logic functionality originating from stray conducting paths formed by misaligned CNTs. This SNA‐mediated method thus holds great potential for fabricating scalable CNT arrays for nanoelectronics. [ABSTRACT FROM AUTHOR]

Development of new nanostructured materials has shown high impact for improving the performance of chemical and biological sensors. In this work, we show that by controlling the dimensions of the gold flower microelectrode (GFME), it is possible to regulate detection sensitivity of a sensor for rapid analysis of chemical species. A ~13-fold increase in sensitivity was achieved by enlarging the dimension of GFMEs from 70 to 330 μm, whereas the response dynamics are dimension-independent, with the signal attaining saturation ~20 s. Due to the intrinsic nanostructure on the microelectrode surface, our GFME exhibits excellent anti-interference property when applied to detect dopamine (DA) in the presence of 10-fold excess of ascorbic acid (AA). The regulable sensitivity, fast response dynamics, and excellent anti-interference property will make GFME an ideal sensing platform for biomedical applications. [ABSTRACT FROM AUTHOR]

Natural ion channels on cell membrane can gate the transport of ions and molecules by the conformational alteration of transmembrane proteins to regulate the normal physiological activities of cells. Inspired by the similarity of the conformation change under specific stimuli, here we introduce an ion channel gating model on a single nanoelectrode by anchoring DNA-gated switches on the very nanotip of gold nanoelectrode to mimic the response-to-stimulus behaviors of ion channels on bio-membranes. The surface-tethered DNA ion channels can be switched on by the Watson-Crick base pairing, which can alter the conformation of the tethered DNA from lying state to upright state. And these conformational alterations of the anchored DNA switches can effectively gate the transport of potassium ferricyanide onto the electrode interface. By continuously initiating the gates with DNA of different concentrations, we achieved the stepping gating of ion channels on a single nanoelectrode. Further, we demonstrated that the ion gating system on nanoelectrode showed excellent sensing performance. For example, the response kinetic was very fast with the signal saturation time of ~1 min, the reproducibility of the OFF/ON switch was robust enough to sustain for two cycles, and simultaneously, the specificity was high enough to distinguish complementary DNA and noncomplementary DNA. When used for label-free DNA detection, the limit of detection can be as low as 10 pM. This study provides a promising avenue to achieve label free and real-time detection of multiple biomolecules. • Stimulus responsive ion channels on nanoelectrode interface. • Stepping gating of ion channels by DNA hybridization. • Fast response kinetics, high specificity and excellent reproducibility of the ion gating system. • Label-free DNA detection with the LOD of 10 pM. [ABSTRACT FROM AUTHOR]

Highly efficient transmembrane transport of exogenous reagents into cells is of vital importance for developing drug‐delivery systems. Conventionally, transmembrane transport of exogenous reagents was accomplished with the assistance of transfection agents or other artificial means. However, the high toxicity and low transport efficiency of current delivery techniques still remain to be solved. In this work, by anchoring artificial receptors onto cell membranes with a mild chemical reaction, we demonstrated that the exogenous reagent framework nucleic acids, namely tetrahedral DNA nanostructures (TDN) can bind onto cell membranes effectively by the hybridization between single‐stranded DNA (ssDNA) and pendant ssDNA of TDN. The transport rate was greatly enhanced, with the endocytosis time could be as fast as 0.5 h. Furthermore, the transport quantity was prominently improved, with around 30 % of TDN endocytosed within 4 h. Owing to its rapid transmembrane transport speed and improved endocytosis quantity, this artificial‐receptor‐mediated transmembrane transport is a promising tool for achieving rapid and highly efficient transmembrane transport of exogenous reagents. [ABSTRACT FROM AUTHOR]

Abstract DNA-gold nanoparticles (AuNPs) conjugate is one of the most versatile bionanomaterials for biomedical and clinical diagnosis. However, to finely tune the hybridization ability and precisely control the orientation and conformation of surface-tethered oligonucleotides on AuNPs remains a hurdle. In this work, we developed a poly adenine-mediated spherical nucleic acid (polyA-mediated SNA) strategy by assembling di-block DNA probes on gold nanoparticles (AuNPs) to spatially control interdistance and hybridization ability of oligonucleotides on AuNPs. By modulating length of poly A bound on the SNA with different degrees of constructing, we presented significant improved biosensing performance including high hybridization efficiency, and expanded dynamic range of analytes with more sensitive detection limit. Furthermore, this polyA design could facilitate the programmable detection for DNA in serum environment and simultaneous multicolor detection of three different microRNAs associated with pancreatic carcinoma. The demonstration of the link between modulation of SNA assembly strategy and biodetection capability will increase the development of high performance diagnostic tools for translational biomedicine. Highlights • Poly adenines (polyA)-mediated spherical nucleic acid assembly strategy was developed. • Poly adenines assembly could systematically modulate the lateral spacing and surface density of DNA on AuNPs. • A panel of three pancreatic carcinoma associated miRNAs was simultaneously detected. [ABSTRACT FROM AUTHOR]

Abstract: Weak ligand–receptor recognition events are often amplified by recruiting multiple regulatory biomolecules to the action site in biological systems. However, signal amplification in in vitro biomimetic systems generally lack the spatiotemporal regulation in vivo. Herein we report a framework nucleic acid (FNA)‐programmed strategy to develop valence‐controlled signal amplifiers with high modularity for ultrasensitive biosensing. We demonstrated that the FNA‐programmed signal amplifiers could recruit nucleic acids, proteins, and inorganic nanoparticles in a stoichiometric manner. The valence‐controlled signal amplifier enhanced the quantification ability of electrochemical biosensors, and enabled ultrasensitive detection of tumor‐relevant circulating free DNA (cfDNA) with sensitivity enhancement of 3–5 orders of magnitude and improved dynamic range. [ABSTRACT FROM AUTHOR]

Abstract: Weak ligand–receptor recognition events are often amplified by recruiting multiple regulatory biomolecules to the action site in biological systems. However, signal amplification in in vitro biomimetic systems generally lack the spatiotemporal regulation in vivo. Herein we report a framework nucleic acid (FNA)‐programmed strategy to develop valence‐controlled signal amplifiers with high modularity for ultrasensitive biosensing. We demonstrated that the FNA‐programmed signal amplifiers could recruit nucleic acids, proteins, and inorganic nanoparticles in a stoichiometric manner. The valence‐controlled signal amplifier enhanced the quantification ability of electrochemical biosensors, and enabled ultrasensitive detection of tumor‐relevant circulating free DNA (cfDNA) with sensitivity enhancement of 3–5 orders of magnitude and improved dynamic range. [ABSTRACT FROM AUTHOR]

Electrochemical DNA biosensor has unique advantages for on-site pathogenic microorganism detection, yet the detection of long DNA towards genome DNA (gDNA) analysis remains challenge. In this work, we report a novel electrochemical biosensor for the ultrasensitive analysis of mecA DNA on methicillin-resistant Staphylococcus aureus (MRSA) genome, using a multi-signal probes (MSP) system. The MSP consists of 7 biotin-labelled signal probes that will combine to the target DNA in a prehybridization step, and then the complex will be captured by a DNA tetrahedron structure probe (TSP) on the electrode surface. Then, after the introduction of the streptavidin-labelled HRP enzyme, a catalysis current signal is detected that is found to be corresponding to the concentration of the target DNA. MSP in this work plays a critical role not only for the signal amplification through bringing 7 biotins, but also dramatically improves the accessibility of the target sequence embedded in the double-strand DNA molecules and complex second structures. The 3-D DNA TSP here provides steady support and optimized surface density for the very "large" complex of MSP system and gDNA, as a base of the capture probe. Finally, as low as 10 fM synthetic target DNA was successfully detected, which is at least 3 magnitudes lower than that using single signal probe. Most importantly, we demonstrated the practicability of our analysis method by analyzing a 57 fM MRSA gDNA sample showing excellent selectivity, and the reliability of the analysis was also demonstrated by digital PCR. [ABSTRACT FROM AUTHOR]

Precise control over the valency of quantum dots (QDs) is critical and fundamental for quantitative imaging in living cells. However, prior approaches on valence control of QDs remain restricted to single types of valences. A DNA-programmed general strategy is presented for valence engineering of QDs with high modularity and high yield. By employing a series of programmable DNA scaffolds, QDs were generated with tunable valences in a single step with near-quantitative yield (>95 %). The use of these valence-engineered QDs was further demonstrated to develop 12 types of topologically organized QDs-QDs and QDs-AuNPs and 4 types of fluorescent resonance energy transfer (FRET) nanostructures. Quantitative analysis of the FRET nanostructures and live-cell imaging reveal the high potential of these nanoprobes in bioimaging and nanophotonic applications. [ABSTRACT FROM AUTHOR]

Precise control over the valency of quantum dots (QDs) is critical and fundamental for quantitative imaging in living cells. However, prior approaches on valence control of QDs remain restricted to single types of valences. A DNA-programmed general strategy is presented for valence engineering of QDs with high modularity and high yield. By employing a series of programmable DNA scaffolds, QDs were generated with tunable valences in a single step with near-quantitative yield (>95 %). The use of these valence-engineered QDs was further demonstrated to develop 12 types of topologically organized QDs-QDs and QDs-AuNPs and 4 types of fluorescent resonance energy transfer (FRET) nanostructures. Quantitative analysis of the FRET nanostructures and live-cell imaging reveal the high potential of these nanoprobes in bioimaging and nanophotonic applications. [ABSTRACT FROM AUTHOR]