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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]

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]

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]

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]

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]

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]

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]

DNA is the primary genetic material that is highly compatible with biological system, and its intrinsic property of complementary base pairing can be programmed for analysis. However, single-stranded DNA probes present challenges as they are difficult to internalize into cells and can easily decompose in the cell microenvironment. In recent years, the development of framework nucleic acids (FNAs) has enabled DNA nanostructures to emerge as promising materials for bioimaging, drug delivery, and biosensor design. These probes offer several advantages, including high biological stability, efficient cell internalization, low dynamic limitations, and diverse signal output. Therefore, it is important to review and summarize the critical role of framework design in DNA-based biosensor construction for the advancement of DNA nanotechnology and its application in bioanalysis. This article provides an overview of the development and limitations of DNA nanostructures in different dimensions and highlights the endocytosis of tetrahedral DNA frameworks (TDF) and their applications in biosensing and imaging. Finally, existing signal output modes are introduced to provide a comprehensive understanding of the potential applications of TDF. [Display omitted] • A comprehensive review on the structure and performance of tetrahedral DNA frameworks (TDF) is reported. • Different intracellular targets detected by TDF-based probes are discussed. • Multiple signal output modes using TDF are summarized. • The challenges and clinical barriers of TDF are also listed. [ABSTRACT FROM AUTHOR]

DNA nanostructures are among the most fascinating self-assembled nanostructures in diverse areas of science and technology, because of their nanoscale precision in biomolecule and nanoparticle organization. The implementation of dynamic and spatial regulation in structural morphology and hierarchical assembly upon specific external stimuli will greatly expand their applications in biocomputation, clinical diagnosis, and cancer therapy. Recently, noncanonical nucleic acids, particularly DNA triplexes, i-motifs, and G-quadruplexes, have become powerful tools for biosensing and mechanical switching. Developments in incorporating stimuli-responsive noncanonical nucleic acids into DNA nanostructures provide a promising approach to regulating the spatial organization and hierarchical assembly of DNA nanostructures. In this review, we briefly introduce recent progress in constructing DNA nanostructures with dynamic regulation of the structural transformation and programmable assembly pathways at the nanometer scale by noncanonical nucleic acids and discuss their potential applications and challenges. DNA double helix exploiting Watson–Crick base-pairing lays the foundation of DNA nanotechnology. However, other forms of nucleic acids (e.g., triplex, i-motif, and G-quadruplex) exhibiting noncanonical base-base interactions bring about novel functionality. Here, we review the interplay of naturally occurring noncanonical nucleic acids and artificial DNA nanostructures in biomedical applications that have not been possible by duplex formation alone. [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]

DNA nanostructures have attracted considerable attention as drug delivery carriers. However, the transmembrane kinetics of DNA nanostructures remains less explored. Herein, the dynamic process of transporting single tetrahedral DNA nanostructures (TDNs) is monitored in real time using a force‐tracing technique based on atomic force microscopy. The results show that transporting single TDNs into living HeLa cells need ≈53 pN force and ≈25 ms duration with the average speed of ≈0.6 µm s−1. Interestingly, the dynamic parameters are irrelevant to the size of TDNs, while the larger TDNs rotated slightly during the transporting process. Meanwhile, both the results from single‐molecule force tracing and ensemble fluorescence imaging demonstrate that the different size TDNs transmembrane transporting depends on caveolin‐mediated endocytosis. [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]

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]

DNA-based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)-powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)-based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt-bridge mechanism. The operation of this Exo III-propelled DNA walker was monitored in real time and at the single-particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA-based stochastic DNA walker by exploiting movement-triggered cascade signal amplification. [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]