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Tumor‐derived small extracellular vesicles (sEVs) are proven to play important roles in accelerating the progression of tumors. Destructing the sEVs at tumor sites is therefore a promising route to inhibit tumor progression. Herein, a smart DNA network‐based sEV trap (DNET) is reported, which achieved the specific capture of tumor‐derived sEVs through recognizing sEVs by polyaptamers, and the efficient destruction of sEVs via a photodynamic process at tumor sites. The DNET is constructed through the assembly of two DNA chains generated via rolling circle amplification. The DNA chains contain polyaptamers for capturing sEVs, polyvalent G‐quadruplexes for loading photodynamic reagents, and complementary segments for forming a cross‐linked network. Upon the irradiation of the laser, the captured sEVs in DNET are destructed, causing significant inhibition effects on the migration, invasion, and proliferation of glioblastoma cells. In particular, DNET achieved tumor inhibition rates of 39.70% in the zebrafish tumor model, and 73.10% in the nude mouse tumor model, respectively, demonstrating the significant efficacy of DNET in inhibiting tumor progression. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: Deoxyribonucleic acid (DNA) is a biomacromolecule, as well as a polymeric material, whose sequences with different manipulative structures enable them to implement a series of functions, such as reorganization, target, and catalysis. Compared to existing traditional materials incapable of multifunctional integration, the polymeric DNA network is a form of material that can achieve functional integration while maintaining specific DNA properties. Furthermore, precise target enabled by DNA network is one of the most essential components of cellular manipulation. Hence, the DNA network is indispensable and irreplaceable to cell manipulation that it is a versatile tool for the understanding of basic laws of living life and treatments of diseases, such as cell isolation, cell delivery, and cell interference. Herein, the construction of polymeric DNA network is briefly introduced from the aspects of assembly modules, construction methods, and properties. Subsequently, the applications of DNA network in the field of cell manipulation, including cell isolation and encapsulation, intracellular inference and detection, and tumor therapy are summarized. Finally, we provide some prospects for further research and applications of DNA network for cell manipulation. [ABSTRACT FROM AUTHOR]

Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects.

Organic photoelectrochemical transistor (OPECT) biosensor is now appearing in perspective of public, which characterized by amplified the grating electrode potential by ion transport. In this study, the DNA network formed by the hybridization chain reaction (HCR) detects the target adenosine triphosphate (ATP) by adjusting the surface potential of the new heterojunction of ZnIn 2 S 4 /MXene. The formation of DNA network amplifies the detection signal of ATP. Significantly, OPECT biosensor could further amplify the signal, which calculated the gain achieved 103, which is consistent with the gain signal of the previously reported OPECT biosensor. Furthermore, the OPECT biosensor achieved a highly sensitivity detection of the target ATP, which the linear detection range is 0.03 pM–30 nM, and the detection limit is 0.03 pM, and illustrated a high selectivity to ATP. The proposed OPECT biosensor achieved signal amplification by adjusting the surface potential of ZnIn 2 S 4 /MXene through cascade DNA network, which provides a new direction for the detection of biomolecules. We designed an ultrasensitive method for organic photoelectrochemical transistor detection of ATP based on DNA network structure modulated ZnIn 2 S 4 /MXene schottky junction. [Display omitted] • A new Schottky junction of MXene/ZnIn 2 S 4 is applied to organic phototransistors. • An enzyme-free labelled DNA-assisted isothermal amplification system was designed. • The detection of ATP with organic photoelectrochemical transistor was realized. [ABSTRACT FROM AUTHOR]

Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhang and Sun.)

Abstract: In this paper, a uniform calf thymus deoxyribonucleic acid (DNA) network has been constructed on a bare mica surface using a simple adsorption method. The effect of the immersion time in water on the characteristics of the morphological transitions of DNA molecules adsorbed on the mica surface was investigated by atomic force microscopy. It was found that the DNA molecules underwent conformational transitions from stretched wormlike coil to rod and to network by changing the immersion time in water and the formation mechanism was explained briefly. [Copyright &y& Elsevier]

The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.

• Proximity binding-induced DNA network for thrombin analysis was developed. • DNA network endowed the electrochemical biosensor with high sensitivity. • The biosensor enabled detection of thrombin in serum samples. The abnormal change of thrombin concentration is closely related with various diseases. By using proximity binding-induced DNA network assembled by nonlinear hybridization chain reaction (HCR), we here developed an enzyme-free and ultrasensitive electrochemical strategy for analyzing thrombin in human serums. The binding of the two different aptamers to a thrombin enhanced the local concentration of the aptamers and facilitates the formation of an intact strand. Subsequently, the formed strand caused nonlinear HCR, forming DNA network. The DNA network bound to the capture probes (CP)-modified electrode, producing electrochemical signal of MB. Benefiting from the proximity binding-induced DNA network, the proposed biosensor exhibited a wide linear range from 1.0 pM to 1.0 nM with a low detection limit of 0.56 pM and high specificity. More importantly, the developed enzyme-free electrochemical biosensor has been used to detect thrombin in serum samples with good performance. This makes such a strategy possess potential promise in the application of clinical diagnosis. [ABSTRACT FROM AUTHOR]

of molecular species is needed for applications in diagnosis of infections and genetic diseases. Herein, we demonstrate a target DNA-responsive ultrahigh fluorescence signal-on DNA amplification system via periodically programmed building and collapse of DNA networks. In this system, a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP) are utilized. The presence of target DNA firstly hybridizes with PP, allowing the occurrence of rolling circle amplification (RCA) to produce RCA products with tandem repeats in abundance to bind and unfold numbers of PHPs. The conformational change of PHPs enables the building of DNA networks via the intermolecular palindrome pairing, but then makes the DNA networks collapsed via the palindrome-induced strand displacement polymerization. The displaced RCA products are dynamically reused to undergo periodically programmed multiple rounds of DNA network building and collapse. Depend on the bidirectional DNA assembly and disassembly, a strikingly amplified fluorescence can be collected to ultrasensitive and specific detection of target DNA. The practicability has been demonstrated by evaluating target-spiked human serum, saliva, and urine samples with acceptable recoveries and reproducibility. Therefore, this newly explored method opens a promising avenue for the detection of nucleic acids with low abundance in biochemical analysis and diseases diagnosis. Image 1 • A target DNA-responsive amplification system via programmed building and collapse of DNA networks has been built. • The dynamic DNA assembly requires a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP). • The target DNA can be detected depend on the bidirectional manner of DNA assembly and disassembly to amplify fluorescence. • The practicability for analyzing target from human serum, saliva samples has been demonstrated. [ABSTRACT FROM AUTHOR]

• Based on the RCA-DLS strategy of RCA-DNA-AuNPs polymer with network for the ultrasensitive and specific detection of miRNA. • The tandem repeat stem-ring structure of the RCA products induced the self-assembly of DNA-AuNPs. • The RCA-DLS biosensing platform can be used for detection of let-7a in small RNA samples extracted from Hela cells. In this paper, rolling circle amplification (RCA) -based self-assembly DNA network was developed for ultrasensitive and specific detection of microRNA (miRNA) with dynamic light scattering (DLS) technology. A dumbbell-shaped padlock probe was designed, which could be connected with itself as a template under the action of T4 DNA ligase to form a dumbbell-shaped sealed probe. In the presence of the target miRNA, the miRNA bound to the toehold domain of the sealed probe. The sealed probe was activated into a circular probe to start RCA reaction by a spontaneous chain displacement reaction. The DNA functionalized AuNPs probe was hybridized with the RCA products to form RCA-DNA-AuNPs polymer with network, whose diameter was measured by DLS. Not only did this method greatly improve the sensitivity of detection, but the specificity of detection increased by using sealed probe as well. The limit of detection (LOD) was 0.11 fM. Furthermore, this strategy has been successfully used to analyze target miRNA in cancer cell samples, which confirmed that RCA-DLS analysis has broad application prospects in early clinical diagnosis. [ABSTRACT FROM AUTHOR]