Displacement Reaction Research Articles

Discrimination of Multiple Homologous Sequences Based on DNA Logic Gate and Elemental Labeling Technology.

The simultaneous discrimination of multiple homologous sequences faces challenges due to the high similarity of sequences and the complexity of the discrimination system in most reported works. Herein, a simple and ingenious analysis method was developed to identify eight miRNAs of the let-7 family by combining logic gates and entropy-driven catalytic (EDC)-based lanthanide labeling inductively coupled plasma mass spectrometry (ICP-MS) technology. Specifically, eight miRNAs were first divided into four types according to the difference of bases in the domains 2 and 3 on sequences. To identify the type of targets, a DNA logic gate was constructed with two strand displacement reactions on magnetic beads that could be initiated by different types of targets. Based on the difference of the output signals after two strand displacement reactions, the type of targets was distinguished preliminarily. Then, the discrimination of a specific target was achieved with EDC-based lanthanide labeling ICP-MS detection. By labeling the different magnetic probes with different elemental tags, a specific element signal released from magnetic beads after EDC could be detected by ICP-MS, and therefore, simultaneous detection of homologous sequences was completed. This work provided a novel and simple method for highly specific identification of homologous sequences with the assistance of a logic gate and can promote further development of elemental labeling ICP-MS in the field of multiple analysis.

An enzyme-free and ratiometric biosensor for single nucleotide polymorphism with portable electrochemical system

Portable, low-cost and efficient biosensing systems are valuable for single nucleotide polymorphisms (SNPs) analysis, particularly in resource-limited fields. Herein, a rapid, enzyme-free and ratiometric SNPs biosensor with portable electrochemical system enabling simultaneous recognition and signal amplification is proposed. To demonstrate its versatility and effectiveness, we have selected the human cancer-related KRAS gene and the soybean mosaic virus resistance Rsv3 gene as our analysis models. Our biosensor is constructed based on a combination of strand displacement reactions and hybridization chain reactions (HCR). This unique design enables to differentiate between mutant (MT) and wild (WD) sequences based on the differential release of HCR products on the electrode surfaces. Importantly, this enzyme-free SNPs biosensor concurrently achieves both SNPs recognition and signal amplification, significantly reducing the reaction time to just 40 minutes. Furthermore, we have developed a miniaturized biosensor system that incorporates screen printed gold electrodes (SPGE) and smartphones. This system is integrated with a ratiometric strategy with an limit of detection as low as 1.2 fM, enhancing accuracy and eliminating external interference. This simple SNPs biosensing system possesses high reliability, positioning it as a versatile biosensor for the determination of various SNPs mutations.

A DNA circuit that records molecular events.

Characterizing the relative onset time, strength, and duration of molecular signals is critical for understanding the operation of signal transduction and genetic regulatory networks. However, detecting multiple such molecules as they are produced and then quickly consumed is challenging. A MER can encode information about transient molecular events as stable DNA sequences and are amenable to downstream sequencing or other analysis. Here, we report the development of a de novo molecular event recorder that processes information using a strand displacement reaction network and encodes the information using the primer exchange reaction, which can be decoded and quantified by DNA sequencing. The event recorder was able to classify the order at which different molecular signals appeared in time with 88% accuracy, the concentrations with 100% accuracy, and the duration with 75% accuracy. This simultaneous and highly programmable multiparameter recording could enable the large-scale deciphering of molecular events such as within dynamic reaction environments, living cells, or tissues.

Comparative Study of Static and Dynamic Analysis of Multistoried Building

In a moderate seismic activity, relying solely on the static force method to estimate the seismic force assessing the vulnerability and behaviour of RCC buildings under seismic loads is insufficient. The seismic response of the building system is highly influenced by the analysis method adopted. In the past years, static approaches were preferred due to their simplicity, although these methods provided safe design, they may have been overly cautious. Dynamic analysis, on the other hand, is a fundamental aspect of structural mechanics, that describes and predicts the behaviour of structures subjected to dynamic loads. Dynamic load includes wind, imposed load, earthquake, etc. Dynamic analysis techniques, such as modal analysis, time history analysis, and dynamic displacement analysis. RCC structures are mainly designed to resist static load. This process of ignoring dynamic events sometimes becomes the cause of disasters, especially in the case of earthquakes. This research paper provides information on the comparison of various parameters in static and dynamic analysis. Two RCC multistoried residential buildings (g+10 and g+25) acting on seismic zone IV are analyzed using the static analysis method and response spectrum method with ETABS 16. The research investigates the effect on various structural parameters such as story displacement, story drift, and support reactions. The results are compared and evaluated to assess the performance of the response spectrum method over the static analysis method.

Construction of an artificial zinc alloy layer toward stable zinc-metal anode

Aqueous zinc-ion batteries (AZIBs) present a promising option for next-generation batteries given their high safety, eco-friendliness, and resource sustainability. Nonetheless, the practical application of zinc anodes is hindered by inevitable parasitic reactions and dendrite growth. Here, zinc alloy layers (i.e., ZnCo and ZnFe alloys) were rationally constructed on the zinc surface by chemical displacement reactions. The alloying process exposes more (002) planes of the ZnCo anode to guide the preferential and dendrite-free zinc deposition. Furthermore, the ZnCo alloy layer not only effectively inhibits water-induced side reactions but also accelerates electrode kinetics, enabling highly reversible zinc plating/stripping. As a result, the ZnCo anode achieves a Coulombic efficiency of 99.2% over 1300 cycles, and the ZnCo symmetric cell exhibits a long cycle life of over 2000 h at 4.4 mA cm−2. Importantly, the ZnCo//NH4V4O10 full cell retains a high discharge capacity of 218.4 mAh g−1 after 800 cycles. Meanwhile, the ZnFe-based symmetric cell also displays excellent cycling stability over 2500 h at 1.77 mA cm−2. This strategy provides a facile anode modification approach toward high-performance AZIBs.

Dual toeholds regulated CRISPR-Cas12a sensing platform for ApoE single nucleotide polymorphisms genotyping

Single nucleotide polymorphisms (SNPs) are closely associated with many biological processes, including genetic disease, tumorigenesis, and drug metabolism. Accurate and efficient SNP determination has been proved pivotal in pharmacogenomics and diagnostics. Herein, a universal and high-fidelity genotyping platform is established based on the dual toeholds regulated Cas12a sensing methodology. Different from the conventional single stranded or double stranded activation mode, the dual toeholds regulated mode overcomes protospacer adjacent motif (PAM) limitation via cascade toehold mediated strand displacement reaction, which is highly universal and ultra-specific. To enhance the sensitivity for biological samples analysis, a modified isothermal recombinant polymerase amplification (RPA) strategy is developed via utilizing deoxythymidine substituted primer and uracil-DNA glycosylase (UDG) treatment, designated as RPA-UDG. The dsDNA products containing single stranded toehold domain generated in the RPA-UDG allow further incorporation with dual toeholds regulated Cas12a platform for high-fidelity human sample genotyping. We discriminate all the single-nucleotide polymorphisms of ApoE gene at rs429358 and rs7412 loci with human buccal swab samples with 100% accuracy. Furthermore, we engineer visual readout of genotyping results by exploiting commercial lateral flow strips, which opens new possibilities for field deployable implementation.

Label-free and portable detection of HIV-DNA by a handheld luminometer

BackgroundThe human immunodeficiency virus (HIV) remains a major worldwide health problem. Nowadays, many methods have been developed for quantitative detecting human immunodeficiency virus DNA (HIV-DNA), such as fluorescence and colorimetry. However, these methods still have the disadvantages of being expensive and requiring professional technicians. Early diagnosis of pathogens is increasingly dependent on portable instruments and simple point-of-care testing (POCT). Therefore, it is meaningful and necessary to develop portable and cheap methods for detecting disease markers. ResultsIn this work, a label-free chemiluminescence (CL) method was developed for detecting HIV-DNA via a handheld luminometer. To achieve label-free target detection, the CL catalyst, G-triplex-hemin DNAzyme (G3-hemin DNAzyme), was in-situ assembled in the presence of HIV-DNA. For improving sensitivity, HIV-DNA induced the cyclic strand displacement reaction (SDR), which can form three G3-hemin DNAzymes in one cycle. So, the chemiluminescence reaction between luminol and H2O2 was highly effectively catalyzed, and the CL intensity was linearly related with the concentration of HIV-DNA in the range of 0.05–10 nM with a detection limit of 29.0 pM. Due to the high specificity of hairpin DNA, single-base mismatch can be discriminated, which ensured the specific detection of HIV-DNA. SignificanceIn-situ formation of G3-hemin DNAzyme led to label-free and selective detection without complex synthesis and functionalization. Therefore, it offers a cheap, selective, sensitive and portable method for detecting disease-related genes, which is promising for POCT of clinical diagnosis in resource-limited settings.

Study on the corrosion behavior of L245 pipeline steel in 100LL aviation gasoline wastewater

The study investigates the corrosion behavior of L245 pipeline steel exposed to 100LL aviation gasoline-contaminated water. The investigation includes analyzing the corrosion rate, morphological changes, and product composition, as well as changes in wastewater ion concentration. Samples of contaminated water were collected and subjected to analytical techniques such as electrochemical testing, morphology characterization, and component analysis. The findings reveal severe corrosion of the specimens, with significant alterations in morphology and product composition. The study reveals that the specimens experienced severe corrosion in the contaminated water environment, with a corrosion rate reaching 0.387 mm/year. Following corrosion, a relatively complete dark green covering layer formed on the specimen surfaces. Moreover, significant alterations in morphology and product composition were observed. Additionally, changes in wastewater ion concentration before and after the reaction were noted. The failure of corrosion of the specimens is due to oxygen uptake and displacement reactions between the iron in the specimens and the Cu2+ in the wastewater, resulting in the dissolution of the basal iron and an increase in the corrosion rate due to the presence of Cu2+.

Driving inward growth of lithium metal in hollow microcapsule hosts by heteroatom‐controlled nucleation

AbstractThe application of Li metal anodes in rechargeable batteries is impeded by safety issues arising from the severe volume changes and formation of dendritic Li deposits. Three‐dimensional hollow carbon is receiving increasing attention as a host material capable of accommodating Li metal inside its cavity; however, uncontrollable and nonuniform deposition of Li remains a challenge. In this study, we synthesize metal–organic framework‐derived carbon microcapsules with heteroatom clusters (Zn and Ag) on the capsule walls and it is demonstrated that Ag‐assisted nucleation of Li metal alters the outward‐to‐inward growth in the microcapsule host. Zn‐incorporated microcapsules are prepared via chemical etching of zeolitic imidazole framework‐8 polyhedra and are subsequently decorated with Ag by a galvanic displacement reaction between Ag+ and metallic Zn. Galvanically introduced Ag significantly reduces the energy barrier and increases the reaction rate for Li nucleation in the microcapsule host upon Li plating. Through combined electrochemical, microstructural, and computational studies, we verify the beneficial role of Ag‐assisted Li nucleation in facilitating inward growth inside the cavity of the microcapsule host and, in turn, enhancing electrochemical performance. This study provides new insights into the design of reversible host materials for practical Li metal batteries.

Latent Toehold-Mediated DNA Circuits Based on a Bulge-Loop Structure for Leakage Reduction and Its Application to Signal-Amplifying DNA Logic Gates.

DNA circuits based on successive toehold-mediated DNA displacement reactions, particularly entropy-driven DNA circuit (EDC) systems, have attracted considerable attention as powerful enzyme-free tools for dynamic DNA nanotechnology. However, background leakage (noise signal) often occurs when the circuit is executed nonspecifically, even in the absence of the appropriate catalyst DNA (input). This study designed and developed a new latent toehold-mediated DNA circuit (LDC) system that relies on a bulge-loop structure as a latent toehold toward leakage reduction. Furthermore, the number (size) of nucleotides (nt) in the bulge-loop is found to play a significant role in the performance (i.e., leakage, signal, and kinetics) of LDC systems. In fact, the signal rate for the LDC systems increased as the number of nt in the bulge-loop increased from 4 to 8, whereas the leakage rate of the LDC systems with bulge-loops of 7 nt or less was low, but the leakage rate of the LDC system with a bulge-loop of 8 nt increased significantly. Note that the LDC system with the optimal bulge-loop (7 nt) was capable of not only reducing the leakage but also accelerating the circuit speed without any signal loss, unlike methods of reducing the leakage by reducing the signal reported previously for the conventional EDC systems. These facts indicate that the 7 nt bulge-loop acts as a "latent" toehold for the DNA circuit system. By using the amplification function of output signals with an accelerated circuit and reduced leakage, our LDC system with a 7 nt bulge-loop could be applied directly and successfully to signal-amplifying DNA logic gates such as OR and AND gates, and thus, sufficient output signals could be obtained even with a small amount of input. These findings reveal that our LDC systems with a bulge-loop structure can replace the conventional EDC system and have enormous potential in the field of DNA nanotechnology.

A Cu-Ag double-layer coating strategy for stable and reversible Zn metal anodes

Structuring a stable artificial coating to mitigate dendrite growth and side reactions is an effective strategy for protecting the Zn metal anode. Herein, a Cu-Ag double-layer metal coating is constructed on the Zn anode (Zn@Cu-Ag) by simple and in-situ displacement reactions. The Cu layer enhances the bond between the Ag layer and Zn substrate by acting as an intermediary, preventing the Ag coating from detachment. Concurrently, the Ag layer serves to improve the corrosion resistance of Cu metal. During plating, the initial Cu sheets and Ag particles on the surface of Zn@Cu-Ag electrode gradually transform into a flat and smooth layer, resulting in the formation of AgZn, AgZn3, and (Ag, Cu)Zn4 alloys. Alloys play a multifunctional role in inhibiting dendrite growth and side reactions due to decreased resistance, low nucleation barrier, enhanced zincophilicity, and strong corrosion resistance. Consequently, the Zn@Cu-Ag symmetric cell exhibits continuous stable performance for 3750 h at 1 mA cm−2. Furthermore, the Zn@Cu-Ag||Zn3V3O8 full cell achieves an initial capacity of 293.4 mAh g−1 and realizes long cycling stability over 1200 cycles. This work provides new insight into the engineering of an efficient artificial interface for highly stable and reversible Zn metal anodes.

Coarse-grained modeling of DNA-RNA hybrids.

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.

Efficient DNA walker guided by ordered cruciform-shaped DNA track for ultrasensitive and rapid electrochemical detection of lead ion

The rational design of DNA tracks is an effective pathway to guide the autonomous movement and high-efficiency recognition in DNA walkers, showing outstanding advantages for the cascade signal amplification of electrochemical biosensors. However, the uncontrolled distance between two adjacent tracks on the electrode could increase the risk of derailment and interruption of the reaction. Hence, a novel four-way balanced cruciform-shaped DNA track (C-DNT) was designed as a structured pathway to improve the effectiveness and stability of the reaction in DNA walkers. In this work, two kinds of cruciform-shaped DNA were interconnected as a robust structure that could avoid the invalid movement of the designed DNA walker on the electrode. When hairpin H2 was introduced onto the electrode, the strand displacement reaction (SDR) effectively triggered movements of the DNA walker along the cruciform-shaped track while leaving ferrocene (Fc) on the electrode, leading to a significant enhancement of the electrochemical signal. This design enabled the walker to move in an excellent organized and controllable manner, thus enhancing the reaction speed and walking efficiency. Compared to other walkers moving on random tracks, the reaction time of the C-DNT-based DNA walker could be reduced to 20 min. Lead ion (Pb2+) was used as a model target to evaluate the analytical performance of this biosensor, which exhibited a low detection limit of 0.033 pM along with a wide detection ranging from 0.1 pM to 500 nM. This strategy presented a novel concept for designing a high-performance DNA walker-based sensing platform for the detection of contaminants.

A dual-mode biosensor based on silica inverse opal photonic crystals modulated electrochemiluminescence and dye displacement colorimetry for the sensitive detection of synthetic cathinone in water environment

To address the challenges posed by signal capacity limitations and the reliance of sensing methods on single analytical information, this study developed an electrochemiluminescence (ECL) and colorimetric dual-mode sensing platform for the precise detection of 4-chloroethcathinone (4-CEC) in water environments. Firstly, the accurate alignment of the reflection wavelength of appropriately sized silica inverse opal photonic crystals (SIOPCs) with the ECL emission wavelength of luminescent metal-organic frameworks (PCN-224) has been achieved via diameter modulation. This innovative design, which cleverly utilized the band-edge effect, improved the luminous intensity of the ECL sensor, leading to a significant boost in analytical performance. Secondly, the establishment of a colorimetric detection method for confirming the presence of 4-CEC in samples through visual observation of color changes was achieved by employing an aptamer-based dye displacement reaction, utilizing differential binding affinities between the aptamer and both the sulforhodamine B (SRB) and 4-CEC. Under the optimal experimental conditions, the dual-mode sensor demonstrated ECL detection of limits (LOD) of 2.6 × 10−13 g/L and colorimetric LOD of 6.5 ng/L for 4-CEC. These findings highlighted the tremendous potential of developing streamlined and efficient dual-signal readout platforms using ECL aptamer sensors for the precise determination of other Synthetic cathinones (SCs) in water environments.

Framework Nucleic Acids-Based VEGF Signaling Activating System for Angiogenesis: A Dual Stimulation Strategy.

Angiogenesis is crucial for tissue engineering, wound healing, and regenerative medicine. Nanomaterials constructed based on specific goals can be employed to activate endogenous growth factor-related signaling. In this study, based on the conventional single-stranded DNA self-assembly into tetrahedral framework nucleic acids (tFNAs), the Apt02 nucleic acid aptamer and dimethyloxallyl glycine (DMOG) small molecule are integrated into a complex via a template-based click chemistry reaction and toehold-mediated strand displacement reaction. Thus, being able to simulate the VEGF (vascular endothelial growth factor) function and stabilize HIF (hypoxia-inducible factor), a functional whole is constructed and applied to angiogenesis. Cellular studies demonstrate that the tFNAs-Apt02 complex (TAC) has a conspicuous affinity to human umbilical vein endothelial cells (HUVECs). Further incubation with DMOG yields the tFNAs-Apt02-DMOG complex (TACD), which promotes VEGF secretion, in vitro blood vessel formation, sprouting, and migration of HUVECs. Additionally, TACD enhances angiogenesis by upregulating the VEGF/VEGFR and HIF signaling pathways. Moreover, in a diabetic mouse skin defect repair process, TACD increases blood vessel formation and collagen deposition, therefore accelerating wound healing. The novel strategy simulating VEGF and stabilizing HIF promotes blood-vessel formation in vivo and in vitro and has the potential for broad applications in the vascularization field.

The construction of COFs functionalized CRISPR electrochemical sensor for ultrasensitive detection of bacteria by hyper-branched rolling circle amplification

Rapid, sensitive, and low-cost foodborne pathogens detection is crucial for dealing with foodborne diseases caused by bacteria. In this work, we designed a new CRISPR/Cas9-mediated electrochemical biosensor for ultrasensitive detection of Escherichia coli (E. coli) based on multifunctional covalent organic framework-based nanocomposite (GOx-AuNPs-COF-H2) and hyperbranched rolling circle amplification (HB-RCA) reaction. When specific DNA targets were present in the system, the targets could be recognized and cleaved by CRISPR-Cas9 system, which triggered strand displacement reaction (SDR) and HB-RCA reaction. By introducing GOx-AuNPs-COF-H2 nanocomposite, H2 probe could hybridize with RCA products to bind to the electrode surface. After added glucose solution, GOx could catalyze it in the detection system and thus offered significant current signals for bacteria detection. This approach showed high analytical performance for assay of E. coli with the detection limit (LOD) of 10 CFU/mL. Furthermore, real samples were detected by this approach, demonstrating its promising potential for foodborne pathogens detection in food monitoring and clinical diagnosis.

Dynamic control of DNA condensation

Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.

A perovskite-based electrochemiluminescence aptasensor for tetracycline screening.

Tetracyclines are currently the most commonly used class of antibiotics, and their residue issue significantly impacts public health safety. In this study, a surface modification of perovskite with cetyltrimethylammonium bromide led to the generation of stable electrochemiluminescence (ECL) emitters in aqueous systems and improved the biocompatibility of perovskite. A perovskite quantum dot-based ECL sensing strategy was developed. Utilizing the corresponding aptamer of the antibiotics, strain displacement reactions were triggered, disrupting the ECL quenching system composed of perovskite and Ag nanoclusters (Ag NCs) on the electrode surface, generating a signal to achieve quantitative detection of several common tetracycline antibiotics. The perovskite quantum dot provided a strong and stable initial signal, while the efficient catalytic activity of the silver cluster enhanced the recognition sensitivity. Tetracycline, chlortetracycline, and oxytetracycline were used as examples to demonstrate the differentiation and quantitative detection through this method. In addition, the aptasensor exhibited analytical performance with the linear range (0.1-10μM OTC) and good recovery rates of 94.7% to 101.6% in real samples. This approach has the potential to become a sensitive and practical approach for assessing antibiotic residues.

A highly sensitive ratiometric electrochemical aptasensor for prostate specific antigen detection based on toehold-mediated strand displacement reaction

In this work, a novel ratiometric electrochemical aptasensor was designed for prostate specific antigen (PSA) detection based on toehold-mediated strand displacement reaction (TMSDR). For PSA detection, PSA could bind with the aptamer sequence in hairpin probe 1 (HP1), and HP1/PSA complex was obtained. Then, in the presence of S3 DNA, HP1/PSA could trigger two TMSDR processes by hybridizing with Fc-S2/S1 double-stranded DNA, which would generate a large amount of Fc-S2 and recycle HP1/PSA. This enabled the hybridization of Fc-S2 with methylene blue labeled thiolated hairpin probe 2 (MB-HP2) immobilized on the electrode surface, causing MB molecules away from the electrode and Fc close to the electrode. Thus, with the increasing PSA concentrations, the current of MB (IMB) decreased and the current of Fc (IFc) increased. The ratio of IFc/IMB was shown to be linear with the logarithm of PSA concentration from 1 pg mL−1 to 100 ng mL−1, with a detection limit of 0.28 pg mL−1. In addition, the aptasensor had good specificity, reproducibility, repeatability, and stability for PSA detection, and was successfully applied to spiked diluted human serum samples.

A dual-mode biosensor coupling electrochemical and fluorescent measurements of single nucleotide polymorphism with enzyme-free cascade amplification

Enzyme-free amplification techniques empower the easy-operable and cost-effective analysis of single nucleotide polymorphisms (SNPs), which garnered considerable extensive attention. However, the sensitivity and reliability of enzyme-free amplification technology are limited to meet the needs of biomedical diagnosis. Herein, we develop a dual-mode biosensing strategy that combines target-induced double DNA release and enzyme-free amplification for both electrochemical and fluorescent SNP detections. This strategy utilizes mutant SNP to activate entropy-driven amplifier (EDA) system, a cyclic strand displacement reaction, achieving the release of two single-strand DNA. These EDA by-products of target-induced release are ingeniously used as synchronized inputs for electrochemical and fluorescent measurements to fabricate circularly amplified hybridization chain reaction (HCR) and catalytic hairpin reaction (CHA) respectively. Such flexible strategy of dual-mode biosensing platform can not only make effective use of EDA by-products originally wasteful to elevate identification and amplification efficiency, but also improve the detection reliability. Moreover, leveraging the programmability and integration of classical enzyme-free cascaded amplification, this dual “signal-on” biosensor flexibly achieves high sensitivity detection and good selectivity, which holds great promise in the fields of early disease diagnosis.