Exponential strand-displacement amplification for detection of microRNAs

Target-induced multiregion MNAzyme nanowires for ultrasensitive homogeneous detection of microRNAs

A target-induced multiregion MNAzyme nanowire system is designed for the ultrasensitive and homogeneous detection of microRNAs (miRNAs). miRNA-21 and miRNA-375 are chosen as analytes, and a miRNA-induced primer exchange reaction (PER) is utilized to construct a long DNA strand with repetitive sequences. This innovative design enables the efficient anchoring of numerous MNAzymes. This unique architecture significantly boosts the effective local concentration of MNAzymes, thereby enhancing the sensitivity and efficiency of miRNA detection. Notably, the limit of detection (LOD) achieved with our target-induced multiregion MNAzyme nanowire approach is over an order of magnitude lower than most other MNAzyme-based methods, while the MNAzyme reaction time is reduced from several hours to 50 min. The method has demonstrated successful applications in quantitatively determining the expression levels of two miRNAs in cell lysates of MCF-7, HeLa and MCF-10 A cells, highlighting its potential for assaying miRNA biomarkers in clinical samples.

Synergy of Target-Induced Magnetic Network and Single-Drop Chromogenic System for Ultrasensitive "All-in-Tube" Detection of miRNA in Whole Blood

The development of liquid biopsy methods for the accurate and reliable detection of miRNAs in whole blood is critical for the early diagnosis and monitoring of diseases. However, accurate quantification of miRNA expression levels remains challenging due to the complex matrix and low abundance of miRNAs in blood samples. Herein, we report a contactless signal output strategy with low background interference that ensures "zero-contact" between the reaction system and the colorimetry system. The designed target-induced magnetic ZnS/ZIF-90/ZnS network can serve as a unique signal amplifier and transducer. It releases hydrogen sulfide (H2S) gas in an acidic solution which can be concentrated in a droplet of only a few microliters in volume, etching the silver layer of Au@Ag nanostars (NSTs) in the droplet. This will lead to changes in the localized surface plasmon resonance signals of the NSTs. Finally, quantitative detection of let-7a is realized by measuring the offset value of the UV-vis absorption peak. Therefore, by virtue of the synergistic action of quadruple signal amplification methods, including catalytic hairpin assembly, ZnS/ZIF-90/ZnS, magnetic separation, and microextraction, the "All-in-Tube" ultrasensitive detection of low-abundance let-7a in whole blood is achieved with a detection limit as low as the aM level. In addition, the "zero-contact" signal output mode effectively solves the problem of complex matrix interference, demonstrating the great potential of this method for miRNA quantification in complex samples, such as whole blood.

One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe

In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.

Multifunctional self-priming hairpin probe-based isothermal nucleic acid amplification and its applications for COVID-19 diagnosis

We herein present a multifunctional self-priming hairpin probe-based isothermal amplification, termed MSH, enabling one-pot detection of target nucleic acids. The sophisticatedly designed multifunctional self-priming hairpin (MSH) probe recognizes the target and rearranges to prime itself, triggering the amplification reaction powered by the continuously repeated extension, nicking, and target recycling. As a consequence, a large number of double-stranded DNA (dsDNA) amplicons are produced that could be monitored in real-time using a dsDNA-intercalating dye. Based on this unique design approach, the nucleocapsid (N) and the open reading frame 1 ab (ORF1ab) genes of SARS-CoV-2 were successfully detected down to 1.664 fM and 0.770 fM, respectively. The practical applicability of our method was validated by accurately diagnosing 60 clinical samples with 93.33% sensitivity and 96.67% specificity. This isothermal one-pot MSH technique holds great promise as a point-of-care testing protocol for the reliable detection of a wide spectrum of pathogens, particularly in resource-limited settings.

Coupling Exponential to Linear Amplification for Endpoint Quantitative Analysis

Exponential DNA amplification techniques are fundamental in ultrasensitive molecular diagnostics. These systems offer a wide dynamic range, but the quantification requires real-time monitoring of the amplification reaction. Linear amplification schemes, despite their limited sensitivity, can achieve quantitative measurement from a single end-point readout, suitable for low-cost, point-of-care, or massive testing. Reconciling the sensitivity of exponential amplification with the simplicity of end-point readout would thus break through a major design dilemma and open a route to a new generation of massively scalable quantitative bioassays. Here a hybrid nucleic acid-based circuit design is introduced to compute a logarithmic function, therefore providing a wide dynamic range based on a single end-point measurement. CELIA (Coupling Exponential amplification reaction to LInear Amplification) exploits a versatile biochemical circuit architecture to couple a tunable linear amplification stage - optionally embedding an inverter function - downstream of an exponential module in a one-pot format. Applied to the detection of microRNAs, CELIA provides a limit of detection in the femtomolar range and a dynamic range of six decades. This isothermal approach bypasses thermocyclers without compromising sensitivity, thereby opening the way to applications in various diagnostic assays, and providing a simplified, cost-efficient, and high throughput solution for quantitative nucleic acid analysis.

Highly sensitive miRNA-21 detection with enzyme-free cascade amplification biosensor

In this study, we present an enzyme-free fluorescence biosensor for the highly sensitive detection of miRNA-21, a crucial biomarker in clinical diagnosis. Our innovative approach combines catalytic hairpin assembly (CHA) and entropy-driven amplification into a cascade amplification strategy. MicroRNA initiates the catalytic hairpin assembly reaction, liberating the trigger region needed for the entropy-driven amplification reaction. This triggers a series of strand displacement reactions, resulting in the separation of the fluorescence resonance energy transfer pair and an amplified fluorescence signal from FAM. Our cascade amplification strategy achieves ultra-sensitive microRNA detection, with an impressive limit of detection (LOD) of 1.3 fM, approximately 100-fold lower than CHA alone. Additionally, we successfully applied this biosensor for microRNA quantification in human serum and cell lysates, demonstrating its practicality and potential for early diagnosis.

Spherical Nucleic Acid-Mediated Spatial Matching-Guided Nonenzymatic DNA Circuits for the Prediction and Prevention of Malignant Tumor Invasion

Detection of intracellular miRNAs, especially sensitive imaging of in vivo miRNAs, is vital to the precise prediction and timely prevention of tumorgenesis but remains a technical challenge in terms of nuclease resistance and signal amplification. Here, we demonstrate a gold nanoparticle-based spherical nucleic acid-mediated spatial matching-guided nonenzymatic DNA circuit (SSDC) for efficient screening of intracellular miRNAs and, in turn, finding cancerous tissues in living organisms before the appearance of clinical symptoms. Due to the substantially enhanced nuclease resistance, the false positive signal is avoided even in a complex biological medium. Target miRNA can straighten out the hairpin DNA probe to be linear, allowing the probe to penetrate into the internal region of a core/shell DNA-functionalized signal nanoampfilier and initiate a strand displacement reaction, generating an amplified fluorescence signal. The detection limit is as low as 17 pM, and miRNA imaging is in good accordance with the gold standard polymerase chain reaction method. The ability to image intracellular miRNAs is substantially superior to that of conventional fluorescence in situ hybridization techniques, making in vivo SSDC-based imaging competent for the precise prediction of tumorigenesis. By intratumoral chemotherapy guided by SSDC-based imaging, tumorigenesis and progression are efficiently controlled before the onset of clinical symptoms.

A Simple and Robust Exponential Amplification Reaction (EXPAR)-Based Hairpin Template (exp-Hairpin) for Highly Specific, Sensitive, and Universal MicroRNA Detection

Specific and sensitive detection of microRNAs continues to encounter significant challenges, especially in the development of rapid and efficient isothermal amplification strategies for point-of-care settings. The exponential amplification reaction (EXPAR) has garnered significant attention owing to its simplicity and rapid amplification of signals within a short period. However, a substantial loss of amplification efficiency, difficulty in distinguishing closely related homologous sequences, and adapting the designed templates to other targets seriously hamper the practical application of the EXPAR. In this work, a hairpin template tailored for the EXPAR system (exp-Hairpin) was constructed by adding identical trigger sequences and enzyme cleavage sites on two arms of the hairpin, achieving theoretically more than 2n amplification efficiency and minimal background amplification of EXPAR. Modulating the stability of the exp-Hairpin template by increasing the stem length, the specificity of detecting target miRNA in highly homologous sequences could be significantly improved. Using miRNA let-7a as a target model, the exp-Hairpin with 8 bp stem length for EXPAR amplification curves could effectively distinguish target let-7a and nontarget let-7b/7c/7f/7g/7i homologous sequences. This strategy enabled the sensitive and accurate analysis of let-7a in diluted human serum with satisfactory recoveries. By simply replacing the loop recognition sequence of exp-Hairpin, the specific detection of miR-200b was also achieved, demonstrating the universality of this strategy. The exp-Hairpin EXPAR accelerates simple and rapid molecular diagnostic applications for short nucleic acids.

Cyclic Multiple Primer Generation Rolling Circle Amplification Assisted Capillary Electrophoresis for Simultaneous and Ultrasensitive Detection of Multiple Pathogenic Bacteria

Efficient, accurate, and economical detection of pathogenic bacteria is crucial in ensuring food safety and preventing foodborne illnesses. How to fulfill the highly sensitive and simultaneous detection of multiple trace pathogenic bacteria is a big challenge. In this work, capillary electrophoresis coupled with a cyclic multiple primer generation rolling circle amplification (cyclic MPG-RCA) was studied for highly sensitive and simultaneous detection of three kinds of pathogenic bacteria. The cyclic MPG-RCA was based on a carefully designed clover-shaped DNA probe, in which three "leaves" corresponded to three types of aimed pathogenic bacteria: Shigella dysenteriae (S. dysenteriae), Salmonella enterica subsp. enterica serovar Typhi (S. Typhi), and Vibrio parahaemolyticus (V. parahaemolyticus). Under the optimal experimental conditions, the limits of detection (S/N = 3) of this method for bacterial target DNA were 11.4 amol·L-1 (S. dysenteriae), 4.88 amol·L-1 (S. Typhi), and 14.9 amol·L-1 (V. parahaemolyticus), and the conversion concentrations for the target bacteria were 10 colony-forming units (CFU)·mL-1 (S. dysenteriae), 3 CFU·mL-1 (S. Typhi), and 12 CFU·mL-1 (V. parahaemolyticus). This method had been applied to the detection of tap water samples with good results, which proved that it could be used as an effective tool for trace pathogenic bacteria monitoring in foods, environments, and medicines.

CRISPR-based Biosensors for Human Health: A Novel Strategy to Detect Emerging Infectious Diseases

Infectious diseases (such as sepsis, influenza, and malaria), caused by various pathogenic bacteria and viruses, are widespread across the world. Early and rapid detection of disease-related pathogens is necessary to reduce their spread in the world and prevent their potential global pandemics. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, as the next-generation molecular diagnosis technique, holds immense promise in the detection of infectious diseases because of its remarkable advantages, including supreme flexibility, sensitivity, and specificity. While numerous CRISPR-based biosensors have been developed for application in environmental monitoring, food safety, and point-of-care diagnosis, there remains a critical need to summarize and explore their potential in human health. This review aims to address this gap by focusing on the latest advancements in CRISPR-based biosensors for infectious disease detection. We provide an overview of the current status, pre-amplification methods, the unique feature of each CRISPR system, and the design of CRISPR-based biosensing strategies to detect disease-associated nucleic acids. Last but not least, the review analyzes the current challenges and provides future perspectives, which will contribute to developing more effective CRISPR-based biosensors for human health.

Acoustofluidics for simultaneous droplet transport and centrifugation facilitating ultrasensitive biomarker detection

Trace biological sample detection is critical for the analysis of pathologies in biomedicine. Integration of microfluidic manipulation techniques typically strengthens biosensing performance. For instance, using isothermal amplification reactions to sense trace miRNA in peripheral circulation lacks a sufficiently complex pretreatment process that limits the sensitivity of on-chip detection. Herein we propose an orthogonal tunable acoustic tweezer (OTAT) to simultaneously actuate the transportation and centrifugation of μ-droplets on a single device. The OTAT enables diversified modes of droplet transportation such as unidirectional transport, multi-direction transport, round-trip transport, tilt angle movement, multi-droplet fusion, and continuous centrifugation of the dynamic droplets simultaneously. The multiplicity of modalities enables the focusing of a loaded analyte at the center of the droplet or constant rotation about the center axis of the droplet. We herein demonstrate the OTAT's ability to actuate transportation, fusion, and centrifugation-based pretreatment of two biological sample droplets loaded with miRNA biomarkers and multiple mixtures, as well as facilitating the increase of fluorescence detection sensitivity by an order of magnitude compared to traditional tube reaction methods. The results herein demonstrate the OTAT-based droplet acoustofluidic platform's ability to combine a wide range of biosensing mechanisms and provide a higher accuracy of detection for one-stop point-of-care disease diagnosis.

Detection of Escherichia coli by capillary electrophoresis assisted by large volume sample stacking and nicking endonuclease signal amplification

Efficient, accurate and economical detection of pathogenic bacteria is crucial in ensuring food safety and preventing foodborne illnesses. In this study, a capillary electrophoresis coupled laser-induced fluorescence assay (CE-LIF) was developed for the detection of Escherichia coli (E. coli) by detecting its specific DNA. The CE-LIF was assisted by both online enrichment and offline amplification to improve the detection sensitivity of bacterial DNA. Here the online amplification was performed by large volume sample stacking (LVSS), while the offline amplification was nicking endonuclease signal amplification (NESA). Under the optimal experimental conditions, the detection limit of bacterial target DNA was 2.5 fM, and the conversion concentration of E. coli was 3 CFU · mL-1. The method had been applied to the detection of commercially available skim milk samples with good results, which proved that it could be used as an effective tool for food and environmental bacteria monitoring.

A Novel miRNA Detection Method Using Loop-Mediated Isothermal Amplification

A novel ligation-based loop-mediated isothermal amplification has been developed for miRNA detection. Two stem-loop structure DNA linker A/B probes which hybridized with miRNA were designed to establish a rapid and ultrasensitive miRNA-LAMP system for miRNA detection. Target miR-200a was used to template the ligation of Linker A/B probes with SplintR Ligase and used as a dumbbell-shaped amplicon. By adding BIP/FIP and Bst 2.0 DNA polymerase, the LAMP reaction was carried out, which brought greatly improved amplification efficiency. The double-stranded DNA fluorescent dye EvaGreen was added for the detection of amplification product to achieve the quantification of the target miRNA. This method can detect miRNA in a linear range of seven orders of magnitude, with a detection limit of 100 fM. Therefore, this ultrasensitive miRNA-LAMP assay provides a new path for the highly sensitive quantitative analysis of miRNA, thereby bringing convenience to clinical diagnosis and prognostic research.

Isothermal nucleic acid amplification and its uses in modern diagnostic technologies

Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.

A DNAzyme-enhanced nonlinear hybridization chain reaction for sensitive detection of microRNA

As a typical biomarker, the expression of microRNA is closely related to the occurrence of cancer. However, in recent years, the detection methods have had some limitations in the research and application of microRNAs. In this paper, an autocatalytic platform was constructed through the combination of a nonlinear hybridization chain reaction and DNAzyme to achieve efficient detection of microRNA-21. Fluorescently labeled fuel probes can form branched nanostructures and new DNAzyme under the action of the target, and the newly formed DNAzyme can trigger a new round of reactions, resulting in enhanced fluorescence signals. This platform is a simple, efficient, fast, low-cost, and selective method for the detection of microRNA-21, which can detect microRNA-21 at concentrations as low as 0.004 nM and can distinguish sequence differences by single-base differences. In tissue samples from liver cancer patients, the platform shows the same detection accuracy as real-time PCR but with better reproducibility. In addition, through the flexible design of the trigger chain, our method could be adapted to detect other nucleic acids biomarkers.

Target-promoted specific activation of m6A-DNAzyme for SPEXPAR-amplified and highly sensitive non-label electrochemical assay of FTO demethylase

The demethylase of fat mass and obesity related protein (FTO) is critical to regulate the dynamic N⁶-methyladenosine (m6A) modification of eukaryotic mRNAs, and its overexpression has found to be closely related to the initiation of several cancers. On the basis of a target-promoted specific activation of DNAzyme strategy coupled with self-primer exponential amplification reaction (SPEXPAR) cycles and DNA supersandwich assemblies, the highly sensitive and label-free electrochemical FTO assay approach is established. The modification of the catalytic core nucleobase of the DNAzyme probe by m6A can inhibit its cleavage activity. The presence of target FTO catalyzes the elimination of the methyl group to restore the DNAzyme activity, which cleaves the hairpin substrates to trigger the SPEXPAR for yielding many ssDNAs. The capture of these DNAs on the sensor electrode leads to the initiation of supersandwich assembly formation of long dsDNAs. Tremendous electrochemical signal probe of [Ru(NH₃)₆]Cl₃ are then absorbed on these dsDNAs to produce highly amplified catalytic currents with the assistance of K₃[Fe(CN)₆] for detecting trace FTO with 63.1 fM detection limit. Furthermore, the sensor can be employed for selective assay of FTO in cell lysates, revealing the great potential of this sensing strategy for biomedical and biological study applications.

A hairpin probe-mediated exponential amplification reaction for highly sensitive and specific detection of microRNAs

In this work, we propose a hairpin probe-mediated exponential amplification reaction (HEAR) strategy that combines DNA strand displacement with a "who triggers, who gets generated" mode, providing excellent single-base discrimination and a reduced background signal. The detection limit is 19 aM, which is reduced by 3 orders of magnitude compared to traditional exponential amplification approaches. This one-pot strategy also exhibits a wide dynamic range, high specificity and short detection time. It is expected to become a powerful tool for clinical diagnosis.

High-Efficiency 3D DNA Walker Immobilized by a DNA Tetrahedral Nanostructure for Fast and Ultrasensitive Electrochemical Detection of MiRNA

Herein, by directly limiting the reaction space, an ingenious three-dimensional (3D) DNA walker (IDW) with high walking efficiency is developed for rapid and sensitive detection of miRNA. Compared with the traditional DNA walker, the IDW immobilized by the DNA tetrahedral nanostructure (DTN) brings stronger kinetic and thermodynamic favorability resulting from its improved local concentration and space confinement effect, accompanied by a quite faster reaction speed and much better walking efficiency. Once traces of target miRNA-21 react with the prelocked IDW, the IDW could be largely activated and walk on the interface of the electrode to trigger the cleavage of H2 with the assistance of Mg²⁺, resulting in the release of amounts of methylene blue (MB) labeled on H2 from the electrode surface and the obvious decrease of the electrode signal. Impressively, the IDW reveals a conversion efficiency as high as 9.33 × 10⁸ in 30 min with a much fast reaction speed, which is at least five times beyond that of typical DNA walkers. Therefore, the IDW could address the inherent challenges of the traditional DNA walker easily: slow walking speed and low efficiency. Notably, the IDW as a DNA nanomachine was utilized to construct a sensitive sensing platform for rapid miRNA-21 detection with a limit of detection (LOD) of 19.8 aM and realize the highly sensitive assay of biomarker miRNA-21 in the total RNA lysates of cancer cell. The strategy thus helps in the design of a versatile nucleic acid conversion and signal amplification approach for practical applications in the areas of biosensing assay, DNA nanotechnology, and clinical diagnosis.

An immobilization-free electrochemical aptamer-based assay for zearalenone based on target-triggered dissociation of DNA from polydopamine nanospheres with strand displacement amplification

Zearalenone (ZEN), a widespread mycotoxin, can cause great harm to people's health. In order to assay ZEN, an immobilization-free electrochemical sensor has been developed. A multifunctional hairpin DNA has been carefully designed, including three functions: the aptamer for zearalenone (ZEN), primer, and template sequence. This hairpin DNA can anchor on polydopamine nanospheres (PDANSs), which can protect DNA against the digestion of enzymes and prevent the occurrence of strand displacement amplification (SDA). In the presence of ZEN, the hairpin DNA is dissociated from PDANSs due to the interaction between ZEN and the aptamer, and the SDA reaction is initiated with the help of endonuclease and polymerase. During the SDA process, substantial amounts of negatively charged dsDNA are generated. The MB molecules are embedded into the dsDNA grooves to obtain the complex with a negative charge. The confined MB is repelled on the surface of the negatively charged ITO electrode, leading to the decline of the current. This immobilization-free method possesses high sensitivity (LOD of 0.18 pg mL^-1) and good selectivity and can be applied to assay ZEN in corn flour.

Detection of miRNAs

MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression. They play an important role in many biological processes including human diseases. However, miRNAs are challenging to detect due to their short sequence length and low copy number. A number of conventional (e.g., Northern blot, microarray, and RT-qPCR) and emerging (e.g., nanostructured materials and electrochemical methods) techniques have been developed to detect miRNA, each with their own strengths and weaknesses. Some of these techniques have been combined to detect miRNAs as disease biomarkers in point-of-care (POC) settings. Nonetheless, there is still potential for further innovation to facilitate the detection of miRNAs.

Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion

MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

Hairpin-inserted cross-shaped DNA nanoprobe for ultrasensitive microRNA detection based on built-in target analogue cycle amplification

It remains technically challenging to develop a sensitive assay system to isothermally amplify the signal for miRNA detection because of its low abundance in tested sample, sequence similarities and existence in complex biological environments. In this study, using miRNA-21 as target model, a hairpin-inserted cross-shaped DNA nanoprobe (CP) with four functional arms is constructed for the ultrasensitive detection of miRNA via one-step built-in target analogue (BTA) cycle-mediated signal amplification. BTA is pre-locked in one arm of CP probe and inactive. In the presence of target miRNA, BTA can be unlocked and initiate an isothermal amplification process. Utilizing as-designed CP probe, miRNA-21 can be detected to down to 500 fM, and the linear response range spans over five orders of magnitude. The nonspecific signal is less than 1% upon nontarget miRNAs. CP probe exhibits ∼six times enhancement in resistance to nuclease degradation and no obvious degradation-induced fluorescence change is detected during the assay period. The recovery yield ranges from 98.2～105.5% in FBS solution. Because of the high sensitivity, desirable specificity, strong anti-interference ability and substantial increase in nuclease resistance, CP probe is a promising tool for the detection of miRNAs in a complex biological milieu.

Plasmonic Au nanocube enhanced SERS biosensor based on heated electrode and strand displacement amplification for highly sensitive detection of Dam methyltransferase activity

In this work, a novel "turn-on" mode Au nanocubes (AuNCs) enhanced surface-enhanced Raman scattering (SERS) biosensing platform coupled with heated Au electrode (HAuE) and strand displacement amplification (SDA) strategy was proposed for highly sensitive detection of DNA adenine methylation (Dam) Methyltransferase (MTase) activity. The Dam MTase and DpnI enzyme activities were significantly increased by elevating the HAuE surface temperature, resulting in the rapid production of template DNA for later SDA. During the SDA process, the released single-stranded DNA (ssDNA) could be amplified exponentially, and its concentration was positively related to the Dam MTase activity. The plasmonic AuNCs in SERS tags could provide significant SERS enhancement due to their "lightning rod" effect resulting from the sharp feature of the edges and corners of AuNCs. Because of these factors, the proposed biosensors exhibited high sensitivity in detecting the Dam MTase activity. The limit of detection was estimated to be 8.65 × 10^-5 U mL^-1, which was lower than that in most of the sensors for detection of Dam MTase activity in the literature. This SERS biosensor could also be used to screen inhibitors of Dam MTase and had the potential for detecting Dam MTase activity in real biological samples.

Circulating Abnormal Extracellular Vesicles: Their Mechanism for Crossing Blood-Brain Barrier, Effects on Central Nervous System and Detection Methods

Central nervous system (CNS) diseases are difficult to treat and harmful. Many CNS diseases are secondary to peripheral diseases, such as tumor brain metastases (BMS), viral infections and inflammation of the brain, and their pathogenic factors travel through the circulatory system to the brain, eventually leading to lesions. Extracellular vesicles (EVs) play an important role in this process. Recent studies have shown that, extracellular EVs can effectively cross the blood- brain barrier (BBB) through endocytosis and they transmit molecular signals in cell-to-cell communication. Abnormal EVs produced in the lesion portion transport pathogenic factors, including miRNAs, proteins, and virions into the CNS. These pathogenic factors participate in cellular pathways to interfere with homeostasis or are themselves pathogens that directly damage CNS. In addition, different or specific pathological molecules in EVs are potential disease markers. We herein reviewed pathways through which the abnormal EVs cross BBB and adverse effects of abnormal exosomes. We also and summarized their existing detection techniques, so as to provide basis for prevention and early diagnosis of secondary diseases.

Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier

Herein, a programmable dual-catalyst hairpin assembly (DCHA) for realizing the synchronous recycle of two catalysts is developed, displaying high reaction rate and outstanding conversion efficiency beyond traditional nucleic acid signal amplifications (NASA). Once catalyst I interacts with the catalyst II, the DCHA can be triggered to realize the simultaneous recycle of catalysts I and II to keep the highly concentrated intermediate product duplex I-II instead of the steadily decreased one in typical NASA, which can accomplish in about only 16 min and achieves the outstanding conversion efficiency up to 4.54 × 108 , easily conquering the main predicaments of NASA: time-consuming and low-efficiency. As a proof of the concept, the proposed DCHA as a high-speed and hyper-efficiency DNA signal magnifier is successfully applied in the rapid and ultrasensitive detection of miRNA-21 in cancer cell lysates, which exploits the new generation of universal strategy for the applications in biosensing assay, clinic diagnose, and DNA nanobiotechnology.

A portable system for isothermal amplification and detection of exosomal microRNAs

Exosomal microRNAs (miRNAs) play a key role in cell-cell communication to regulate gene expression in target cells and have great potential as biomarkers for disease diagnosis. This paper reports an on-chip exosomal miRNA amplification and detection system for rapid analysis of exosomal miRNAs. The compact system consists of two connected flow cells for processing exosomes and detecting miRNAs, respectively. The miRNAs extracted from exosomes were quantitatively measured using the on-chip exponential amplification reaction (EXPAR) assay. The sensor chip was designed to store multiple oligonucleotide templates for the EXPAR, mix sample and reagent, and simultaneously analyze multiple exosomal miRNAs of interest. To facilitate the miRNA analysis, a portable detection instrument was built on an IoT platform using a low-cost microcontroller to execute the EXPAR assay, collect fluorescent images, and analyze amplification curves. Here, we studied the miRNA profiles carried by exosomes derived from three different phenotypes of tissue macrophages. The affordable instrument, rapid assay, multiplexed analysis, as well as disposable sensor chip, would boost the development of point-of-care liquid biopsy tests using exosomal miRNAs.

Visible-light and near-infrared fluorescence and surface-enhanced Raman scattering point-of-care sensing and bio-imaging: a review

This review article deals with the concepts, principles and applications of visible-light and near-infrared (NIR) fluorescence and surface-enhanced Raman scattering (SERS) in in vitro point-of-care testing (POCT) and in vivo bio-imaging. It has discussed how to utilize the biological transparency windows to improve the penetration depth and signal-to-noise ratio, and how to use surface plasmon resonance (SPR) to amplify fluorescence and SERS signals. This article has highlighted some plasmonic fluorescence and SERS probes. It has also reviewed the design strategies of fluorescent and SERS sensors in the detection of metal ions, small molecules, proteins and nucleic acids. Particularly, it has provided perspectives on the integration of fluorescent and SERS sensors into microfluidic chips as lab-on-chips to realize point-of-care testing. It has also discussed the design of active microfluidic devices and non-paper- or paper-based lateral flow assays for in vitro diagnostics. In addition, this article has discussed the strategies to design in vivo NIR fluorescence and SERS bio-imaging platforms for monitoring physiological processes and disease progression in live cells and tissues. Moreover, it has highlighted the applications of POCT and bio-imaging in testing toxins, heavy metals, illicit drugs, cancers, traumatic brain injuries, and infectious diseases such as COVID-19, influenza, HIV and sepsis.

Ultrasensitive electrochemical aptasensor based on palindromic sequence mediated bidirectional SDA and a DNAzyme walker for kanamycin detection

An electrochemical biosensing platform for kanamycin analysis based on SDA and a DNA walker.

MicroRNA detection using light-up aptamer amplification based on nuclease protection transcription

The quantification of microRNAs (miRNAs) is important because the miRNA expression level is closely associated with the occurrence and development of diseases. Here, we report a simple nuclease protection transcription...

Ratiometric fluorescent probe: a sensitive and reliable reporter for the CRISPR/Cas12a-based biosensing platform

Using a ratiometric probe as the reporter for the CRISPR-Cas12a based biosensing system, the change of two fluorescence intensities can be monitored, while the TaqMan probe appears only one signal.

Ultra-specific nucleic acid testing by target-activated nucleases

Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.

A copper-free and enzyme-free click chemistry-mediated single quantum dot nanosensor for accurate detection of microRNAs in cancer cells and tissues

MicroRNAs (miRNAs) play key roles in the post-transcriptional regulation of genes, and their aberrant expression may disturb the normal gene regulation network to induce various diseases, and thus accurate detection of miRNAs is essential to early clinical diagnosis. Herein, we develop for the first time a single-quantum dot (QD)-based Förster resonance energy transfer (FRET) nanosensor to accurately detect miRNAs based on copper-free and enzyme-free cycling click chemistry-mediated tricyclic ligase chain reaction (LCR) amplification. We design four DNA probes namely DNA probes 1-4, with DNA probes 1 and 3 being modified with azide (N3) and DNA probes 2 and 4 being modified with dibenzocyclooctyne (DBCO). When target miRNA is present, DNA probes 1 and 2 can proceed via copper-free and enzyme-free click chemistry to generate the probes 1-2 ligation product. Subsequently, DNA probes 3 and 4 can hybridize with the probes 1-2 ligation product to generate the probes 3-4 ligation product. Both the probes 1-2 ligation product and probes 3-4 ligation product can act as the templates to initiate cycling click chemistry-mediated tricyclic LCR amplification whose products can be easily measured by the single-QD-based FRET nanosensor. This assay does not involve any enzymatic reverse transcription, copper catalyst, and ligase enzyme, and it exhibits excellent selectivity, high sensitivity, and the capability of differentiating even single-base mismatches. Moreover, this nanosensor can accurately quantify miRNA-155 even at the single-cell level, and it can distinguish the miRNA-155 expression in tissues of healthy persons and nonsmall cell lung cancer (NSCLC) patients.

MiRNA Detection Using a Rolling Circle Amplification and RNA-Cutting Allosteric Deoxyribozyme Dual Signal Amplification Strategy

A microRNA (miRNA) detection platform composed of a rolling circle amplification (RCA) system and an allosteric deoxyribozyme system is proposed, which can detect miRNA-21 rapidly and efficiently. Padlock probe hybridization with the target miRNA is achieved through complementary base pairing and the padlock probe forms a closed circular template under the action of ligase; this circular template results in RCA. In the presence of DNA polymerase, RCA proceeds and a long chain with numerous repeating units is formed. In the presence of single-stranded DNA (H1 and H2), multi-component nucleic acid enzymes (MNAzymes) are formed that have the ability to cleave substrates. Finally, substrates containing fluorescent and quenching groups and magnesium ions are added to the system to activate the MNAzyme and the substrate cleavage reaction, thus achieving fluorescence intensity amplification. The RCA-MNAzyme system has dual signal amplification and presents a sensing platform that demonstrates broad prospects in the analysis and detection of nucleic acids.

Engineering a Rolling-Circle Strand Displacement Amplification Mediated Label-Free Ultrasensitive Electrochemical Biosensing Platform

In this work, an original rolling-circle strand displacement amplification (RC-SDA) was developed by introducing a circle DNA with two recognition domains as a template instead of the limited liner DNA template in traditional strand displacement amplification (SDA), which displayed much shorter reaction time down to 30 min and quite higher conversion efficiency of more than 1.77 × 10⁸ compared with those of traditional strand displacement amplification (SDA) and could be applied to construct a label-free biosensor for ultrasensitive detection of an HIV DNA fragment. Once the target HIV DNA fragment interacts with the template circle DNA, the RC-SDA could be activated to dramatically output amounts of mimic target DNA with the assistance of the Phi29 DNA polymerase and Nb.BbvCI enzyme. In application, while the output products were captured by the DNA tetrahedral nanoprobe (DTNP) modified electrode, the electrochemical tag silver nanoclusters (AgNCs) on DTNP would be released from the electrode surface, accompanied with an obviously decreased electrochemical signal. This way, the developed signal-off biosensor was successfully applied to realize the rapid and ultrasensitive detection of target HIV DNA fragment with a detection limit down to 0.21 fM, which exploits the new generation of a universal strategy beyond the traditional ones for applications in biosensing assay, clinic diagnosis, and DNA nanobiotechnology.

Ladder-shape melting temperature isothermal amplification of nucleic acids

A novel method, termed ladder-shape melting temperature isothermal amplification (LMTIA), was developed in this study. As a proof of concept, one pair of primers or two pairs of nested primers and a thermostable DNA polymerase were employed to amplify the internal transcribed spacer of Oryza sativa with the ladder-shape melting temperature curve. Our results demonstrated that the LMTIA assay with nested primers was 50-fold more sensitive than the LAMP assay with the same level of specificity. The LMTIA method has the potential to be used for the prevention and control of emerging epidemics caused by different types of pathogens.

Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage

The market for using and storing digital data is growing, with DNA synthesis emerging as an efficient way to store massive amounts of data. Storing information in DNA mainly consists of two steps: data writing and reading. The writing step requires encoding data in DNA, building one nucleotide at a time as a form of single-stranded DNA (ssDNA). Once the data needs to be read, the target DNA is selectively retrieved and sequenced, which will also be in the form of an ssDNA. Recently, enzyme-based DNA synthesis is emerging as a new method to be a breakthrough on behalf of decades-old chemical synthesis. A few enzymatic methods have been presented for data memory, including the use of terminal deoxynucleotidyl transferase. Besides, enzyme-based amplification or denaturation of the target strand into ssDNA provides selective access to the desired dataset. In this review, we summarize diverse enzymatic methods for either synthesizing ssDNA or retrieving the data-containing DNA.

An innovative and user-friendly smartphone-assisted molecular diagnostic approach for rapid detection of canine vector-borne diseases

Present-day diagnostic tools and technologies for canine diseases and other vector-borne parasitic diseases hardly meet the requirements of an efficient and rapid diagnostic tool, which can be suitable for use at the point-of-care in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been always a method of choice in the development and validation of quick, precise, and sensitive diagnostic assays for pathogen detection and to reorganize point-of-care (POC) molecular diagnostics. In this study, we have demonstrated an efficient detection system for parasitic vector-borne pathogens like Ehrlichia canis and Hepatozoon canis by linking the LAMP assay to a smartphone via a simple, inexpensive, and a portable “LAMP box,” All the components of the LAMP box were connected to each other wirelessly. This LAMP box was made up of an isothermal heating pad mounted below an aluminum base which served as a platform for the reaction tubes and LAMP assay. The entire setup could be connected to a smartphone via an inbuilt Wi-Fi that allowed the user to establish the connection to control the LAMP box. A 5 V USB power source was used as a power supply. The sensitivity of the LAMP assay was estimated to be up to 10⁻⁶ dilution limit using the amplified, purified, and quantified specific DNA templates. It can also serve as an efficient diagnostic platform for many other veterinary infectious or parasitic diseases of zoonotic origin majorly towards field-based diagnostics.

Graphene oxide assisted light-up aptamer selection against Thioflavin T for label-free detection of microRNA

We selected an aptamer against a fluorogenic dye called Thioflavin T (ThT). Aptamers are single-stranded DNA that can bind a specific target. We selected the ThT aptamer using graphene oxide assisted SELEX and a low-cost Open qPCR instrument. We optimized, minimized, and characterized the best aptamer candidate against ThT. The aptamer, ThT dye, and the enzymatic strand displacement amplification (SDA) were used in a label-free approach to detect the micro RNA miR-215 in saliva and serum. The aptamer confers higher specificity than intercalating dyes but without expensive covalently modified DNA probes. This isothermal, low-cost, simple method can detect both DNA and RNA. The target, miR-215, was detected with a limit of detection of 2.6 nM.

Ultrasensitive isothermal method to detect microRNA based on target-induced chain amplification reaction

We herein describe an ultrasensitive isothermal method to detect microRNA (miRNA) by utilizing target-induced chain amplification reaction (CAR). The hairpin probe (HP) employed in this strategy is designed to be opened upon binding to target miRNA. The exponential amplification reaction (EXPAR) template (ET) then binds to the exposed stem of HP and DNA polymerase (DP) promotes the extension reactions for both HP and ET, consequently producing intermediate double-stranded DNA product (IP) and concomitantly recycling target miRNA to open another intact HP. The IPs would produce a large number of target-mimicking probes (TMPs) and trigger probes (TPs) through the continuously repeated nicking and extension reactions at the two separated nicking sites within the IP. TMP triggers another CAR cycle by binding to intact HP as target miRNA did while TP promotes conventional EXPAR by independently binding to free ET. As a consequence of these interconnected reaction systems, a large number of final double-stranded DNA products (FPs) are produced, which can be monitored by measuring the fluorescent signal produced from duplex-specific fluorescent dye. Based on this unique design principle, the target miRNA was successfully determined down to even a single copy with high selectivity against non-specific miRNAs. The practical applicability of this method was also verified by reliably detecting target miRNA included in the total RNA extracted from the human cancer cell.

Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To counter COVID-19 spreading, an infrastructure to provide rapid and thorough molecular diagnostics and serology testing is the cornerstone of outbreak and pandemic management. We hereby review the clinical insights with regard to using molecular tests and immunoassays in the context of COVID-19 management life cycle: the preventive phase, the preparedness phase, the response phase and the recovery phase. The spatial and temporal distribution of viral RNA, antigens and antibodies during human infection is summarized to provide a biological foundation for accurate detection of the disease. We shared the lessons learned and the obstacles encountered during real world high-volume screening programs. Clinical needs are discussed to identify existing technology gaps in these tests. Leverage technologies, such as engineered polymerases, isothermal amplification, and direct amplification from complex matrices may improve the productivity of current infrastructure, while emerging technologies like CRISPR diagnostics, visual end point detection, and PCR free methods for nucleic acid sensing may lead to at-home tests. The lessons learned, and innovations spurred from the COVID-19 pandemic could upgrade our global public health infrastructure to better combat potential outbreaks in the future.

Gelatin nanoparticles transport DNA probes for detection and imaging of telomerase and microRNA in living cells

Telomerase and microRNA (miRNA) are biomarkers closely related to tumors. Simultaneous detection of both markers can improve accuracy and reliability of early diagnosis. Based on the mechanism of fluorescence resonance energy transfer (FRET), two fluorescent DNA probes were designed for telomerase and miRNA-21. The probes were wrapped by gelatin through electrostatic interaction to form nanoparticles. After that, we synthesized molecularly imprinted coating of transferrin on the surface of gelatin nanoparticles, which can avoid the immune stress response and macrophage phagocytosis to help gelatin nanoparticles enter into the cells smoothly through endocytosis. Following with the degradation of gelatin in the cells, DNA probes were released to react with telomerase and miRNA-21 and lead to the change of the fluorescence signal. Thereby the simultaneous imaging of telomerase and miRNA-21 were successfully achieved in HeLa cells and HepG2 cells. The proposed strategy shows the simultaneous imaging for different biological markers with DNA probes by preventing them from being hydrolyzed with nucleases before the determination and achieves reliable method for early diagnosis of cancer.