Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants

Split T7 switch-based orthogonal logic operation of fluorogenic RNA aptamer for small molecules detection

Recent advances in fluorescent biosensors have stimulated the development of molecular detection. We herein developed a new orthogonal logic operation of fluorescent biosensor with cell-free to accomplish the detection of atrazine (ATZ) and tetrachlorobiphenyls (PCB77). The transcriptional process to generate fluorescent RNA aptamers (Mango) was controlled by molecules-probe bindings, which regulate split T7 promoter transcription switches ON or OFF. Leveraging the rapid in vitro T7 transcription process and high signal-to-background ratio of the Mango-TO1-Biotin complex, this biosensor demonstrates remarkable sensitivity in detecting ATZ and PCB77, with detection limit of 1.56 pM and 10.2 pM. Moreover, the orthogonality of four logic gates (AND, NOR, INHIBT, NIMPLY) were utilized the ATZ and PCB77 as input to construct, which could be activated by utilizing the target probe-driven association. The output of the fluorescence signal was controlled by split/intact fluorescent RNA aptamer (Mango) to achieve flexible and sensitive orthogonal operations. Significantly, the development of two-input logic gates has enabled the modular detection of various small molecules, offering a promising approach to intelligent multi-input analysis. Predictably, with the advantages of sensitivity, flexibility and easy-to-operate, this orthogonal logic gate platform holds immense potential in small molecules detection.

Engineering thermostable fluorescent DNA aptamer for the isothermal amplification of nucleic acids

Isothermal amplification-based nucleic acid detection technologies have become rapid and efficient tools for molecular diagnostics. Sequence-specific monitoring methods are crucial for isothermal amplification, as they help identify the occurrence of extended primer dimers, which can lead to false positive results. Fluorescent aptamers are promising tools for real-time monitoring of isothermal amplification but are inherently limited by thermostability. Here, we report an engineered fluorescent DNA aptamer variant, named thermostable Lettuce (TS-Lettuce), with a 5 °C higher melting temperature and 20 times greater fluorescence at 60 °C, ideal for real-time monitoring of sequence-specific isothermal amplification. Using molecular dynamics simulations for structural analyses, we introduced mutations to wild-type Lettuce to redesign the non-core sequences of the aptamer structure for tightly stabilizing its folding, thereby enhancing thermostability. The TS-Lettuce offers greater versatility and ease of design for coupling with isothermal amplification for all-in-one nucleic acid detection. We demonstrated three applications of TS-Lettuce in isothermal amplification: fluorescent turn-off, fluorescent turn-on, and fluorescent aptamer switch, facilitating the sequence-specific detection of nucleic acids. In addition, the results generated by TS-Lettuce are visible to the naked eye, enhancing the utility of isothermal amplification reactions in resource-constrained areas. The thermostable fluorescent DNA aptamers can be further utilized in more isothermal amplification methods.

DNA Tetrahedron-enhanced single-particle counting integrated with cascaded CRISPR Program for ultrasensitive dual RNAs logic sensing

CRISPR-Cas-based technology, emerging as a leading platform for molecular assays, has been extensively researched and applied in bioanalysis. However, achieving simultaneous and highly sensitive detection of multiple nucleic acid targets remains a significant challenge for most current CRISPR-Cas systems. Herein, a CRISPR Cas12a based calibratable single particle counting-mediated biosensor was constructed for dual RNAs logic and ultra-sensitive detection in one tube based on DNA Tetrahedron (DTN)-interface supported fluorescent particle probes coupled with a novel synergistic cascaded strategy between CRISPR Cas13a system and strand displacement amplification (SDA). As expected, our platform enables dual RNA molecules intelligent detection using only one crRNA of Cas13a, achieving a sensitivity enhancement of three orders of magnitude assisted with multiple signal amplification and accurate fluorescence particle counting with DTN mediated nano-biointerface enhancement, compared to traditional bulk Cas13a assays. Moreover, the effectiveness and universality of our strategy are experimentally investigated and demonstrated through the detection of mRNAs (cervical cancer swab clinical samples and cultured cancer cells) and bacterial 16s rRNAs. This work not only proposes a highly promising avenue for designing CRISPR-based multiplex detection systems that excel in ultra-sensitivity, specificity, and clinical molecular diagnostics, but also provide new insights into the potential applications of nanotechnology in molecular diagnostics, functional surface engineering, and interface-mediated bioreactions.

A sensitive miRNA detection method based on a split-T7 switch modulating CRISPR/Cas12a system

This study presents a novel method for sensitive miRNA detection based on a split-T7 switch modulating CRISPR/Cas12a system. By integrating the split-T7 promoter-mediated transcription with the CRISPR/Cas12a system, this method can achieve femtomolar detection of the target miRNA within 1 h and successfully analyze miR-21 in samples from various cell lines, demonstrating its potential for clinical applications.

A minimal transcription template-based amplification-free CRISPR-Cas13a strategy for DNA detection

CRISPR-Cas13a has shown great potential for the rapid and accurate detection of pathogen nucleic acids. However, conventional CRISPR-Cas13a-based assays typically require pre-amplification, which can introduce aerosol contamination and operational complexities. In this study, we developed a Minimalist transcription template-based Amplification-free CRISPR-Cas13a strategy for DNA detection (MAD). This strategy facilitates the release of pathogen DNA and its annealing with primers from nasopharyngeal swab samples in a straightforward manner, followed by T7 transcription and CRISPR-Cas13a detection, completing the entire process within 40 min. MAD eliminates the need for DNA extraction and pre-amplification while maintaining high sensitivity after optimization, allowing for result visualization via lateral flow strips. Furthermore, evaluation of 167 clinical pediatric samples identified 18 positive cases of human adenovirus, demonstrating a 99.4% concordance in detection compared to standard qPCR. We believe that MAD offers new insights into CRISPR-Cas diagnostics and, due to its simplicity, rapidity, and safety, is poised for widespread application in clinical practice.

Current biosensing strategies based on in vitro T7 RNA polymerase reaction

Recently, a unique behavior of T7 RNA polymerase has expanded its functionality as a biosensing platform. Various biosensors utilizing T7 RNA polymerase, combined with fluorescent aptamers, electrochemical probes, or CRISPR/Cas systems, have been developed to detect analytes, including nucleic acids and non-nucleic acid target, with high specificity and low detection limits. Each approach demonstrates unique strengths, such as real-time monitoring and minimal interference, but also presents challenges in stability, cost, and reaction optimization. This review provides an overview of T7 RNA polymerase's role in biosensing technology, highlighting its potential to advance diagnostics and molecular detection in diverse fields.

A one-pot isothermal Fluorogenic Mango II arrays-based assay for label-free detection of miRNA

The capability to detect a small number of miRNAs in clinical samples with simplicity, selectivity, and sensitivity is immensely valuable, yet it remains a daunting task. Here, we described a novel Mango II aptamers-based sensor for the one-pot, sensitive and specific detection of miRNAs. Target miRNA-initiated mediated catalyzed hairpin assembly (CHA) would allow for the production of plenty of DNA duplexes and the formation of the complete T7 promoter, motivating the rolling circle transcription (RCT). Then, the subsequent RCT process efficiently generates a huge number of repeating RNA Mango II aptamers, brightened by the incorporation of fluorescent dye TO1-B for miRNA quantification, realizing label-free and high signal-to-background ratio. Moreover, this assay possesses a remarkable ability to confer high selectivity, enabling the distinction of miRNAs among family members with mere 1- or 2- nucleotide (nt) differences. By employing the proposed assay, we have successfully achieved a sensitive evaluation of miR-21 content in diverse cell lines and clinical serum samples. This offers a versatile approach for the sensitive assay of miRNA biomarkers in molecular diagnosis.

Engineering Gene-Specific DNAzymes for Accessible and Multiplexed Nucleic Acid Testing

The accurate and timely detection of disease biomarkers at the point-of-care is essential to ensuring effective treatment and epidemiological surveillance. Here, we report the selection and engineering of RNA-cleaving DNAzymes that respond to specific genetic markers and amplify detection signals. Because the target-specific activation of gene-specific DNAzymes (gDz) is like the trans-cleavage activity of clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated (Cas) machinery, we further developed a CRISPR-like assay using RNA-cleaving DNAzyme coupled with isothermal sequence and signal amplification (CLARISSA) for nucleic acid detection in clinical samples. Building on the high sequence specificity and orthogonality of gDzs, CLARISSA is highly versatile and expandable for multiplex testing. Upon integration with an isothermal recombinase polymerase amplification, CLARISSA enabled the detection of human papillomavirus (HPV) 16 in 189 cervical samples collected from cervical cancer screening participants (n = 189) with 100% sensitivity and 97.4% specificity, respectively. A multiplexed CLARISSA further allowed the simultaneous analyses of HPV16 and HPV18 in 46 cervical samples, which returned clinical sensitivity of 96.3% for HPV16 and 83.3% for HPV18, respectively. No false positives were found throughout our tests. Besides the fluorescence readout using fluorogenic reporter probes, CLARISSA is also demonstrated to be fully compatible with a visual lateral flow readout. Because of the high sensitivity, accessibility, and multiplexity, we believe CLARISSA is an ideal CRISPR-Dx alternative for clinical diagnosis in field-based and point-of-care applications.

Tetrahedral DNA nanostructures enhance transcription isothermal amplification for multiplex detection of non-coding RNAs

This study introduces an innovative detection system for multiple cancer biomarkers, employing transcription isothermal amplification methods in conjunction with a tetrahedral DNA nanostructure (TDN). We demonstrate that TDN enhances various transcription isothermal amplification methods by placing DNA probes in proximity. Notably, the TDN-enhanced split T7 promoter-based isothermal transcription amplification with light-up RNA aptamer (STAR) system stands out for its optimal performance and operational simplicity, especially in identifying non-coding RNAs such as microRNAs and long non-coding RNAs (lncRNAs). Multiplex detection of lncRNAs was also achieved by generating distinct light-up RNA aptamers, each emitting unique fluorescence signals. The system effectively identified the target lncRNAs, demonstrating high sensitivity and selectivity in both cell lines and clinical samples. The system, utilizing the single enzyme T7 RNA polymerase, can be easily tailored for alternative targets by substituting target-specific sequences in DNA probes and seamlessly integrated with other isothermal amplification methods for greater sensitivity and accuracy in the detection of multiple cancer biomarkers.

Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis

Rapid and simple nucleic acid detection is significant for disease diagnosis and pathogen screening, especially under specific conditions. However, achieving highly sensitive and specific nucleic acid detection to meet the time and equipment demand remains technologically challenging. In this study, we proposed a magnetic separation enhanced colorimetry biosensor based on a toehold-containing three-way junction (TWJ) induced multiple isothermal exponential amplification and the CRISPR/Cas14a (C-TEC) biosensor. The TWJ template was designed as a Y-X-Y structure. In the presence of the target, the formation of toehold-containing TWJ complex induced primer extension, leading to the generation of amplified single-stranded DNA; this amplified DNA could then bind to either the free TWJ template for EXPAR reaction or the toehold of the TWJ complex for toehold-mediated strand displacement, thereby enabling the recycling of the target. The amplification products could trigger CRISPR/Cas14a for efficient trans-cleavage and release the magnetically bound gold nanoparticle probes for colorimetry detection. Using Mycobacterium tuberculosis 16S rDNA as the target, the proposed C-TEC could detect 16S rDNA down to 50 fM by the naked eye and 20.71 fM by UV-vis detector at 520 nm within 90 min under optimal conditions. We successfully applied this biosensor to clinical isolates of Mycobacterium tuberculosis. In addition, the C-TEC biosensor also showed feasibility for the detection of RNA viruses. In conclusion, the proposed C-TEC is a convenient, fast, and versatile platform for visual detection of pathogen DNA/RNA and has potential clinical applications.

Aptamer-Based Switching System for Communication of Non-Interacting Proteins

Biological macromolecules, such as DNA, RNA, and proteins in living organisms, form an intricate network that plays a key role in many biological processes. Many attempts have been made to build new networks by connecting non-communicable proteins with network mediators, especially using antibodies. In this study, we devised an aptamer-based switching system that enables communication between non-interacting proteins. As a proof of concept, two proteins, Cas13a and T7 RNA polymerase (T7 RNAP), were rationally connected using an aptamer that specifically binds to T7 RNAP. The proposed switching system can be modulated in both signal-on and signal-off manners and its responsiveness to the target activator can be controlled by adjusting the reaction time. This study paves the way for the expansion of biological networks by mediating interactions between proteins using aptamers.

Lighting up Lipidic Nanoflares with Self-Powered and Multivalent 3D DNA Rolling Motors for High-Efficiency MicroRNA Sensing in Serum and Living Cells

Intelligent DNA nanomachines are powerful and versatile molecular tools for bioimaging and biodiagnostic applications; however, they are generally constrained by complicated synthetic processes and poor reaction efficiencies. In this study, we developed a simple and efficient molecular machine by coupling a self-powered rolling motor with a lipidic nanoflare (termed RMNF), enabling high-contrast, robust, and rapid probing of cancer-associated microRNA (miRNA) in serum and living cells. The lipidic nanoflare is a cholesterol-based lipidic micelle decorated with hairpin-shaped tracks that can be facilely synthesized by stirring in buffered solution, whereas the 3D rolling motor (3D RM) is a rigidified tetrahedral DNA scaffold equipped with four single-stranded "legs" each silenced by a locking strand. Once exposed to the target miRNA, the 3D RM can be activated, followed by self-powered precession based on catalyzed hairpin assembly (CHA) and lighting up of the lipidic nanoflare. Notably, the multivalent 3D RM that moves using four DNA legs, which allows the motor to continuously and acceleratedly interreact with DNA tracks rather than dissociate from the surface of the nanoflare, yielded a limit of detection (LOD) of 500 fM at 37 °C within 1.5 h. Through the nick-hidden and rigidified structure design, RMNF exhibits high biostability and a low false-positive signal under complex physiological settings. The final application of RMNF for miRNA detection in clinical samples and living cells demonstrates its considerable potential for biomedical imaging and clinical diagnosis.

Fluorescent and visual sensing of sodium dodecylbenzene sulfonate with an aminosilane self-condensation promoting and electrostatic attraction effect-based ratiometric probe

BACKGROUND

Increasing attention has been paid to sodium dodecylbenzene sulfonate (SDBS) detection because it could cause damage to human body and environmental water. For example, SDBS must not be detected on tableware surface according to national standard of China (GB 14934-2016). However, there is no report heretofore addressing SDBS sensing on surfaces. More importantly, the interferents often affect the sensing performance of analytical approaches. Hence, there is an urgent need to establish a method with good anti-interference ability for SDBS detection both on tableware surfaces and in water.

RESULTS

Inspired by a finding that SDBS could cause the generation of white turbidity in (3-aminopropyl)trimethoxysilane (APTMS, an aminosilane) aqueous solution, APTMS modified Mn doped ZnS quantum dots (QDs) and fluorescent (FL) whitening agent (FWA) were constructed as a ratiometric probe for FL and visual sensing of SDBS. The modified QDs aggregated and settled in presence of SDBS, which was likely to be connected to the stimulatory effect of SDBS on the APTMS self-condensation and the electrostatic attraction. The FL emission from the QDs at 605 nm then decreased dramatically, whereas that at 425 nm was virtually constant owing to FWA. SDBS sensing could be achieved by calculating the ratio change of their FL intensities. The detection limits of FL and visual methods were found to be 0.011 and 10 μg/L, respectively, making it one of the most sensitive approaches in literature. Finally, it was successfully utilized for SDBS detection on tableware surfaces and in water.

SIGNIFICANCE

Herein, the specific interaction between SDBS and APTMS was reported and the reaction mechanisms were explored for the first time. The proposed probe based on the effect described above provided a promising potential for SDBS analysis owing to high sensitivity, selectivity, anti-interference ability, and stability (in 20 days).

Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor

The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.

Development of extension-mediated self-folding isothermal amplification technology for SARS-CoV-2 diagnosis

The coronavirus disease (COVID-19) pandemic has highlighted the importance of rapid and accurate diagnosis, and loop-mediated isothermal amplification (LAMP) has become a popular method because of its powerful amplification ability using a simple instrument such as a heater or water bath. However, LAMP has limitations such as the complexity of primer design and the difficulty of designing sequence-specific probes, leading to non-specific amplicons and false-positive results. To overcome these limitations, we developed a novel isothermal amplification system called the Extension-mediated self-folding Isothermal amplification Technology (ExIT). ExIT uses a newly designed, self-folding primer (SP) with two key functions. Hairpin structures are formed when the extended strand of the SP hybridizes, exposing the priming site for continuous binding of the new SP. This results in exponential amplification with only two primers, unlike conventional LAMP primer systems. Additionally, an unnatural base was introduced into the SP, which terminated the extension of polymerase and generated a ssDNA amplicon. This makes it easier to design and apply probes, reducing the possibility of false-positive results even if non-specific amplicons are produced. Through this strategy, we confirmed a sensitivity of 90 copies (3.6 copies/μL) and verified the specificity by testing for the presence or absence of non-complementary targets. Therefore, the validation of the ExIT was completed. In conclusion, ExIT will be key to solving the complexity of conventional LAMP design and offers great potential for successfully introducing sequence-specific probes to improve false positives.

Hairpin Switches-Based Isothermal Transcription Amplification for Simple, Sensitivity Detection of MicroRNA

The ability to simply, selectively, and sensitively detect low numbers of miRNAs in clinical samples is highly valuable but remains a challenge. In this work, we present a novel miRNA detection system by using the elaborately designed hairpin switch, where the T7 primer, template, target recognize sequence, and light-up RNA aptamer template are edited and embedded in one single-stranded DNA hairpin structure. In the beginning, the hairpin switch maintained the hairpin structure 1, in which the ds promoter of T7 polymerase was disrupted, thus the transcription reaction of T7 polymerase was inhibited. After binding to the target, the hairpin switch 1 was unfolded and turned to the hairpin structure 2. This switch initiates the in vitro T7 transcription reaction, producing plenty of RNA transcripts containing RNA aptamers. Consequently, transcribed tremendous RNA aptamers lighted up the fluorophore for quantitative analysis. Compared with the existing T7 polymerase-based amplification system, this strategy exhibits several advantages, including simplicity, convenience, and high selectivity and sensitivity. The experimental results demonstrated that we could achieve the quantification of miRNA in buffer and complex biological samples.

Label-Free Detection of T4 Polynucleotide Kinase Activity and Inhibition via Malachite Green Aptamer Generated from Ligation-Triggered Transcription

Polynucleotide kinase (PNK) is a key enzyme that is necessary for ligation-based DNA repair. The activity assay and inhibitor screening for PNK may contribute to the prediction and improvement of tumor treatment sensitivity, respectively. Herein, we developed a simple, low-background, and label-free method for both T4 PNK activity detection and inhibitor screening by combining a designed ligation-triggered T7 transcriptional amplification system and a crafty light-up malachite green aptamer. Moreover, this method successfully detected PNK activity in the complex biological matrix with satisfactory outcomes, indicating its great potential in clinical practice.

Low-Temperature Loop-Mediated Isothermal Amplification Operating at Physiological Temperature

Loop-mediated isothermal amplification (LAMP) is one of the most widely used isothermal amplification technologies in molecular diagnostics. However, LAMP operates at a high temperature of 65 °C; thus, operating LAMP at a lower temperature is desirable to maximize its usefulness for on-site diagnosis. In this study, we propose a new version of LAMP, termed low-temperature LAMP, which operates at the physiological temperature of 37 °C. Low-temperature LAMP differs from conventional LAMP operating at 65 °C in terms of the concentrations of MgSO₄ and deoxyribonucleoside triphosphates (dNTPs), as well as the lengths of DNA probes, which are crucial for the execution of low-temperature LAMP. Under the optimal conditions, the amplification efficiency of low-temperature LAMP is comparable to that of conventional LAMP. In addition, the ligation reaction at 37 °C, which is necessary to detect actual target nucleic acids, is combined without altering the temperature, enabling the identification of miR-21, a cancer-promoting oncogenic miRNA, with high sensitivity and selectivity. The method described in this paper does not require expensive DNA modifications or special additives and would facilitate the widespread application of LAMP in facility-limited or point-of-care settings, paving the way to improvements in other isothermal-amplification-based techniques.

FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12

Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/μL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.

Mix-and-Detection Assay with Multiple Cyclic Enzymatic Repairing Amplification for Rapid and Ultrasensitive Detection of Long Noncoding RNAs in Breast Tissues

Long noncoding RNAs (lncRNAs) are valuable biomarkers and therapeutic targets, and they play essential roles in various pathological and biological processes. So far, the reported lncRNA assays usually suffer from unsatisfactory sensitivity and time-consuming procedures. Herein, we develop a mix-and-read assay based on multiple cyclic enzymatic repairing amplification (ERA) for sensitive and rapid detection of mammalian metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1). In this assay, we design two three-way junction (3WJ) probes including a 3WJ template and a 3WJ primer to specifically recognize lncRNA MALAT1, and the formation of a stable 3WJ structure induces cyclic ERA to generate triggers. The resulting triggers subsequently hybridize with a free 3WJ template and act as primers to initiate new rounds of cyclic ERA, generating abundant triggers. The hybridization of triggers with signal probes forms stable double-stranded DNA duplexes that can be specifically cleaved by apurinic/apyrimidinic endonuclease 1 to produce a high fluorescence signal. This assay can be carried out in a mix-and-read manner within 10 min under an isothermal condition (50 °C), which is the rapidest and simplest method reported so far for the lncRNA MALAT1 assay. This method can sensitively detect lncRNA MALAT1 with a limit of detection of 0.87 aM, and it can accurately measure endogenous lncRNA MALAT1 at the single-cell level. Moreover, this method can distinguish lncRNA MALAT1 expression in breast cancer patient tissues and their corresponding healthy adjacent tissues. Importantly, the extension of this assay to different RNAs detection can be achieved by simply replacing the corresponding target recognition sequences.

Rapid, specific and sensitive detection of Vibrio parahaemolyticus in seafood by accelerated strand exchange amplification

Vibrio parahaemolyticus infectious diseases caused by seafood contamination may be life-threatening to people with weak immunity. The detection of the Vibrio parahaemolyticus pathogen in aquatic foods is critical for reducing the outbreak of human Vibrio parahaemolyticus-associated diseases. In this study, a highly sensitive, specific, and time-saving real-time narrow thermal-cycling amplification detection method was developed based on accelerated strand exchange amplification (ASEA). It can detect cultured Vibrio parahaemolyticus at concentrations as low as 25 CFU mL^-1. In addition, for artificially spiked scallop meat, the detection limit was 1.8 × 10³ CFU g^-1 without pre-culture and 18 CFU g^-1 of initial inoculum after 3 h enrichment. The whole assay, starting from DNA extraction, can be completed within 20 min. The ASEA detection method established in this study is an effective tool for the rapid detection of Vibrio parahaemolyticus strains in a large number of seafood samples.

Construction and Application of Orthogonal T7 Expression System in Eukaryote: An Overview

The T7 system is an orthogonal transcription-system, which is characterized by simplicity, higher efficiency, and higher processivity, and it is used for protein or mRNA synthesis in various biological-systems. In comparison with prokaryotes, the construction of the T7 expression system is still on-going in eukaryotes, but it shows greatly applicable prospects. In the present paper, development of T7 expression system construction in eukaryotes is reviewed, including its construction in animal (mammalian cells, trypanosomatid protozoa, Xenopus oocytes, zebrafish), plant, and microorganism and its application in vaccine production and gene therapy. In addition, the innate challenges of T7 expression system construction in eukaryote and its potential application in vaccine production and gene therapy are discussed.

A functional RNA/DNA circuit for one-pot detection of SARS-CoV-2 RNA

A simple method is proposed in this work for the detection of SARS-CoV-2 RNA based on a functional RNA/DNA circuit. By ingeniously integrating the nucleic acid circuit technology and CRISPR/cas12a system, this method can achieve femtomolar detection of the target RNA in one step and successfully distinguish COVID-19 positive cases from clinical samples, proving its great potential for clinical application.

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.

An Update on Detection Technologies for SARS-CoV-2 Variants of Concern

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the global epidemic of Coronavirus Disease 2019 (COVID-19), with a significant impact on the global economy and human safety. Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard for detecting SARS-CoV-2, but because the virus's genome is prone to mutations, the effectiveness of vaccines and the sensitivity of detection methods are declining. Variants of concern (VOCs) include Alpha, Beta, Gamma, Delta, and Omicron, which are able to evade recognition by host immune mechanisms leading to increased transmissibility, morbidity, and mortality of COVID-19. A range of research has been reported on detection techniques for VOCs, which is beneficial to prevent the rapid spread of the epidemic, improve the effectiveness of public health and social measures, and reduce the harm to human health and safety. However, a meaningful translation of this that reduces the burden of disease, and delivers a clear and cohesive message to guide daily clinical practice, remains preliminary. Herein, we summarize the capabilities of various nucleic acid and protein-based detection methods developed for VOCs in identifying and differentiating current VOCs and compare the advantages and disadvantages of each method, providing a basis for the rapid detection of VOCs strains and their future variants and the adoption of corresponding preventive and control measures.

Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method

Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 poses a significant threat to global public health. Early detection with reliable, fast, and simple assays is crucial to contain the spread of SARS-CoV-2. The real-time reverse transcription-polymerase chain reaction (RT-PCR) assay is currently the gold standard for SARS-CoV-2 detection; however, the reverse transcription loop-mediated isothermal amplification method (RT-LAMP) assay may allow for faster, simpler and cheaper screening of SARS-CoV-2. In this study, the triple-target RT-LAMP assay was first established to simultaneously detect three different target regions (ORF1ab, N and E genes) of SARS-CoV-2. The results revealed that the developed triplex RT-LAMP assay was able to detect down to 11 copies of SARS-CoV-2 RNA per 25 µL reaction, with greater sensitivity than singleplex or duplex RT-LAMP assays. Moreover, two different indicators, hydroxy naphthol blue (HNB) and cresol red, were studied in the colorimetric RT-LAMP assay; our results suggest that both indicators are suitable for RT-LAMP reactions with an obvious color change. In conclusion, our developed triplex colorimetric RT-LAMP assay may be useful for the screening of COVID-19 cases in limited-resource areas.

Single-tube isothermal label-free fluorescent sensor for pathogen detection based on genetic signatures

We report on a single-tube biosensor for real-time detection of bacterial pathogens with multiplex capabilities. The biosensor consists of two DNA probes, which bind to the complementary fragment of a bacterial RNA to form a three-way junction (3WJ) nucleic acid structure. One of the probes encodes a fluorescent light-up RNA aptamer under T7 promoter. It allows for generation of multiple aptamer copies due to elongation and transcription of the 3WJ structure in the presence of the complementary target. The aptamer coordinates and thereby enhances fluorescence of a cognate fluorogenic dye, allowing for fluorescent detection of the RNA target. Multiple aptamer copies can be produced from a single target-dependent 3WJ structure allowing for amplification and visual observation of the signal. The limit of detection depended on the assay time and was found to be 1.7 nM or 0.6 nM for 30-min or 60-min assay, respectively, when N-methylmesoporphyrin IX (NMM) was used as a fluorescent indicator. The sensor is excellent in analyzing folded RNA targets and differentiating between closely related sequences due to the multicomponent character of the target-interrogating probe. Response to unamplified samples of total bacterial RNA from Mycobacterium tuberculosis complex or Escherichia coli was observed with excellent selectivity within 30 min under isothermal conditions at 50°C in a one-tube one-step assay. Several bacterial species can be detected in multiplex by utilizing biosensors with the template strands encoding different light-up aptamers. The isothermal one-tube-one-step format of the assay and the possibility to monitor the signal visually makes it amenable to use in a point-of-care scenario.

A Rotatable Paper Device Integrating Reverse Transcription Loop-Mediated Isothermal Amplification and a Food Dye for Colorimetric Detection of Infectious Pathogens

In this study, we developed a rotatable paper device integrating loop-mediated isothermal amplification (RT-LAMP) and a novel naked-eye readout of the RT-LAMP results using a food additive, carmoisine, for infectious pathogen detection. Hydroxyl radicals created from the reaction between CuSO4 and H2O2 were used to decolor carmoisine, which is originally red. The decolorization of carmoisine can be interrupted in the presence of DNA amplicons produced by the RT-LAMP reaction due to how DNA competitively reacts with the hydroxyl radicals to maintain the red color of the solution. In the absence of the target DNA, carmoisine is decolored, owing to its reaction with hydroxyl radicals; thus, positive and negative samples can be easily differentiated based on the color change of the solution. A rotatable paper device was fabricated to integrate the RT-LAMP reaction with carmoisine-based colorimetric detection. The rotatable paper device was successfully used to detect SARS-CoV-2 and SARS-CoV within 70 min using the naked eye. Enterococcus faecium spiked in milk was detected using the rotatable paper device. The detection limits for the SARS-CoV-2 and SARS-CoV targets were both 103 copies/µL. The rotatable paper device provides a portable and low-cost tool for detecting infectious pathogens in a resource-limited environment.

Easy Express Extraction (TripleE)-A Universal, Electricity-Free Nucleic Acid Extraction System for the Lab and the Pen

The complexity of the current nucleic acid isolation methods limits their use outside of the modern laboratory environment. Here, we describe a fast and affordable method (easy express extraction, called TripleE) as a centrifugation-free and electricity-free nucleic acid isolation method. The procedure is based on the well-established magnetic-bead extraction technology using an in-house self-made magnetic 8-channel and a rod cover. With this extraction system, nucleic acids can be isolated with two simple and universal protocols. One method was designed for the extraction of the nucleic acid in resource-limited “easy labs”, and the other method can be used for RNA/DNA extraction in the field for so-called molecular “pen-side tests”. In both scenarios, users can extract up to 8 samples in 6 to 10 min, without the need for any electricity, centrifuges or robotic systems. In order to evaluate and compare both methods, clinical samples from various viruses (African swine fever virus; lumpy skin disease virus; peste des petits ruminants virus; bluetongue virus), matrices and animals were tested and compared with standard magnetic-bead nucleic acid extraction technology based on the KingFisher platform. Hence, validation data were generated by evaluating two DNA viruses as well as one single-stranded and one double-stranded RNA virus. The results showed that the fast, easy, portable and electricity-free extraction protocols allowed rapid and reliable nucleic acid extraction for a variety of viruses and most likely also for other pathogens, without a substantial loss of sensitivity compared to standard procedures. The speed and simplicity of the methods make them ideally suited for molecular applications, both within and outside the laboratory, including limited-resource settings.

Highly Efficient DNA Reporter for CRISPR/Cas12a-Based Specific and Sensitive Biosensor

In addition to cis-cleavage activity that recognizes and cleaves nucleic acid sequences, a trans-cleavage activity that indiscriminately and non-specifically cleaves single-stranded DNA or RNA has been discovered in some Cas proteins, including Cas12a and Cas13a. Various detection methods using this activity have been widely reported. Herein, we describe a new highly efficient DNA reporter (5'-TTATT-CCCCC-3'; TTATT-5C) that outperformed the existing AT-rich DNA reporter (5'-TTATT-3') used in most Cas12a-based target nucleic detection assays. By systematically investigating the effect of DNA reporter length and sequence on the trans-cleavage activity of Cas12a, we achieved up to a 100-fold increase in fluorescence signal intensity derived from the trans-cleavage activity of Cas12a compared to that achieved using the existing AT-rich DNA reporter. The new DNA reporter was also applied, along with the existing AT-rich DNA reporter, for the detection of the Salmonella enterotoxin (stn) gene. Importantly, both detection speed and limit were significantly enhanced with the new DNA reporter. In addition, polymerase chain reaction (PCR) was adopted to the CRISR/Cas-Based system of the new DNA reporter, thereby confirming its practical applicability. The high-efficiency DNA reporter described herein can pave the way for further improving the trans-cleavage activity of other Cas proteins, as well as the sensitivity of CRISPR/Cas-Based systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13206-022-00081-0.