Simple and sensitive detection of microRNAs with ligase chain reaction

Entropy-Driven Catalytic G-Quadruple Cycle Amplification Integrated with Ligases for Label-Free Detection of Single Nucleotide Polymorphisms

G-Quadruplex/thioflavin (G4/THT) has become a very promising label-free fluorescent luminescent element for nucleic acid detection due to its good programmability and compatibility. However, the weak fluorescence efficiency of single-molecule G4/THT limits its potential applications. Here, we developed an entropy-driven catalytic (EDC) G4 (EDC-G4) cycle amplification technology as a universal label-free signal amplification and output system by properly programming classical EDC and G4 backbone sequences, preintegrated ligase chain reaction (LCR) for label-free sensitive detection of single nucleotide polymorphisms (SNPs). First, the positive strand LCR enabled specific transduction and preliminary signal amplification from single-base mutation information to single-strand information. Subsequently, the EDC-G4 cycle amplification reaction was activated, accompanied by the production of a large number of G4/THT luminophores to output fluorescent signals. The EDC-G4 system was proposed to address the weak fluorescence of G4/THT and obtain a label-free fluorescence signal amplification. The dual-signal amplification effect enabled the LCR-EDC-G4 detection system to accurately detect mutant target (MT) at concentrations as low as 22.39 fM and specifically identify 0.01% MT in a mixed detection pool. Moreover, the LCR-EDC-G4 system was further demonstrated for its potential application in real biological samples. Therefore, this study not only contributes ideas for the development of label-free fluorescent biosensing strategies but also provides a high-performance and practical SNP detection tool in parallel.

Light-activated CRISPR-Cas12a for amplified imaging of microRNA in cell cycle phases at single-cell levels

An ortho-nitrobenzyl phosphate ester-caged nucleic acid hairpin structure coupled to the CRISPR-Cas12a complex is introduced as a functional reaction module for the light-induced activation of the CRISPR-Cas12a (LAC12a) machinery toward the amplified fluorescence detection of microRNA-21 (miRNA-21). The LAC12a machinery is applied for the selective, in vitro sensing of miRNA-21 and for the intracellular imaging of miRNA-21 in different cell lines. The LAC12a system is used to image miRNA-21 in different cell cycle phases of MCF-7 cells. Moreover, the LAC12a machinery integrated in cells enables the two-photon laser confocal microscopy-assisted, light-stimulated spatiotemporal, selective activation of the CRISPR-Cas12a miRNA-21 imaging machinery at the single-cell level and the evaluation of relative expression levels of miRNA-21 at distinct cell cycle phases. The method is implemented to map the distribution of cell cycle phases in an array of single cells.

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.

Ligation-Based High-Performance Mimetic Enzyme Sensing Platform for Nucleic Acid Detection

G-quadruplex (G4)/hemin DNAzyme is a promising candidate to substitute horseradish peroxidase in biosensing systems, especially for the detection of nucleic acids. However, the relatively suboptimal catalytic capacity limits its potential applications. This makes it imperative to develop an ideal signal for the construction of highly sensitive biosensing platforms. Herein, we integrated a novel chimeric peptide-DNAzyme (CPDzyme) with the ligase chain reaction (LCR) for the cost-efficient and highly sensitive detection of nucleic acids. By employing microRNA (miRNA) and single-nucleotide polymorphism detection as the model, we designed a G4-forming sequence on the LCR probe with a terminally labeled amino group. Subsequently, asymmetric hemin with carboxylic arms allowed assembly with the LCR products and peptide to form CPDzyme, followed by the magnetic separation of the extraneous components and chemiluminescence detection. Compared with the conventional G4/hemin signaling-based method, the LCR-CPDzyme system demonstrated 3 orders of magnitude improved sensitivity, with accurate quantification of as low as 25 aM miRNA and differentiation of 0.1% of mutant DNA from the pool containing a large amount of wild-type DNA. The proposed LCR-CPDzyme strategy is a potentially powerful method for in vitro diagnostics and serves as a reference for the development of other ligation- or hybridization-based nucleic acid amplification assays.

Electrochemiluminescent bioassay based on Ru@Zr-BTC-MOFs nanoparticles for determination of let-7a miRNA using the hybridization chain reaction

Carboxyl-rich tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) ([Ru(dcbpy)3]2+) and 1,3,5-phenyl tricarboxylic acid (H3BTC) were used as the organic ligand to synthesize the metal-organic frameworks by a simple one-pot hydrothermal method with ZrCl4 as metal ion source. Subsequently, the excellent electrochemiluminescence (ECL) luminophore (denoted as Ru@Zr-BTC-MOFs) was obtained. The Ru@Zr-BTC-MOFs displayed outstanding ECL properties, and a sensitive ECL bioassay based on Ru@Zr-BTC-MOFs was designed for the detection of let-7a microRNA (miRNA) using hybrid chain reaction (HCR). Under the optimal experimental conditions, the proposed bioassay exhibited a good linear relationship in the range from 50.0 fM to 5.00 × 102 pM with a detection limit of 3.71 fM. Besides, the proposed sensor exhibited satisfactory performance in real samples. The recovery was 91 ~ 108%, and the relative standard deviation was less than 5.6%. It might have potential clinical applications for detecting miRNA in biomedical research and clinical diagnosis. The schematic diagram of the preparation of Ru@Zr-BTC-MOFs (a) and ECL sensor for detecting let -7a (b).

Real-time detection of SARS-CoV-2 in clinical samples via ultrafast ligation-dependent RNA transcription amplification

RNA has been recognized as an important biomarker of many infectious pathogens; thus, sensitive, simple and rapid detection of RNA is urgently required for the control of epidemics. Herein, we report an ultrafast ligation-dependent RNA transcription amplification assay with high sensitivity and specificity for real-time detection of SARS-CoV-2 in real clinical samples, termed splint-based cascade transcription amplification (SCAN). Target RNA is first recognized by two DNA probes, which are then ligated together by SplintR, followed by the binding of the T7 promotor and T7 RNA polymerase to the ligated probe and the start of the transcription process. By introducing a vesicular stomatitis virus (VSV) terminator in the ligated probe, large amounts of RNA transcripts are rapidly produced within 10 min, which then directly hybridize with molecular beacons (MBs) and trigger the conformational switch of the MBs to generate a fluorescence signal that can be monitored in real time. The SCAN assay, which can be completed within 30-50 min, has a limit of detection of 10⁴ copies per mL, while exhibiting high specificity to distinguish the target pathogen from those causing similar syndromes. More importantly, the results of SCAN for SARS-CoV-2 detection in clinical samples display great agreement with the most used qRT-PCR and qRT-LAMP, indicating great potential in the diagnosis of pathogens in clinical practice.

A duplex-specific nuclease (DSN) and catalytic hairpin assembly (CHA)-mediated dual amplification method for miR-146b detection

A novel method for detecting miRNA has been developed using a combination of duplex-specific nuclease signal amplification (DSNSA) and a catalytic hairpin assembly (CHA). In this work, a biotinylated trigger release (BTR) probe with a biotin group at the 3'-end and a CHA reaction sequence trigger as an initiator (catalyst I) at the 5'-end was designed to hybridize target miRNA. The DSN enzyme was introduced to initiate the DSNSA. The miRNA was released to consume more BTR probes and amplify the signals. Subsequently, streptavidin-coated magnetic beads (SA-MBs) were added to the DSNSA reaction solution to remove excess BTR probes that did not hybridize with miRNA, which would then separate BTR probes and catalyst-I, to ensure detection with high selectivity and sensitivity. The catalyst-I remaining in the solution could trigger the CHA reaction to enable signal amplification in the second step. The developed method exhibits a sensitive detection limit and excellent selectivity in identifying a high sequence homology among family members.

Advances in microRNA from adipose-derived mesenchymal stem cell-derived exosome: focusing on wound healing

Skin wounds are a common condition causing economic burden and they represent an urgent clinical need, especially chronic wounds. Numerous studies have been conducted on the applications of stem cell therapy in wound healing, with adipose-derived mesenchymal stem cells (ADMSCs) playing a major role since they can be isolated easily, yielding a high number of cells, the less invasive harvesting required, the longer life span and no ethical issues. However, the lack of standardized doses and protocols, the heterogeneity of clinical trials, as well as the incompatibility of the immune system limit its application. Recent studies have demonstrated that specific stem cell functions depend on paracrine factors, including extracellular vesicles, in which microRNAs in exosomes (Exo-miRNAs) are essential in controlling their functions. This paper describes the application and mechanism whereby ADMSC-Exo-miRNA regulates wound healing. ADMSC-Exo-miRNA is involved in various stages in wounds, including modulating the immune response and inflammation, accelerating skin cell proliferation and epithelialization, promoting vascular repair, and regulating collagen remodeling thereby reducing scar formation. In summary, this acellular therapy based on ADMSC-Exo-miRNA has considerable clinical potential, and provides reference values for developing new treatment strategies for wound healing.

Point-of-Care Tests for HIV Drug Resistance Monitoring: Advances and Potentials

HIV/AIDS is a global public health crisis that is yet to be contained. Effective management of HIV drug resistance (HIVDR) supported by close resistance monitoring is essential in achieving the WHO 95-95-95 targets, aiming to end the AIDS epidemic by 2030. Point-of-care tests (POCT) enable decentralized HIVDR testing with a short turnaround time and minimal instrumental requirement, allowing timely initiation of effective antiretroviral therapy (ART) and regimen adjustment as needed. HIVDR POCT is of particular significance in an era when ART access is scaling up at a global level and enhanced HIVDR monitoring is urgently needed, especially for low-to-middle-income countries. This article provides an overview of the currently available technologies that have been applied or potentially used in HIVDR POCT. It may also benefit the continued research and development efforts toward more innovative HIVDR diagnostics.

Integration of the Ligase Chain Reaction with the CRISPR-Cas12a System for Homogeneous, Ultrasensitive, and Visual Detection of microRNA

The ligase chain reaction (LCR), as a classic nucleic acid amplification technique, is popular in the detection of DNA and RNA due to its simplicity, powerfulness, and high specificity. However, homogeneous and ultrasensitive LCR detection is still quite challenging. Herein, we integrate the LCR with a CRISPR-Cas12a system to greatly promote the application of the LCR in a homogeneous fashion. By employing microRNA as the model target, we design LCR probes with specific protospacer adjacent motif sequences and the guide RNA. Then, the LCR is initiated by target microRNA, and the LCR products specifically bind to the guide RNA to activate the Cas12a system, triggering secondary signal amplification to achieve ultrasensitive detection of microRNA without separation steps. Moreover, by virtue of a cationic conjugated polymer, microRNA can not only be visually detected by naked eyes but also be accurately quantified based on RGB ratio analysis of images with no need of sophisticated instruments. The method can quantify microRNA up to 4 orders of magnitude, and the determination limit is 0.4 aM, which is better than those of other reported studies using CRISPR-Cas12a and can be compared with that of the reverse-transcription polymerase chain reaction. This study demonstrates that the CRISPR-Cas12a system can greatly expand the application of the LCR for the homogeneous, ultrasensitive, and visual detection of microRNA, showing great potential in efficient nucleic acid detection and in vitro diagnosis.

Label-free and sensitive MiRNA detection based on turn-on fluorescence of DNA-templated silver nanoclusters coupled with duplex-specific nuclease-assisted signal amplification

A novel strategy for microRNAs (miRNAs) detection has been developed utilizing duplex-specific nuclease-assisted signal amplification (DSNSA) and guanine-rich DNA-enhanced fluorescence of DNA-templated silver nanoclusters (AgNCs). The combination between target miRNA, DSNSA, and AgNCs is achieved by the unique design of DNA sequences. Target miRNA opens the hairpin structure of the Hairpin DNA probe (HP) by hybridizing with the HP and initiates the duplex-specific nuclease-assisted signal amplification (DSNSA) reaction. The DSNSA reaction generates the release of the guanine-rich DNA sequence, which can turn on the fluorescence of the dark AgNCs by hybridizing with the DNA template of the dark AgNCs. The fluorescence intensity of AgNCs corresponds to the dosage of the target miRNA. This is measured at 630 nm by exciting at 560 nm. The constructed method exhibits a low detection limit (~8.3 fmol), a great dynamic range of more than three orders of magnitude, and excellent selectivity. Moreover, it has a good performance for miR-21 detection in complex biological samples. A novel strategy for microRNAs (miRNAs) detection has been developed utilizing duplex-specific nuclease-assisted signal amplification (DSNSA) and guanine-rich DNA-enhanced fluorescence of DNA-templated silver nanoclusters (AgNCs).

Graphene Oxide Biosensors Based on Hybridization Chain Reaction Signal Amplification for Detecting Biomarkers of Radiation-Resistant Nasopharyngeal Carcinoma and Imaging in Living Cells

Since microRNA-205 (miRNA-205) is a predictive biomarker for antiradiation of nasopharyngeal carcinoma (NPC), quantitative detection of miRNA-205 is important for developing personalized strategies for the treatment of NPC. In this investigation, based on the graphene oxide (GO) sensor and hybridization chain reaction (HCR) for fluorescence signal amplification, a highly sensitive and selective detection method for miRNA-205 was designed. A target-recycling mechanism is employed, where a single miRNA-205 target triggers the signal amplification of many DNA signal probes. The biosensor shows the ability to analyze miRNA-205 in solution, and it can detect miRNA-205 at concentrations as low as 311.96 pM. Furthermore, the method is specific in that it distinguishes between a target miRNA and a sequence with single-, double-, and three-base mismatches, as well as other miRNAs. Considering its simplicity and superior sensitivity, it was also verified in 1‰ serum with a detection limit of 111.65 pM. Importantly, the method successfully demonstrated that miRNA-205 could be imaged in living cells, which provided the possibility of localizing target molecules in live cell imaging applications. This method has great clinical application potential in the determination of miRNA-205, a biomarker for radiation-resistant NPC.

Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV

Infectious diseases caused by viruses such as SARS-CoV-2 and HPV have greatly endangered human health. The nucleic acid detection is essential for the early diagnosis of diseases. Here, we propose a method called PLCR (PfAgo coupled with modified Ligase Chain Reaction for nucleic acid detection) which utilizes PfAgo to only use DNA guides longer than 14-mer to specifically cleave DNA and LCR to precisely distinguish single-base mismatch. PLCR can detect DNA or RNA without PCR at attomolar sensitivities, distinguish single base mutation between the genome of wild type SARS-CoV-2 and its mutant spike D614G, effectively distinguish the novel coronavirus from other coronaviruses and finally achieve multiplexed detection in 70 min. Additionally, LCR products can be directly used as DNA guides without additional input guides to simplify primer design. With desirable sensitivity, specificity and simplicity, the method can be extended for detecting other pathogenic microorganisms.

Ultrasensitive homogeneous detection of microRNAs in a single cell with specifically designed exponential amplification

We firstly developed an ultrasensitive method based on specifically designed exponential amplification for miRNA detection with simple operation in homogeneous solutions. The proposed assay can detect miRNAs at a concentration as low as 1 aM and can be successfully applied for routine miRNA detection in a single cell.

Real-time quantification of fusion transcripts with ligase chain reaction by direct ligation of adjacent DNA probes at fusion junction

Gene fusions, produced by aberrant juxtapositions of two or more genes even in different chromosomes, play important roles in the primary oncogenic mechanism and have been demonstrated to be typically associated with many cancers. So the fused genes or the transcripts can be specific predictive biomarkers for cancer diagnosis and therapy. Herein, we develop a direct ligation- and ligase chain reaction (LCR)-based method for a fusion transcript assay. In virtue of the high selectivity of ligase and the exponential amplification capacity of LCR, the proposed method can detect as low as 1 fM fusion transcripts with high specificity and has been successfully applied to real samples. With the real-time fluorescence measurements, the fusion transcripts can be assayed in a simple way. Therefore, the proposed method can provide a simple and cost-effective platform for fusion transcript detection in routine laboratories and clinical diagnosis.

Polysaccharide-enhanced ARGET ATRP signal amplification for ultrasensitive fluorescent detection of lung cancer CYFRA 21-1 DNA

An ultrasensitive fluorescence biosensor for detecting cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA of non-small cell lung carcinoma (NSCLC) is designed using polysaccharide and activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) signal amplification strategy. Thiolated peptide nucleic acid (PNA) is fixed on magnetic nanoparticles (MNPs) by a cross-linking agent and hybridized with CYFRA 21-1 DNA. Hyaluronic acid (HA) is linked to PNA/tDNA heteroduplexes in the form of carboxy-Zr⁴⁺-phosphate. Subsequently, multiple 2-bromo-2-methylpropionic acid (BMP) molecules are linked with HA to initiate ARGET ATRP reaction. Finally, a large number of fluorescein o-acrylate (FA) monomers are polymerized on the macro-initiators, and the fluorescence signal is significantly amplified. Under optimal conditions, this biosensor shows a significant linear correlation between the fluorescence intensity and logarithm of CYFRA 21-1 DNA concentration (0.1 fM to 0.1 nM), and the limit of detection is as low as 78 aM. Furthermore, the sensor has a good ability to detect CYFRA 21-1 DNA in serum samples and to recognize mismatched bases. It suggests that the strategy has broad application in early diagnosis by virtue of its high sensitivity and selectivity. Graphical abstract A novel and highly sensitive fluorescence biosensor for quantitatively detecting CYFRA 21-1 DNA via dual signal amplification of hyaluronic acid and ARGET ATRP reaction was developed. This proposed method has a low detection limit, wide detection range, high selectivity, and strong anti-interference.

Direct and sensitive detection of circulating miRNA in human serum by ligase-mediated amplification

MicroRNAs (miRNA) involve in regulating different physiological processes whose dysregulation is associated with a wide range of diseases including cancers, diabetes and cardiovascular problems. Herein, we report a direct, sensitive and highly selective detection assay for circulating microRNA (miRNA). This detection strategy employs magnetic nanoparticles as the reaction platform which can not only allow online pre-concentration and selective separation but also integrates ligation reaction with amplification to enhance the sensitivity of the detection assay. With the presence of the target miRNA, the locked nucleic acid (LNA)-modified molecular beacon (MB) opens up, exposing the binding sites at two ends. The 3'- and 5'-end of the MB responsible for the attachment onto the magnetic nanoparticles, and reporting probe for the attachment of the pair of amplification probes respectively. The ligase ligate RNA to DNA enhance the amplification efficiency. Upon labelled with intercalating fluorophores (YOYO-1) on the hybrids, the quantification of the target miRNA was determined by measuring the fluorescence intensity. A detection limit of 314 fM was achieved with trace amount of sample consumption (~20 μL). As a proof of concept, miRNA-149 was chosen as the target miRNA. This assay is capable of discriminating single-base and reliably quantifying circulating miRNA-149 in both healthy and cancer patient's serums. The result obtained was comparable with that of quantitative reverse transcription polymerase chain reaction (qRT-PCR), suggesting that this direct and sensitive assay can be served as a promising, non-invasive tool for early diagnosis of breast cancer and colorectal cancer.

Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses

We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.

Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.

Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA

A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N₃, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N₃-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.

A simple and isothermal ligase-based amplification approach based on a ligation-activated cleavage reaction

We develop a simple and isothermal ligase-based cyclic amplification approach for the sensitive detection of polynucleotide kinase, DNA, proteins and ATP.

Recent advances in microRNA detection

Recent advances in miRNA detection methods and new applications.

An enzyme-free flow cytometric bead assay for the sensitive detection of microRNAs based on click nucleic acid ligation-mediated signal amplification

An enzyme-free flow cytometric assay is developed for the sensitive detection of microRNAs based on click nucleic acid ligation-mediated signal amplification.

One-step detection of microRNA with high sensitivity and specificity via target-triggered loop-mediated isothermal amplification (TT-LAMP)

A target-triggered loop-mediated isothermal amplification (TT-LAMP) mechanism is developed for simple one-step but highly sensitive detection of microRNAs.

A simple molecular beacon with duplex-specific nuclease amplification for detection of microRNA

A target recycling amplification method based on a simple molecular beacon and duplex-specific nuclease has been developed for microRNA detection.

Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction

We have developed a new ligase chain reaction-based colorimetric assay for detection of DNA methylation with ultrahigh sensitivity and selectivity. Using the proposed assay, as low as 0.01 fM methylated DNA can be detected by visualization of color changes of gold nanoparticles with the naked eye.

One-Step Ligation on RNA Amplification for the Detection of Point Mutations

The detection of point mutations is required in the diagnosis of many human diseases. The conformal specificity of DNA ligases was elegantly used to distinguish single-nucleotide mismatches. However, to detect point mutations in RNA retroviruses, conventional ligase-mediated approaches require the reverse transcription of viral genomes before separate ligation and amplification steps. We developed one-step ligation on RNA amplification (LRA) for the direct detection of RNA point mutations. The process combines the ligase-mediated joining of two oligonucleotides and subsequent hot start amplification into a single-tube reaction. We report that modifications to the structure of the oligonucleotide ligation probes improve the rate of ligation and the specificity of mutation detection on RNA. We applied LRA to the detection of a common, clinically relevant HIV-1 reverse transcriptase drug-resistant point mutation, K103N, and compared it with allele-specific PCR and pyrosequencing. LRA achieved a limit of specific quantitation of 1:100 (1%), and a limit of specific detection for mutant K103N RNA transcripts among excess wild-type strands of 1:10,000 (0.01%). LRA also exhibited good detection threshold of 5 × 10(2) copies/μL K103N RNA transcripts. LRA is a novel point mutation detection method, with potential utilization in HIV drug resistance detection and early diagnostics of genetic disorders associated with other infectious diseases and cancer.

"Signal-on" photoelectrochemical biosensor for sensitive detection of human T-Cell lymphotropic virus type II DNA: dual signal amplification strategy integrating enzymatic amplification with terminal deoxynucleotidyl transferase-mediated extension

A novel "signal-on" photoelectrochemical (PEC) biosensor for sensitive detection of human T-cell lymphotropic virus type II (HTLV-II) DNA was developed on the basis of enzymatic amplification coupled with terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. The intensity of the photocurrent signal was proportional to the concentration of the HTLV-II DNA-target DNA (tDNA) by dual signal amplification. In this protocol, GR-CdS:Mn/ZnS nanocomposites were used as photoelectric conversion material, while pDNA was used as the tDNA recognizing unit. Moreover, the TdT-mediated extension and the enzymatic signal amplification technique were used to enhance the sensitivity of detection. Using this novel dual signal amplification strategy, the prototype of PEC DNA sensor can detect as low as ∼0.033 fM of HTLV-II DNA with a linear range of 0.1-5000 fM, with excellent differentiation ability even for single-base mismatches. This PEC DNA assay opens a promising platform to detect various DNA targets at ultralow levels for early diagnoses of different diseases.

A simple and highly sensitive fluorescence assay for microRNAs

A simple and highly sensitive assay for miRNAs using magnetic bead-carried DNA probes coupled with DSN-facilitated isothermal target cycling is reported.

Homogeneous and sensitive detection of microRNA with ligase chain reaction and lambda exonuclease-assisted cationic conjugated polymer biosensing

A simple and homogeneous microRNA assay is developed by integration of ligase chain reaction (LCR) and lambda exonuclease-assisted cationic conjugated polymer (CCP) biosensing. LCR is utilized for exponential amplification of microRNA, and lambda exonuclease is introduced to degrade excess fluorescein-labeled probes in LCR for eliminating background signal. After addition of CCP, efficient fluorescence resonance energy transfer from CCP to fluorescein in LCR products occurs. The method is sensitive enough to detect 0.1 fM target microRNA and specific to discriminate one-base difference of microRNAs, which paves a new way for homogeneous microRNA detection and molecular diagnosis.

Highly sensitive and specific multiplexed microRNA quantification using size-coded ligation chain reaction

As important regulators of gene expression, microRNAs (miRNAs) are emerging as novel biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. There is a great demand for flexible multiplexed miRNA quantification methods that can quantify very low levels of miRNA targets with high specificity. For further analysis of miRNA signatures in biological samples, we describe here a highly sensitive and specific method to detect multiple miRNAs simultaneously in total RNA. First, we rationally design one of the DNA probes modified with two ribonucleotides, which can greatly improve the ligation efficiency of DNA probes templated by miRNAs. With the modified DNA probes, the ligation chain reaction (LCR) can be well applied to miRNA detection and as low as 0.2 fM miRNA can be accurately determined. High specificity to clearly discriminate a single nucleotide difference among miRNA sequences can also be achieved. By simply coding the DNA probes with different length of oligo (dA) for different miRNA targets, multiple miRNAs can be simultaneously detected in one LCR reaction. In our proof of principle work, we detect three miRNAs: let-7a, mir-92a, and mir-143, which can also be simultaneously detected in as small as 2 ng of total RNA sample.

Ligase chain reaction coupled with rolling circle amplification for high sensitivity detection of single nucleotide polymorphisms

We present a highly sensitive and homogeneous assay for the detection of single nucleotide polymorphisms (SNPs) by ligase chain reaction (LCR) coupled with rolling circle amplification (RCA). The LCR probes include one pair of probes and a padlock probe (PLP). In the LCR, one pair of probes composed of X and Y, perfectly hybridize with the upper strand of the target DNA after thermal denaturation. They are then ligated by the thermostable ligase to form the ligation product of XY. At the same time, the PLP hybridizes with the lower strand of the target DNA and are ligated to form the circular PLP (cPLP). After repeated cycles of denaturation, annealing, and ligation, the target DNA is amplified exponentially to generate a large number of XY and cPLPs. Subsequently, RCA is triggered by the cPLP as a template and XY as a primer, producing large numbers of long strand DNA products, which are detected by binding with the fluorescent dye, SYBR Green I, in a homogeneous manner. This method is simple, and avoids the need for detection of the LCR products with labeled probes and complex separation steps. The assay is sensitive and specific enough to detect a 1 fM target DNA molecule. It is possible to accurately determine the allele frequency as low as 1.0%. The LCR coupled with RCA assay extends the application of the LCR and RCA, and provides a new strategy for detecting SNPs as well as nucleic acid analysis, immunoassay, and molecular diagnosis.

Graphene surface-anchored fluorescence sensor for sensitive detection of microRNA coupled with enzyme-free signal amplification of hybridization chain reaction

A new enzyme-free signal amplification-based assay for microRNA (miRNA) detection is developed by using hybridization chain reaction (HCR) coupled with a graphene oxide (GO) surface-anchored fluorescence signal readout pathway. MiRNAs can efficiently initiate HCR between two species of fluorescent hairpin probes. After HCR, both of the excess hairpin probes and the HCR products will be anchored on the GO surface. The fluorescence of the hairpin probes can be completely quenched by GO, whereas the HCR products maintain strong fluorescence. Therefore, integrating HCR strategy for signal amplification with selective fluorescence quenching effects of GO provides a versatile miRNA assay.

A homogeneous fluorescence sensing platform with water-soluble carbon nanoparticles for detection of microRNA and nuclease activity

Based on the high efficiency of fluorescence quenching and the different affinities of water-soluble carbon nanoparticles (CNPs) towards single-stranded DNA (ssDNA) and double-stranded DNA/RNA hybrid, a novel, rapid and cost-effective assay for detection of microRNA and nuclease activity was developed. The fluorescein-labeled ssDNA probe (FAM-P) could be adsorbed on the surface of CNPs through π-π stacking interaction giving rise to fluorescence quenching. By introduction of microRNA complementary to the DNA probe, the double-stranded DNA/miRNA hybrid could be formed and released from the surface of CNPs resulting in the fluorescence recovery. Thus, microRNA was successfully detected in homogenous fashion without any amplification or enzyme-involving reactions. Moreover, we demonstrated that the nuclease activities of RNase H and DNase I could also be sensitively monitored by using CNPs based on the fluorescence changing of the DNA probe. So, the CNPs provide an excellent homogeneous sensing platform for studying molecular diagnosis and therapeutics.

Graphene oxide for rapid microRNA detection

We have developed a fluorescence quenching based approach using graphene oxide (GO) for rapid detection of miRNAs. This GO-based method has been demonstrated to be highly specific to homogenous miRNAs, and is reverse transcription free which simplifies the detection procedures and reduces the total analysis time and cost.