Mutation detection and single-molecule counting using isothermal rolling-circle amplification

Mathematical model to reduce loop mediated isothermal amplification (LAMP) false-positive diagnosis

Loop mediated isothermal amplification (LAMP) is a nucleic acid amplification technique performed under isothermal conditions. The output of this amplification technique includes multiple different sizes of deoxyribonucleic acid (DNA) structures which are identified by a banding pattern on gel electrophoresis plots. Although this is a specific amplification technique, the complexity of the primer design and amplification still lead to the issue of obtaining false‐positive results, especially when a positive reading is determined solely by whether there is any banding pattern in the gel electrophoresis plot. Here, we first performed extensive LAMP experiments and evaluated the DNA structures using microchip electrophoresis. We then developed a mathematical model derived from the various components that make up an entire LAMP structure to predict the full LAMP structure size in base pairs. This model can be implemented by users to make predictions for specific, DNA size dependent, banding patterns on their gel electrophoresis plots. Each prediction is specific to the target sequence and primers used and therefore reduces incorrect diagnosis errors through identifying true‐positive and false‐positive results. This model was accurately tested with multiple primer sets in house and was also translatable to different DNA and RNA types in previously published literature. The mathematical model can ultimately be used to reduce false‐positive LAMP diagnosis errors for applications ranging from tuberculosis diagnostics to E. coli to numerous other infectious diseases.

Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics

Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.

Universal identification of lethal amanitas by using Hyperbranched rolling circle amplification based on α-amanitin gene sequences

Hyperbranched rolling circle amplification (HRCA) with a padlock probe (PLP) targeting the α-amanitin (α-AMA) gene, as a screening tool for the universal identification of lethal amanitas, was established in this study. With the isothermal HRCA assay, all of the lethal Amanita species tested from Phalloideae (10) were positive, while the non-Phalloideae Amanita species (15) and three amanitin-containing Lepiota and Galerina species were negative. Furthermore, the PLP based on α-AMA sequences from lethal Amanita species was effective for Amanita α-AMA, but not Amanita β-AMA or non-Amanita α-AMA. HRCA sensitivity was 100-fold higher than conventional PCR with a detection limit of 100 copies (recombinant plasmid containing α-AMA), and 0.2% lethal amanitas could be detected in dry mushroom blends. The HRCA method presented provided a rapid, specific, sensitive and low-cost identification tool for lethal amanitas.

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

Fluorescence in situ hybridization (FISH) reveals the abundance and positioning of nucleic acid sequences in fixed samples. Despite recent advances in multiplexed amplification of FISH signals, it remains challenging to achieve high levels of simultaneous amplification and sequential detection with high sampling efficiency and simple workflows. Here we introduce signal amplification by exchange reaction (SABER), which endows oligonucleotide-based FISH probes with long, single-stranded DNA concatemers that aggregate a multitude of short complementary fluorescent imager strands. We show that SABER amplified RNA and DNA FISH signals (5- to 450-fold) in fixed cells and tissues. We also applied 17 orthogonal amplifiers against chromosomal targets simultaneously and detected mRNAs with high efficiency. We then used 10-plex SABER-FISH to identify in vivo introduced enhancers with cell-type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit for rapid and cost-effective multiplexed imaging of nucleic acid targets.

Allele-Specific Loop-Mediated Isothermal Amplification for the Detection of IVSII-I G>A Mutation On β-Globin Gene

BACKGROUND

Thalassemia is one of the most common genetic health problems in the world. More than 200 different mutations have been identified in the beta-globin gene and among the 24 β-globin gene mutations in β-thalassemia carriers in the north of Iran IVSII-I G>A mutation has the highest frequency. Using fast, inexpensive, simple and reliable methods for the detection of the mutations in β-thal carriers is very important in prenatal diagnosis, and introduction of alternative methods to the existing ones can help to simplify the detection of mutations. Since its introduction, different methods derived from LAMP have been widely used for SNPs detection.

AIM

This study was aimed to design a new method for the detection of IVSII-I G>A mutation on β-globin gene based on AS - LAMP technique.

METHODS

Primer explorer V5 software was used for the design of LAMP primers. Three sets of primers were designed. In the first set, the BIP primers were exactly complementary to the normal and mutant alleles. In the second set, 1 nucleotide (T) was inserted at the 5' end of BIP primers, and in the last set, one nucleotide at the 5' end of BIP primer was changed. The other required primers for the LAMP reaction (FIP, B3, and F3) were the same for all 3 sets of primers. The LAMP reaction was applied on three DNA samples (Wild type, Heterozygote and Homozygote for IVSII-I G>A mutation) and synthetic DNA.

RESULTS

The results of the present study showed that LAMP reaction using three sets of primers could not successfully detect the IVSII-I G > A mutation among subjects DNA sample and synthetic DNA.

CONCLUSION

Although several studies have successfully used ARMS-LAMP method to detect the SNPs, and other studies use a variety of methods to identify IVSII-I G>A mutation, the present study was unable to differentiate between a normal allele and IVSII-I G>A mutation. Hence further studies are recommended to consider redesigning of primer set, DNA concentration and using commercial LAMP Master Mix to detect the mutation.

Label-free visual biosensor based on cascade amplification for the detection of Salmonella

Salmonella is a widely distributed, extremely harmful bacteria, the presence of which requires confirmation via an on-site visual biosensor. In this study, we constructed a label-free, cascade amplification visualization biosensor for the sensitive and rapid detection of Salmonella enterica subsp. enterica serovar typhimurium based on the RDTG principle (recombinase polymerase amplification (RPA), duplex-specific enzyme (DSN) cleavage, terminal deoxynucleotidyl transferase (TdT) extension and G-quadruplexes output). Following DNA extraction of Salmonella spp., the first step in the construction involved the recognition and amplification of nucleic acids, carried out by RPA, to achieve the first signal amplification within 10 min. This RPA product was then specifically cleaved by DSN to produce a large number of small double-stranded DNA (dsDNA) products with 3'-OH within 15 min to achieve the second signal amplification. Thereafter, TdT was employed to empower these small 3'-OH dsDNA products to extend and produce a large number of long G-rich single-stranded DNAs (ssDNAs) within 20 min, thus realizing the third signal increase. These long G-rich ssDNA products displayed a color change that could be directly observed through the naked eye by adding H₂O₂/3,3',5,5'-tetramethylbenzidine (TMB). The RDTG biosensor for the detection of Salmonella spp. has several advantages, including a low limit of 6 cfu/mL. It is an isothermal-free instrument, simple to operate, with a rapid detection time of less than 1.5 h. Furthermore, it can be visually characterized and quantified by a microplate reader to detect Salmonella spp., in food and environmental samples, and it has broad application prospects.

An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification

We have developed an ingenious method, termed Cas9 nickase-based amplification reaction (Cas9nAR), to amplify a target fragment from genomic DNA at a constant temperature of 37 °C. Cas9nAR employs a sgRNA:Cas9n complex with a single-strand nicking property, a strand-displacing DNA polymerase, and two primers bearing the cleavage sequence of Cas9n, to promote cycles of DNA replication through priming, extension, nicking, and displacement reaction steps. Cas9nAR exhibits a zeptomolar limit of detection (2 copies in 20 μL of reaction system) within 60 min and a single-base discrimination capability. More importantly, the underlying principle of Cas9nAR offers simplicity in primer design and universality in application. Considering the superior sensitivity and specificity, as well as the simple-to-implement, rapid, and isothermal features, Cas9nAR holds great potential to become a routine assay for the quantitative detection of nucleic acids in basic and applied studies.

Detection of helminths by loop-mediated isothermal amplification assay: a review of updated technology and future outlook

BACKGROUND

Helminths are endemic in more than half of the world's countries, raising serious public health concerns. Accurate diagnosis of helminth infection is crucial to control strategies. Traditional parasitological methods, serological tests and PCR-based assays are the major means of the diagnosis of helminth infection, but they are time-consuming and/or expensive, and sometimes provide inaccurate results. Loop mediated isothermal amplification (LAMP) assay, a sensitive, simple and rapid method was therefore developed for detection of helminths. This study aims to discuss the current status of application of LAMP on helminths detection and to make a comprehensive evaluation about this updated technology and its future outlook by comparing with several other diagnostic methods.

MAIN BODY

This review summarizes LAMP assay applied for helminth detection and helminthiasis surveillance. The basic principle of LAMP is introduced to help better understand its characteristics and each reported assay is assessed mainly based on its detection sensitivity, specificity and limitations, in comparison with other common diagnostic tests. Moreover, we discuss the limitations of the assays so as to clarify some potential ways of improvement.

CONCLUSIONS

Here, we summarize and discuss the advantages, disadvantages and promising future of LAMP in heliminth detection, which is expected to help update current knowledge and future perspectives of LAMP in highly sensitive and specific diagnosis and surveillance of helminthiasis and other parasitic diseases, and can contribute to the elimination of the diseases from endemic areas.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry

Advances in single-cell analysis technologies are providing novel insights into phenotypic and functional heterogeneity within seemingly identical cell populations. RNA within single cells can be analyzed using unbiased sequencing protocols or through more targeted approaches using in situ hybridization (ISH). The proximity ligation assay for RNA (PLAYR) approach is a sensitive and high-throughput technique that relies on in situ and proximal ligation to measure at least 27 specific RNAs by flow or mass cytometry. We provide detailed instructions for combining this technique with antibody-based detection of surface/internal protein, allowing simultaneous highly multiplexed profiling of RNA and protein expression at single-cell resolution. PLAYR overcomes limitations on multiplexing seen in previous branching DNA-based RNA detection techniques by integration of a transcript-specific oligonucleotide sequence within a rolling-circle amplification (RCA). This unique transcript-associated sequence can then be detected by heavy metal (for mass cytometry)- or fluorophore (for flow cytometry)-conjugated complementary detection oligonucleotides. Included in this protocol is methodology to label oligonucleotides with lanthanide metals for use in mass cytometry. When analyzed by mass cytometry, up to 40 variables (with scope for future expansion) can be measured simultaneously. We used the described protocol to demonstrate intraclonal heterogeneity within primary cells from chronic lymphocytic leukemia patients, but it can be adapted to other primary cells or cell lines in suspension. This robust, reliable and reproducible protocol can be completed in 2-3 d and can be paused at several stages for convenience.

Visualized Detection of Vibrio parahaemolyticus in Food Samples Using Dual-Functional Aptamers and Cut-Assisted Rolling Circle Amplification

A biosensor using two aptamers (Dual-Apt) and cut-assisted rolling circle amplification (CA-RCA) for rapid and visualized detection of Vibrio parahaemolyticus was established. The anchoring aptamer (A-Apt) that specifically binds to the surface of V. parahaemolyticus was applied to separate and enrich the bacterium from the food matrix with the help of streptavidin magnetic beads. While the detecting aptamer (D-Apt), binding on the different sites of the cell surface, was used as a signal reporter. CA-RCA with an enhanced amplification rate was fabricated here to amplify the D-Apt to produce the monomeric G4 sequence that catalyzes the oxidation of ABTS^2-, resulting in the coloration visible to the naked eye. Under optimal conditions, as low as 10 colony-forming units (CFU)/mL (g) of V. parahaemolyticus can be visibly detected in real food samples. Free from DNA extraction, visualized signal output and no need for expensive instruments enable Dual-Apt and CA-RCA to be a promising strategy for on-spot rapid detection.

Exonuclease III-assisted multiple cycle amplification for the sensitive detection of DNA with zero background signal

Detection of low-abundant DNA is essential for disease diagnosis and treatment. DNA polymerase-based amplification is frequently used due to its excellent sensitivity, but it suffers from time-consuming and labour-intensive procedures, complex template/primer design, and inherent nonspecific amplification. Alternatively, Exonuclease III (Exo III)-assisted target recycling provides a new approach for DNA assay because of its simplicity and general applicability, but it suffers from high background signal due to the nonspecific Exo III digestion and poor sensitivity due to single cycle signal amplification. Herein, we demonstrate the development of Exo III-assisted multiple cycle amplification (exonuclease chain reaction) for the sensitive detection of DNA with zero background signal. The binding of single-stranded DNA binding protein (SSB) to the hairpin probes can protect them from nonspecific digestion by Exo III, resulting in near zero background signal. The presence of the target DNA initiates the Exo III-triggered multiple cycle amplification, enabling the achievement of high sensitivity with a detection limit of 3 fM and excellent selectivity with single base mismatch discrimination capability, holding great potential in disease diagnosis and biomedical research.

Single cell transcriptomics: moving towards multi-omics

Single-cell multi-omics analysis helps characterize multiple layers of molecular features at a single-cell scale to provide insights into cellular processes and functions.

Liquid biopsy in combination with solid-state electrochemical sensors and nucleic acid amplification

Solid-state electrochemical sensors are developing as a new platform for liquid biopsy, combining detection and analysis of nucleic acids with isothermal nucleic acid amplification reactions.

Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods

This review describes the features of molecular biology techniques for single-cell RNA sequencing (scRNA-seq), including methods developed in our laboratory. Existing scRNA-seq methods require the conversion of first-strand cDNA to amplifiable cDNA followed by whole-transcript amplification. There are three primary strategies for this conversion: poly-A tagging, template switching, and RNase H-DNA polymerase I-mediated second-strand cDNA synthesis for in vitro transcription. We discuss the merits and limitations of these strategies and describe our Reverse Transcription with Random Displacement Amplification technology that allows for direct first-strand cDNA amplification from RNA without the need for conversion to an amplifiable cDNA. We believe that this review provides all users of single-cell transcriptome technologies with an understanding of the relationship between the quantitative performance of various methods and their molecular features.

On-chip conductometric detection of short DNA sequences via electro-hydrodynamic aggregation

Fluorescence measurement is the main technology for post-amplification DNA detection in automated systems. Direct electrical reading of DNA concentration in solution could be an interesting alternative to go toward more miniaturized or less expensive devices, in particular in the pathogen detection field. Here we present the detection of short bacterial biomarkers with a direct impedancemetric measurement, within solutions of amplified and elongated DNA sequences in a microchannel. This technology relies on the electrohydrodynamic instability occurring in solutions of long charged macromolecules in a strong electric field. This instability specifically induces the aggregation of long DNAs and triggers conductivity variations that can be monitored by on-contact conductometry. An innovative isothermal amplification and elongation strategy was developed, combining SDA and HRCA reactions, in order to yield long DNAs suitable to be detected by the above principle, from a dilute initial DNA target. In contrast with previous label-free detection methods, this new strategy is very robust to matrix effects, thanks to the unique molecular weight dependence of the instability, coupled with this specific DNA amplification strategy. We demonstrate the detection of a 1 pM gene sequence specific to Staphylococcus aureus, in a portable system.

Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation

Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.

HCV Detection, Discrimination, and Genotyping Technologies

According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.

Ratiometric Fluorescence Coding for Multiplex Nucleic Acid Amplification Testing

Although nucleic acid amplification testing (NAAT) has become the cornerstone for molecular diagnosis of diseases, expanding the multiplexed detection capacity of NAAT remains an important objective. To this end, encoding each nucleic acid target with a specific fluorescently labeled probe has been the most mature approach for multiplexed detection. Unfortunately, the number of targets that can be differentiated via this one-target-one-fluorophore multiplexed detection approach is restricted by spectral overlaps between fluorophores. In response, we present herein a new multiplexed detection approach termed ratiometric fluorescence coding, in which we encode each nucleic acid target with a specific ratio between two standard fluorophores. In ratiometric fluorescence coding, we employ the padlock probe chemistry to encode each nucleic acid target with a specific number of binding sites for two probes labeled with different fluorophores. Coupling the padlock probes with either rolling circle amplification (RCA) or hyperbranched rolling circle amplification (HRCA), we transform each nucleic acid target into a specific template that allows hybridization with the fluorescently labeled probes at predesigned ratios, thereby achieving multiplexed detection. For demonstration, we detected DNA targets from six infectious diseases and demonstrated the potential for further expanding the multiplexing capability of our approach. With further development, ratiometric fluorescence coding has the potential to enable highly multiplexed detection of nucleic acid targets and facilitate molecular diagnosis of diseases.

Multistage Chemical Heating for Instrument-Free Biosensing

Improving the portability of diagnostic medicine is crucial for alleviating global access-to-care deficiencies. This requires not only designing devices that are small and lightweight, but also autonomous and independent of electricity. Here, we present a strategy for conducting automated multistep diagnostic assays using chemically generated, passively regulated heat. Ligation and polymerization reagents for rolling circle amplification of nucleic acids are separated by meltable phase-change partitions, thus replacing precise manual reagent additions with automated partition melting. To actuate these barriers and individually initiate the various steps of the reaction, field ration heaters exothermically generate heat in a thermos, whereas fatty acids embedded in a carbonaceous matrix passively buffer the temperature around their melting points. Achieving multistage temperature profiles extend the capability of instrument-free diagnostic devices and improve the portability of reaction automation systems built around phase-change partitions.

Hyperbranched rolling circle amplification (HRCA)-based fluorescence biosensor for ultrasensitive and specific detection of single-nucleotide polymorphism genotyping associated with the therapy of chronic hepatitis B virus infection

Detection of specific genes related to drug action can provide scientific guidance for personalized medicine. Taking the detection of a single-nucleotide polymorphism (SNP) genotyping related to the chronic hepatitis B virus (HBV) therapy as an example, a novel biosensor with high sensitivity and selectivity was developed based on the hyperbranched rolling circle amplification (HRCA) in this work. The single-base mutant DNA (mutDNA) sequence can perfectly hybridize with the specially designed discrimination padlock probe and initiate the HRCA reaction. Subsequently, a great abundant of double-strand DNA sequences were released and a strong fluorescence signal can be detected after adding SYBR Green I. In particular, the enhanced fluorescence intensity exhibits a linear relationship with the logarithm of mutDNA concentration ranging from 0.1 nM to 40 nM with a low detection limit of 0.05 nM. However, when there was even a single base mismatch in the target DNA, the HRCA was suppressed and fluorescence response process could not occur, resulting in a high selectivity of this biosensor. Moreover, this detection strategy also performs well in human serums, demonstrating its potential application in detecting SNPs in real biological samples.

Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in situ assay applications. These amplification techniques eliminate the need for temperature cycling, as required for the polymerase chain reaction (PCR), while achieving comparable amplification yields. We highlight here recent advances in the exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. The incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables the highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from nonspecific template interactions, must be addressed to further improve isothermal and exponential amplification techniques.

No Structure-Switching Required: A Generalizable Exonuclease-Mediated Aptamer-Based Assay for Small-Molecule Detection

The binding of small molecules to double-stranded DNA can modulate its susceptibility to digestion by exonucleases. Here, we show that the digestion of aptamers by exonuclease III can likewise be inhibited upon binding of small-molecule targets and exploit this finding for the first time to achieve sensitive, label-free small-molecule detection. This approach does not require any sequence engineering and employs prefolded aptamers which have higher target-binding affinities than structure-switching aptamers widely used in current small-molecule detecting assays. We first use a dehydroisoandrosterone-3-sulfate-binding aptamer to show that target binding halts exonuclease III digestion four bases prior to the binding site. This leaves behind a double-stranded product that retains strong target affinity, whereas digestion of nontarget-bound aptamer produces a single-stranded product incapable of target binding. Exonuclease I efficiently eliminates these single-stranded products but is unable to digest the target-bound double-stranded product. The remaining products can be fluorescently quantified with SYBR Gold to determine target concentrations. We demonstrate that this dual-exonuclease-mediated approach can be broadly applied to other aptamers with differing secondary structures to achieve sensitive detection of various targets, even in biological matrices. Importantly, each aptamer digestion product has a unique sequence, enabling the creation of multiplex assays, and we successfully demonstrate simultaneous detection of cocaine and ATP in a single microliter volume sample in 25 min via sequence-specific molecular beacons. Due to the generality and simplicity of this assay, we believe that different DNA signal-reporting or amplification strategies can be adopted into our assay for target detection in diverse analytical contexts.

Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations

With the continuous development and application of targeted drugs, it is particularly desirable to find a non-invasive diagnostic approach to screen patients for precision treatment. Specifically, detection of multiple cancer-related mutations is very important for targeted therapy and prediction of drug resistance. Although numerous advanced PCR methods have been developed to discriminate single nucleotide polymorphisms, their drawbacks significantly limit their application, such as low sensitivity and throughput, complicated operations, and expensive costs. In order to overcome these challenges, in this study, we developed a method combining multiplex and sensitive real-time PCR assay with rolling circle amplification. This allows specific and sensitive discrimination of the single nucleotide mutation and provides convenient multiplex detection by real-time PCR assay. The clinical potential of the MPRP assay was further demonstrated by comparing samples from 8 patients with a digital PCR assay. The coincident results between these two methods indicated that the MPRP assay can provide a specific, sensitive, and convenient method for multiplex detection of cancer-related mutations.

SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants

Immune cell heterogeneity due to the differential expression of RNA splicing variants still remains unexplored. This is mainly because single-cell imaging technologies of splicing variants with precise sequence or base resolution are now not readily available. Herein, we design a splice-junction anchored padlock-probe-mediated rolling circle amplification assay (SpliceRCA) for single-cell imaging of splice isoforms of essential regulatory immune gene (CD45) upon T-cell activation. Two recognition regions in the padlock probe can target the splice-junction sequence, resulting in a close proximity for triggering in situ one-target-one-amplicon amplification. With the read length of ∼30 nucleotides, this method allows discrimination of isoforms with single-base precision and quantification of isoforms with single-molecule resolution. We applied SpliceRCA to single-cell image splice variants of essential regulatory immune gene (CD45) upon T-cell activation. It is found that CD45RO isoform presents a distal nuclear spatial distribution and is coregulated with CD45RB upon activation. Our strategy provides a single-cell analysis platform to investigate the mechanism of complex immune responses and may further guide immunotherapy.

Ultrahigh-throughput droplet microfluidic device for single-cell miRNA detection with isothermal amplification

Analysis of microRNA (miRNA), a pivotal primary regulator of fundamental cellular processes, at the single-cell level is essential to elucidate regulated gene expression precisely. Most single-cell gene sequencing methods use the polymerase chain reaction (PCR) to increase the concentration of the target gene for detection, thus requiring a barcoding process for cell identification and creating a challenge for real-time, large-scale screening of sequences in cells to rapidly profile physiological samples. In this study, a rapid, PCR-free, single-cell miRNA assay is developed from a continuous-flow microfluidic process employing a DNA hybridization chain reaction to amplify the target miRNA signal. Individual cells are encapsulated with DNA amplifiers in water-in-oil droplets and then lysed. The released target miRNA interacts with the DNA amplifiers to trigger hybridization reactions, producing fluorescence signals. Afterward, the target sequences are recycled to trigger a cyclic cascade reaction and significantly amplify the fluorescence signals without using PCR thermal cycling. Multiple DNA amplifiers with distinct fluorescence signals can be encapsulated simultaneously in a droplet to measure multiple miRNAs from a single cell simultaneously. Moreover, this process converts the lab bench PCR assay to a real-time droplet assay with the post-reaction fluorescence signal as a readout to allow flow cytometry-like continuous-flow measurement of sequences in a single cell with an ultrahigh throughput (300-500 cells per minute) for rapid biomedical identification.

Helix loop-mediated isothermal amplification of nucleic acids

Isothermal nucleic acid amplification has played a key role in the point of care test (POCT). In this study, a helix loop-mediated isothermal amplification (HAMP) method with high specificity, efficiency and rapidity was developed. The MERS-Cov orf1b gene was chosen for the validation and optimization of HAMP. The HAMP analysis was performed at a constant temperature of 61-65 °C and yielded a self-primed spiral structure with no introduction of exogenous gene sequence by two pairs of specially designed primers. The primers for helix loop formation were composed of two complementary primers including the helix forward primer and the helix reverse primer, the 3' ends of which were complementary to their respective target nucleic acids. HAMP assay can be monitored by fluorescence signals with the addition of Eva Green in the reaction mixture. In addition, an accelerated HAMP was developed after the addition of acceleration probe, which could be finished within 75 min with a sensitivity of 10 copies per reaction. Further, a reverse transcription-HAMP (RT-HAMP) was proven to be feasible for RNA detection by combining the reverse transcriptase with DNA polymerase. Finally, both the HAMP and RT-HAMP assay were visually conducted by using Hydroxynaphthol blue (HNB) as a chromogenic indicator. All in all, it is suggested that the HAMP assay would have great potential in POCT applications.

A molecular multi-gene classifier for disease diagnostics

Despite its early promise as a diagnostic and prognostic tool, gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Here, we introduce a molecular computation strategy for analysing the information contained in complex gene expression signatures without the need for costly instrumentation. Our workflow begins by training a computational classifier on labelled gene expression data. This in silico classifier is then realized at the molecular level to enable expression analysis and classification of previously uncharacterized samples. Classification occurs through a series of molecular interactions between RNA inputs and engineered DNA probes designed to differentially weigh each input according to its importance. We validate our technology with two applications: a classifier for early cancer diagnostics and a classifier for differentiating viral and bacterial respiratory infections based on host gene expression. Together, our results demonstrate a general and modular framework for low-cost gene expression analysis.

dPCR: A Technology Review

Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods.

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.

Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication

Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions, where the lack of thermal cycling reduces equipment needs and improves the time to answer, especially for point-of-care applications. In order to improve the function of strand-displacing polymerases, we have developed an emulsion-based directed evolution scheme, high-temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand-displacing polymerase variant that performs well in loop-mediated isothermal amplification and rolling circle amplification, even after thermal challenges of up to 95 °C that lead to better primer annealing. The new enzyme (v5.9) is also capable of a variety of new reactions, including isothermal hyperbranched rolling circle amplification. The HTI-CSR method should now prove useful for evolving additional beneficial phenotypes in strand-displacing polymerases.

Multi-DNAzymes-functionalized gold nanoparticles for ultrasensitive chemiluminescence detection of thrombin on microchip

Herein, a chemiluminescence assay with dual signal amplification has been developed based on multi-DNAzymes-functionalized gold nanoparticles (AuNPs) using in situ rolling circle amplification (RCA) for ultrasensitive detection of thrombin on microchip. In this assay, AuNPs was functionalized by aptamer and multi-RCA primer for amplification, and thrombin was sandwiched between the aptamer modified on the microchannel and the aptamer linked AuNP. The further amplification was realized by in situ RCA to expand specific oligonucleotides chains on the AuNPs and produce particular multi-DNAzymes. Enhanced chemiluminescence signal was achieved by the catalytic effect of DNAzymes in the luminol-H₂O₂ system. The sensitivity of detection was greatly improved by the dual amplification of multi-RCA primer modified AuNPs, and RCA. The whole strategy was applied for ultrasensitive and specific detection of thrombin. The chemiluminesce assay of thrombin performed a good linear range of 1-25 pM and the limit of detection was as low as 0.55 pM. The successful determination of thrombin in real human serum sample indicated a great potential in clinical study.

Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips

Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.

A simple and ultrasensitive fluorescence assay for single-nucleotide polymorphism

In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). Briefly, a designed padlock probe is first circularized by a DNA ligase when it perfectly complements to a mutant gene. Then, the mutant gene functions as a primer to initiate branched rolling circle amplification reaction (BRCA), generating a large number of branched DNA strands and a lot of pyrophosphate molecules which is equivalent to the number of nucleotides consumed. With the addition of a terpyridine-Zn(II) complex, pyrophosphate molecules can be sensitively detected owing to the formation of a fluorescent terpyridine-Zn(II)-pyrophosphate complex. The fluorescence intensity is directly associated with the content of the mutant gene in a sample solution. On the other hand, the circulation of the padlock probe is prohibited when it hybridizes with the wild-type gene. In this assay, the accumulative nature of the BRCA process produces a detection limit of 0.1 pM and an excellent selectivity factor of 1000 toward SNP. As little as 0.1% mutant in the wild-type gene can be successfully detected. The simple procedure, high sensitivity, and high selectivity of this assay offer a potentially viable alternative for routine SNP analysis. Graphical abstract A simple and label-free fluorescence assay for SNP detection by coupling BRCA with selective fluorescence detection of pyrophosphate using the terpyridine-Zn(II) complex.

Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes

We have redesigned probes for in situ proximity ligation assay (PLA), resulting in more efficient localized detection of target proteins. In situ PLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes –UnFold probes – where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic “unfolding” step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.

Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors

As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.