Ambient temperature detection of PCR amplicons with a novel sequence-specific nucleic acid lateral flow biosensor

Development of nucleic acid based lateral flow assays for SARS-CoV-2 detection

SARS-CoV-2 is still threat for humanity and its detection is crucial. Although real time reverse transcriptase polymerase chain reaction is the most reliable method for detection of N protein genes, alternative methods for molecular detection are still needed. Thus, lateral flow assay models for 2019-nCoV_ N3 were developed for molecular detection. Briefly, gold nanoparticles were used as label and three sandwich models (1A, 1B, and 1.2) were designed. Prob concentrations on gold nanoparticles, types of sandwich model and membrane, limit of detection of target gene and buffer efficiency were studied. Model 1B has shown the best results with M170 membrane. Lower limit of detection was achieved by model 1.2 as 5 pM. All parameters have significant role for molecular detection of SARS-CoV-2 by lateral flow assays, and these results will be useful for nucleic acid based lateral flow assays for viral detection or multiple detection of mutated forms in various detection systems.

Unreacted Labeled PCR Primers Inhibit the Signal in a Nucleic Acid Lateral Flow Assay as Elucidated by a Transport Reaction Model

Factors that affect the performance of the nucleic acid lateral flow assay (NALFA) have not been well studied. In this work, we identify two important phenomena that negatively affect signal intensities during the detection of PCR products using NALFA: (i) the presence of unreacted PCR primers, and (ii) the presence of excess PCR amplicons. This is the first report that highlights the negative effect of unreacted PCR primers on NALFA. The negative effect of excess amplicons, while not explicitly reported for NALFAs, emanates from an identical phenomenon in lateral flow immunoassays known as the "hook effect". We show that the above effects may be alleviated by increasing the concentration of capture antibodies at the test line and the concentration of reporter moieties (gold nanoparticles). To demonstrate these, we utilized a PCR assay in which both primers were end-labeled, to generate dually end-labeled (bi-labeled) PCR amplicons of 230 bp length. To provide mechanistic understanding of these phenomena, we present the first transport-reaction model of NALFA, the results of which qualitatively matched all observed phenomena. Based on these results, we provide recommendations for the optimal design of PCR for NALFA detection.

High sensitivity and rapid detection of hepatitis B virus DNA using lateral flow biosensors based on Au@Pt nanorods in the absence of hydrogen peroxide

Au@Pt nanorods with enhanced oxidase-like activity were designed and used as signal probes to construct LFBs for the high sensitivity detection of hepatitis B virus DNA (HBV-DNA).

Advanced Multiplex Loop Mediated Isothermal Amplification (mLAMP) Combined with Lateral Flow Detection (LFD) for Rapid Detection of Two Prevalent Malaria Species in India and Melting Curve Analysis

Isothermal techniques with lateral flow detection have emerged as a point of care (POC) technique for malaria, a major parasitic disease in tropical countries such as India. Plasmodium falciparum and Plasmodium vivax are the two most prevalent malaria species found in the country. An advanced multiplex loop-mediated isothermal amplification (mLAMP) combined with a lateral flow dipstick (LFD) technique was developed for the swift and accurate detection of P. falciparum and P. vivax, overcoming the challenges of the existing RDTs (rapid diagnostic tests). A single set of LAMP primers with a biotinylated backward inner primer (BIP primer) was used for DNA amplification of both malaria species in a single tube. The amplified DNA was hybridized with fluorescein isothiocyanate (FITC) and digoxigenin-labelled DNA probes, having a complemented sequence for the P. falciparum and P. vivax genomes, respectively. A colour band appeared on two separate LFDs for P. falciparum and P. vivax upon running the hybridized solution over them. In total, 39 clinical samples were collected from ICMR-NIMR, New Delhi. Melting curve analysis, with cross primers for both species, was used to ascertain specificity, and the sensitivity was equated with a polymerase chain reaction (PCR). The results were visualized on the LFD for both species within 60 min. We found 100% sensitivity and specificity, when compared with a traditional PCR. Melting curve analysis of mLAMP revealed the lowest detection limit of 0.15 pg/μL from sample genomic DNA. The mLAMP-LFD assays could be a potential point of care (POC) tool for early diagnosis in non-laboratory conditions, with the convenience of a reduced assay time and the simple interpretation of results.

Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR-Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR-Cas-based nucleic acid detection strategies and the application of CRISPR-Cas as a potential antiviral agent in the context of COVID-19.

Development and Efficacy of Lateral Flow Point-of-Care Testing Devices for Rapid and Mass COVID-19 Diagnosis by the Detections of SARS-CoV-2 Antigen and Anti-SARS-CoV-2 Antibodies

The COVID-19 pandemic is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2020-2021. COVID-19 is becoming one of the most fatal pandemics in history and brings a huge challenge to the global healthcare system. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. Diagnosis via viral nucleic acid amplification tests (NAATs) is frequently employed and considered the standard procedure. However, with an increasing urge for point-of-care tests, rapid and cheaper immunoassays are widely utilized, such as lateral flow immunoassay (LFIA), which can be used for rapid, early, and large-scale detection of SARS-CoV-2 infection. In this narrative review, the principle and technique of LFIA applied in COVID-19 antigen and antibody detection are introduced. The diagnostic sensitivity and specificity of the commercial LFIA tests are outlined and compared. Generally, LFIA antigen tests for SARS-CoV-2 are less sensitive than viral NAATs, the "gold standard" for clinical COVID-19 diagnosis. However, antigen tests can be used for rapid and mass testing in high-risk congregate housing to quickly identify people with COVID-19, implementing infection prevention and control measures, thus preventing transmission. LFIA anti-SARS-CoV-2 antibody tests, IgM and/or IgG, known as serology tests, are used for identification if a person has previously been exposed to the virus or vaccine immunization. Notably, advanced techniques, such as LFT-based CRISPR-Cas9 and surface-enhanced Raman spectroscopy (SERS), have added new dimensions to the COVID-19 diagnosis and are also discussed in this review.

Nucleic acid lateral flow assay for simultaneous detection of hygiene indicator bacteria

A simple and rapid polymerase chain reaction (PCR)-based lateral flow assay (LFA) was developed for multiplex detection of hygiene indicator bacteria. Specifically, new PCR primers were designed for accurately detecting Escherichia coli, coliform bacteria, and total bacteria, and the results obtained as a colorimetric signal (generated by the accumulation of gold nanoparticles at distinct test zones on flow strips) could be identified by the naked eye in <10 min after the completion of PCR. The proposed LFA system did not exhibit any cross-reactivities with 8 distinct bacterial strains and can detect down to 1 colony forming unit (CFU)/mL. Furthermore, three species of cultured bacteria (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) inoculated onto sterilized ham were successfully analyzed using the LFA system, which demonstrated that this system shows sufficient sensitivity and specificity for food hygiene monitoring. The speed and simplicity of this LFA make it suitable for use in the food industry as part of routine screening analysis.

Nucleic Acid-Based Lateral Flow Biosensor for Salmonella Typhi and Salmonella Paratyphi: A Detection in Stool Samples of Suspected Carriers

A multiplex rapid detection system, based on a PCR-lateral flow biosensor (mPCR-LFB) was developed to identify Salmonella Typhi and Salmonella Paratyphi A from suspected carriers. The lower detection limit for S. Typhi and S. Paratyphi A was 0.16 and 0.08 ng DNA equivalent to 10 and 10² CFU/mL, respectively. Lateral flow biosensor was used for visual detection of mPCR amplicons (stgA, SPAint, ompC, internal amplification control) by labeling forward primers with fluorescein-isothiocyanate (FITC), Texas Red, dinitrophenol (DNP) and digoxigenin (DIG) and reverse primers with biotin. Binding of streptavidin-colloidal gold conjugate with the amplicons resulted in formation of a red color dots on the strip after 15-20 min of sample exposure. The nucleic acid lateral flow analysis of the mPCR-LFB was better in sensitivity and more rapid than the conventional agarose gel electrophoresis. Moreover, the mPCR-LFB showed 100% sensitivity and specificity when evaluated with stools spiked with 100 isolates of Salmonella genus and other bacteria. A prospective cohort study on stool samples of 1176 food handlers in outbreak areas (suspected carriers) resulted in 23 (2%) positive for S. Typhi. The developed assay has potential to be used for rapid detection of typhoid carriers in surveillance program.

Simultaneous and accurate visual identification of chicken, duck and pork components with the molecular amplification integrated lateral flow strip

We propose a visual strategy for simultaneous detection of multiple adulterated components in beef by integration of multiple polymerase chain reaction (mPCR) with the lateral flow strip (LFS). The primer sets for adulterated components are uniquely designed with different nucleic acid tags (NAT), enabling the amplicons with specific wobbled sequences at two opposite ends. The wobbled sequences will precisely hybridize with the pre-immobilized capture probes on T lines (T1, T2 and T3) and C line, contributing to the coloration of LFS. Taking advantages of extraordinary amplification efficiency of PCR and simplicity of LFS, common adulterated components including chicken, duck and pork can be easily detected with LOD as low as 0.01% (wt%), which is comparable to that of quantitative real-time polymerase chain reaction (qPCR) but with more simplified operations and reduced costs. The method can be extended to identification of other components by replacing the functional primer set. This method can be a useful candidate for meat quality control at the resource-limited setups.

Simultaneous Detection of Multiple β-Adrenergic Agonists with 2-Directional Lateral Flow Strip Platform

Clenbuterol (CL), salbutamol (SAL) and ractopamine (RAC) are the three common β-adrenergic agonists, which are the main hazards in food safety and affect human health through the food chain. A convenient and efficient method is urgently required to perform on-site detection of multiple β-adrenergic agonists to avoid frequent poisoning incidents. In this paper, a 2-directional lateral flow strip technique (2-directional LFS) is developed for rapid and simultaneous detection of CL, SAL and RAC with single sampling. Compared to the conventional lateral flow strip, this 2-directional LFS technique can realize simultaneous detection of three or more target analytes without any change of intrinsic simplicity of LFS. Furthermore, this 2-directional LFS can effectively avoid the potential intrinsic cross-reactivity among the reagents to analogues. Under the optimized conditions, CL, SAL and RAC were all successfully determined with satisfactory results in both buffer and urine samples with the detection limit as low as 0.5 ng/mL. This 2-directional LFS technique can revolutionize the commercial single-analyte LFS products and can effectively widen the applications of the classic LFS in various fields.

End-point dual specific detection of nucleic acids using CRISPR/Cas12a based portable biosensor

A CRISPR/Cas12a based portable biosensor (Cas12a-PB) was developed to simultaneously visually detect CaMV35S promoter and Lectin gene from genetically modified (GM) soybean powders (Roundup Ready@). The Cas12a-PB, mainly made of polymethylmethacrylate (PMMA) and PMMA tape, has a connection structure, three channels and three detection chambers. The CRISPR/Cas12a detection reagents were preloaded in detection chambers and the reaction tube was connected to the connection structure by screw threads. After amplification, the amplicons were gone into three detection chambers by swinging the Cas12a-PB to conduct dual detection. Positive samples would produce green fluorescence while negative samples were black under the irradiation of 490 nm LED light. In this study, the Cas12a-PB successively combined with ordinary PCR, rapid PCR and loop-mediated isothermal amplification (LAMP) to achieve dual detection, which made detection process more convenient and portable. As low as 0.1% transgenic ingredients in soybean powders could be detected and the specificity of Cas12a-PB was confirmed with GM maize powders (MON810, GA21), GM soybean powders (DP305423), non-GM peanut and rice as targets. In the end, an amplification chamber combining with Cas12a-PB on a PMMA chip was further designed to eliminate the use of reaction tube and mineral oil, which made operation simpler. The established Cas12a-PB would provide a new reliable solution for multiple targets detection in clinic diagnostics, food safety, etc.

Lateral flow biosensors based on the use of micro- and nanomaterials: a review on recent developments

This review (with 187 refs.) summarizes the progress that has been made in the design of lateral flow biosensors (LFBs) based on the use of micro- and nano-materials. Following a short introduction into the field, a first section covers features related to the design of LFBs, with subsections on strip-based, cotton thread-based and vertical flow- and syringe-based LFBs. The next chapter summarizes methods for sample pretreatment, from simple method to membrane-based methods, pretreatment by magnetic methods to device-integrated sample preparation. Advances in flow control are treated next, with subsections on cross-flow strategies, delayed and controlled release and various other strategies. Detection conditionst and mathematical modelling are briefly introduced in the following chapter. A further chapter covers methods for reliability improvement, for example by adding other validation lines or adopting different detection methods. Signal readouts are summarized next, with subsections on color-based, luminescent, smartphone-based and SERS-based methods. A concluding section summarizes the current status and addresses challenges in future perspectives. Graphical abstractRecent development and breakthrough points of lateral flow biosensors.

Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review

Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.

Diagnostic techniques for rapid detection of Vibrio cholerae O1/O139

Cholera caused by the toxigenic Vibrio cholerae is still a major public health problem in many countries. This disease is mainly due to poor sanitation, hygiene and consumption of unsafe water. Several recent epidemics of cholera showed its increasing intensity, duration and severity of the illness. This indicates an urgent need for effective management and preventive measures in controlling the outbreaks and epidemics. In preventing and spread of epidemic cholera, rapid diagnostic tests (RDTs) are useful in screening suspected stool specimens, water/food samples. Several RDTs developed recently are considered as investigative tools in confirming cholera cases, as the culture techniques are difficult to establish and/or maintain. The usefulness of RDTs will be more at the point-of-care facilities as it helps to make appropriate decisions in the management of outbreaks or epidemiological surveillance by the public health authorities. Apart from RDTs, several other tests are available for the direct detection of either V. cholerae or its cholera toxin. Viable but non-culturable (VBNC) state of V. cholerae poses a great challenge in developing RDTs. The aim of this article is to provide an overview of current knowledge about RDT and other techniques with reference to their status and future potentials in detecting cholera/V. cholerae.

Enhancing the Sensitivity of Lateral Flow Immunoassay by Centrifugation-Assisted Flow Control

Lateral flow immunoassay (LFIA) is widely used but is limited by its sensitivity. In this study, a novel centrifugation-assisted lateral flow immunoassay (CLFIA) was proposed that had enhanced sensitivity compared to traditional LFIA based on test strips. For CLFIA, a vaulted piece of nitrocellulose membrane was prepared and inserted into a centrifugal disc. Powered by the centrifugal force, the sample volume on the disc was not limited and the flow rate of the reaction fluid was steady and adjustable at different rotation speeds. It was found that lower rotation speeds and larger sample volumes resulted in greater signal intensity in the nitrocellulose membrane as well as higher sensitivity, indicating that the actively controlled flow on the disc allowed for sensitivity enhancement of CLFIA. To operate CLFIA on the centrifugal disc, a portable and cost-effective operating device was constructed to rotate the disc with a stepper motor and collect the results with a smartphone. The proposed method was successfully applied to detect prostate specific antigen (PSA) in human serum. Standard curves were established for CLFIA and LFIA, and both had correlation coefficients of up to 0.99. Under optimal conditions (1500 rpm rotation speed, 120 μL sample volume), the detection limit of CLFIA reached 0.067 ng/mL, showing a 6.2-fold improvement in sensitivity compared to that of LFIA. With clinical serum samples, a good correlation was observed between PSA concentrations measured by CLFIA and by a bulky commercial instrument in hospital. In summary, this portable, cost-effective, and easy-to-use system holds great promise for biomarker detection with enhanced sensitivity compared to traditional LFIA.

Development of rapid dipstick assay for food pathogens, Salmonella, by optimized parameters

Salmonella is among the very important pathogens threating the human and animal health. Rapid and easy detection of these pathogens is crucial. In this context, antibody (Ab) based lateral flow assays (LFAs) which are simple immunochromatographic point of care test kits were developed by gold nanoparticles (GNPs) as labelling agent for Salmonella detection. For that purpose some critical parameters such as reagent concentrations on the capture zones, conjugate concentrations and ideal membrane type needed for LFAs for whole cell detection were tested for naked eye analysis. Therefore, prepared LFAs were applied to the live and heat inactivated cells when they were used alone or included in different bacterial mixtures. Among the test platforms, membrane 180 (M180) was found as an ideal membrane and 36 nm GNPs showed highly good labelling in the developed LFAs. Diluted conjugates and low concentrations of reagents affected the test signal negatively. Salmonella was detected in different bacterial mixtures, selectively in 4-5 min. The best recognized species by used Ab were S. enteritidis and S. infantis. 5 × 105 S. typhimurium cells were also determined as a limit of detection of this study with mentioned parameters.

Paper-based lateral flow strip assay for the detection of foodborne pathogens: principles, applications, technological challenges and opportunities

As a representative colorimetic biosnesor, paper-based LFSA have emerged as a promising and robust tool that can easily and instansly detect the presence of target biological components in food sample. Recently, LFSAs have gained a considerable attention as an alternative method for rapid diagnosis of foodborne pathogens to the conventional culture-based assays such as plate counting and PCR. One major drawback of the current LFSAs for the detection of pathogenic bacteria is the low sensitivity, limiting its practical applications in POCT. Not like many other protein-based biomarkers that are present in nM or pM range, the number of pathogenic bacteria that cause disease can be as low as few CFU/ml. Here, we review current advances in LFSAs for the detection of pathogenic bacteria in terms of chromatic agents and analyte types. Furthermore, recent approaches for signal enhancement and modifications of the LFSA architecture for multiplex detection of pathogenic bacteria are included in this review, together with the advantages and limitations of each techniques. Finally, the technological challenges and future prospect of LFSA-based POCT for the detection of pathogenic bacteria are discussed.

Biotin-exposure-based immunomagnetic separation coupled with nucleic acid lateral flow biosensor for visibly detecting viable Listeria monocytogenes

Infectious diseases caused by Listeria monocytogenes pose a great threat to public health worldwide. Therefore, a rapid and efficient method for L. monocytogenes detection is needed. In this study, a biotin-exposure-based immunomagnetic separation (IMS) method was developed. That is, biotinylated antibody was first targeted to L. monocytogenes. Then, streptavidin-functionalized magnetic nanoparticles were added and anchored onto L. monocytogenes cells indirectly through the strong noncovalent interaction between streptavidin and biotin. Biotin-exposure-based IMS exhibited an excellent capability to enrich L. monocytogenes. Specifically, more than 90% of L. monocytogenes was captured when the bacterial concentration was lower than 10⁴ colony-forming units (CFU)/mL. Importantly, the antibody dosage was reduced by 10 times of that in our previous study, which used antibody direct-conjugated magnetic nanoparticles. Propidium monoazide (PMA) treatment prior to PCR amplification could eliminate the false-positive results from dead bacteria and detected viable L. monocytogenes sensitively and specifically. For viable L.monocytogenes detection, enriched L. monocytogenes was treated with PMA prior to asymmetric PCR amplification. The detection limits of the combined IMS with nucleic acid lateral flow (NALF) biosensor for viable L. monocytogenes detection were 3.5 × 10³ CFU/mL in phosphate buffer solution and 3.5 × 10⁴ CFU/g in lettuce samples. The whole assay process of recognizing viable L. monocytogenes was completed within 6 h. The proposed biotin-exposure-mediated IMS combined with a disposable NALF biosensor platform posed no health risk to the end user, and possessed potential applications in the rapid screening and identification of foodborne pathogens.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS₂), and tungsten disulfide (WS₂) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS₂ and WS₂ nearly fully retained the fluorescence of the positive samples. The mechanism for MoS₂ and WS₂ to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS₂ can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS₂ could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.

Optimizations needed for lateral flow assay for rapid detection of pathogenic E. coli

Lateral flow assay (LFA), or the immunochromatographic strip test, is popular to use for rapid and sensitive immunoassays. Gold nanoparticles (GNPs), due to tunable optical characteristics and easy manipulation of size or shape, represent an attractive approach for LFA technology. Since most enterohemorrhagic infections result from water and food contaminations of Escherichia coli O157:H7, selective and rapid detection of this organism in environmental and biological complexes is necessary. In this study, optimized parameters of antibody (Ab)-based LFA for rapid detection of pathogenic E. coli O157:H7 are described. GNPs were used as visualizing agents. The measuring parameters include the Ab concentration on the capture lines, the concentration of gold conjugate, and flow rate. M180 and 36 nm were the ideal membrane and GNP size, respectively, for bacterial detection of LFA. The target, E. coli O157:H7, could be detected with a visual limit of detection of 105 cfu/mL in 3-5 min. Selectivity of the system was very high and the target was recognized by developed strips, regardless of its presence singly or in mixed bacterial samples.

Fluorescent carbon nanoparticle-based lateral flow biosensor for ultrasensitive detection of DNA

We report a fluorescent carbon nanoparticle (FCN)-based lateral flow biosensor for ultrasensitive detection of DNA. Fluorescent carbon nanoparticle with a diameter of around 15nm was used as a tag to label a detection DNA probe, which was complementary with the part of target DNA. A capture DNA probe was immobilized on the test zone of the lateral flow biosensor. Sandwich-type hybridization reactions among the FCN-labeled DNA probe, target DNA and capture DNA probe were performed on the lateral flow biosensor. In the presence of target DNA, FCNs were captured on the test zone of the biosensor and the fluorescent intensity of the captured FCNs was measured with a portable fluorescent reader. After systematic optimizations of experimental parameters (the components of running buffers, the concentration of detection DNA probe used in the preparation of FCN-DNA conjugates, the amount of FCN-DNA dispensed on the conjugate pad and the dispensing cycles of the capture DNA probes on the test-zone), the biosensor could detect a minimum concentration of 0.4 fM DNA. This study provides a rapid and low-cost approach for DNA detection with high sensitivity, showing great promise for clinical application and biomedical diagnosis.

Development of a dry-reagent-based nucleic acid-sensing platform by coupling thermostabilised LATE-PCR assay to an oligonucleotide-modified lateral flow biosensor

In this study, we report for the first time the development of a dry-reagent-based nucleic acid-sensing platform by combining a thermostabilised linear-after-the-exponential (LATE)-PCR assay with a one-step, hybridisation-based nucleic acid lateral flow biosensor. The nucleic acid-sensing platform was designed to overcome the need for stringent temperature control during transportation or storage of reagents and reduces the dependency on skilled personnel by decreasing the overall assay complexity and hands-on time. The platform was developed using toxigenic Vibrio cholerae as the model organism due to the bacterium's propensity to cause epidemic and pandemic cholera. The biosensor generates result which can be visualised with the naked eyes and the limit of detection was found to be 1pg of pure genomic DNA and 10CFU/ml of toxigenic V. cholerae. The dry-reagent-based nucleic acid-sensing platform was challenged with 95 toxigenic V. cholerae, 7 non-toxigenic V. cholerae and 66 other bacterial strains in spiked stool sample and complete agreement was observed when the results were compared to that of monosialoganglioside (GM1)-ELISA. Heat-stability of the thermostabilised LATE-PCR reaction mixes at different storage temperatures (4-56°C) was investigated for up to 90days. The dry-reagent-based genosensing platform with ready-to-use assay components provides an alternative method for sequence-specific detection of nucleic acid without any cold chain restriction that is associated with conventional molecular amplification techniques.

Multiplex detection and genotyping of pathogenic bacteria on paper-based biosensor with a novel universal primer mediated asymmetric PCR

Traditionary multiplex asymmetric polymerase chain reaction (PCR) can be applied to detect multiplex target organisms simultaneously, but complex optimizations of primer concentrations and staggered additions of primers are required to achieve equal amplification of multiplex genes. To overcome this shortcoming, we propose a novel method based on multiplex asymmetric PCR and paper-based nucleic acid diagnostics (PBNAD). In the asymmetric PCR, a universal primer was introduced to break the bottlenecks of low sensitivity and self-inhibition among different sets of primers. Amplification using the novel multiplex asymmetric PCR boosted the quantity of single-stranded amplicons, and the amplified products contained the same sequence at the 5' end. Therefore, only one gold nanoparticle-based signal probe was needed for the simultaneous detection of three genes using the PBNAD platform, and the detection signals could be observed with the naked eye. With this highly efficient, novel multiplex asymmetric PCR, as little as 1 pg/μL genomic DNA can be detected. This method can also be applied to genotyping for reliable epidemiological investigations. This proof-of-concept study highlights the potential of the PBNAD platform for cost- and labor-effective applications in the detection of pathogenic bacteria.

Lateral flow devices for nucleic acid analysis exploiting quantum dots as reporters

There is a growing interest in the development of biosensors in the form of simple lateral flow devices that enable visual detection of nucleic acid sequences while eliminating several steps required for pipetting, incubation and washing out the excess of reactants. In this work, we present the first dipstick-type nucleic acid biosensors based on quantum dots (QDs) as reporters. The biosensors enable sequence confirmation of the target DNA by hybridization and simple visual detection of the emitted fluorescence under a UV lamp. The 'diagnostic' membrane of the biosensor contains a test zone (TZ) and a control zone (CZ). The CZ always fluoresces in order to confirm the proper function of the biosensor. Fluorescence is emitted from the TZ, only when the specific nucleic acid sequence is present. We have developed two general types of QD-based nucleic acid biosensors, namely, Type I and Type II, in which the TZ consists of either immobilized streptavidin (Type I) or immobilized oligodeoxynucleotides (Type II). The control zone consists of immobilized biotinylated albumin. No purification steps are required prior to the application of the DNA sample on the strip. The QD-based nucleic acid biosensors performed accurately and reproducibly when applied to (a) the visual detection of PCR amplification products and (b) visual genotyping of single nucleotide polymorphisms (SNPs) in human genomic DNA from clinical samples. As low as 1.5 fmol of double-stranded DNA were clearly detected by naked eye and the dynamic range extended to 200 fmol. The %CV were estimated to be 4.3-8.2.

Rapid and sensitive PCR-dipstick DNA chromatography for multiplex analysis of the oral microbiota

A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.

Fluorescent probe-based lateral flow assay for multiplex nucleic acid detection

Here we report a rapid, low cost, and disposable dipstick-type DNA biosensor that enables multiplex detection in a single assay. The fluorescent probes labeled with different fluorophores were introduced into the lateral flow nucleic acid testing system. In combination with multiple immobilized probes arranged in an array formant on the membrane, a dual-color fluorescent lateral flow DNA biosensor was developed using a portable fluorescence reader. Up to 13 human papillomavirus types could be detected simultaneously by a single-step operation in less than 30 min after linear-after-the-exponential (LATE)-PCR. The sensitivity was determined to be 10-10(2) copies plasmid DNA/μL. The specificity study showed no cross-reactivity among the 31 different common HPV types. In the clinical validation, 95.3% overall agreement showed very good potential for this method in the clinical application when compared to a commercial kit.