Predicting viruses accurately by a multiplex microfluidic loop-mediated isothermal amplification chip

Multiplex gene assay is a valuable molecular tool not only in academic science but also in clinical diagnostics. Multiplex PCR assays, DNA microarrays, and various nanotechnology-based methods are examples of major techniques developed for analyzing multiple genes; none of these, however, are suitable for point-of-care diagnostics, especially in resource-limited settings. In this report, we describe an octopus-like multiplex microfluidic loop-mediated isothermal amplification (mμLAMP) assay for the rapid analysis of multiple genes in the point-of-care format and provide a robust approach for predicting viruses. This assay with the ability of analyzing multiple genes qualitatively and quantitatively is highly specific, operationally simple, and cost/time-effective with the detection limit of less than 10 copies/μL in 2 μL quantities of sample within 0.5 h. We successfully developed a mμLAMP chip for differentiating three human influenza A substrains and identifying eight important swine viruses.     

食品中亚利桑那菌环介导等温扩增检测方法的建立

应用环介导等温扩增(loop mediated isothermal amplification,LAMP)技术,研究建立一种快速、敏感、特异的检测亚利桑那菌(Salmonella arizonae)方法,为食品安全检测工作中亚利桑那菌检测提供一种快速准确工具。针对亚利桑那菌spv A基因中39个保守且特异的碱基序列,设计LAMP特异性引物,利用实时浊度仪对引物及反应条件进行优化,并对检测方法的灵敏度和特异性进行验证。该方法在63℃恒温下作用40 min,亚利桑那菌DNA获得高效率的特异性扩增;其检出限量为培养菌液浓度10~6CFU/m L,敏感性高;通过对25份沙门氏菌阳性食品的LAMP检测,检出2例亚利桑那菌。该文所建立的亚利桑那菌环介导等温扩增LAMP检测方法具有特异、灵敏、简便快捷等特点,适用于食品安全检测中亚利桑那菌的快速筛检。     

Scanning tunneling microscopy of cauliflower-like DNA nanostructures synthesised by loop-mediated isothermal amplification

DNA nanotechnology is a novel approach for synthesis of DNA-based nanostructures. Stem-loops, nanojunctions, sticky-ends and periodic lengths of DNA are the most essential nanostructures in DNA nanofabrications. Loop-mediated isothermal amplification (LAMP) is a powerful technology for repetitive synthesis of double-stranded and cauliflower-like DNAs. The process leads to long and repetitive sequences of DNAs, which are fabricated via loop primers. The authors demonstrate here scanning tunneling micrographs of LAMP-synthesised DNAs deposited on highly ordered pyrolytic graphite. The scans are compared with natural DNAs. Scanning tunneling microscopy (STM) images indicated the creation of periodic long DNAs, stem-looped DNAs and three-way DNA nanojunctions. It is also suggested that such nanomaterials could be promising candidates for use in DNA-based nanodevices.     

Typing of multiple single-nucleotide polymorphisms by a microsphere-based rolling circle amplification assay

The combination of suspension array with rolling circle amplification can lead to a sensitive and specific assay for single-nucleotide polymorphisms (SNPs) detection, as demonstrated in this study. A circular template generated by ligation upon the recognition of a point mutation on DNA targets was amplified isothermally by the Phi29 polymerase on microspheres. The elongation products were labeled with fluorochrome-tagged probes and detected in a flow cytometer, indicating the mutation occurrence. As low as 10 amol of mutated strands was detected by this assay, and positive mutation detection was achieved with a wild-type to mutant ratio of 10 000:1, which could be attributed to the high amplification efficiency of Phi29, the high binding capacity of the microspheres, and the remarkable precision of DNA ligase in distinguishing mismatched bases at the ligation site. A novel design of using two differently labeled detection probes on the same microsphere to target both the wild-type and mutant samples allowed parallel determination of the heterozygosity for two SNPs (K-ras G12C and TP53 R273H) in PCR amplicons prepared from human genomic DNA extracts. This ability lays the groundwork for further enhancing the assay throughput by using multiple fluorophores and microspheres with distinct properties.     

Technique for quantitative detection of specific DNA sequences using alternately binding quenching probe competitive assay combined with loop-mediated isothermal amplification

We describe a novel technique for a simple, rapid, and reliable quantitative detection of specific DNA sequences using an alternately binding quenching probe (AB-QProbe) that binds to either the gene of interest (target) or an internal standard (competitor) in combination with loop-mediated isothermal amplification (LAMP). The AB-QProbe is a singly labeled oligonucleotide bearing a fluorescent dye at the 5' end. The fluorescence intensity of the AB-QProbe reflects the ratio of the LAMP products from the target and competitor. We amplified the target and competitor by LAMP under isothermal conditions with high specificity, efficiency, and rapidity and calculated the starting quantity of the target from the fluorescence intensities at the beginning and end of LAMP. We call this technique alternately binding quenching probe competitive LAMP (ABC-LAMP). We quantified amoA, which encodes the ammonia-oxidizing enzyme in environmental bacteria, as a model target by ABC-LAMP, real-time PCR, and real-time turbidimetry of LAMP. By comparison, the accuracy of ABC-LAMP was found to be similar to that of real-time PCR. Moreover, ABC-LAMP enables the accurate quantification of DNA in the presence of DNA amplification inhibitors such as humic acid, urea, and Triton X-100 that compromise the values measured by real-time PCR and real-time turbidimetry of LAMP.     

Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor

MicroRNAs (miRNAs) play important roles in a wide range of biological processes, and their aberrant expressions are associated with various diseases. Here we develop a rapid, highly sensitive, and specific miRNA assay based on the two-stage exponential amplification reaction (EXPAR) and a single-quantum-dot (QD)-based nanosensor. The two-stage EXPAR involves two templates and two-stage amplification reactions under isothermal conditions. The first template enables the amplification of miRNA, and the second template enables the conversion of miRNA to the reporter oligonucleotide. Importantly, different miRNAs can be converted to the same reporter oligonucleotides, which can hybridize with the same set of capture and reporter probes to form sandwich hybrids. These sandwich hybrids can be assembled on the surface of 605 nm emission QDs (605QDs) to form the 605QD/reporter oligonucleotide/Cy5 complexes, where the 605QD functions as both a fluorescence resonance energy transfer donor and a target concentrator. Upon excitation with a wavelength of 488 nm, distinct Cy5 signals can be observed in the presence of target miRNA. This assay is highly sensitive and specific with a detection limit of 0.1 aM and can even discriminate single-nucleotide differences between miRNA family members. Moreover, in combination with the specific templates, this method can be applied for multiplex miRNA assay by simply using the same set of capture and reporter probes. This highly sensitive and specific assay has potential to become a promising miRNA quantification method in biomedical research and clinical diagnosis.     

Rolling circle amplification and circle-to-circle amplification of a specific gene integrated with electrophoretic analysis on a single chip

We have developed an integrated platform for rolling circle amplification (RCA) and circle-to-circle amplification (C2CA) of circular probe (padlock probe) and subsequent microchip electrophoretic detection of a specific gene on a poly(methyl methacrylate) microchip. RCA and C2CA were successfully carried out at a steady temperature of 37 degrees C in the sample well of the microchip, and their respective product was detected on the same channel of the microchip, which was prefilled with a polymer separation matrix and fluorescent dye. Using a species-specific padlock probe for bacterial pathogen V. cholerae, a 25-ng bacterial genomic DNA could be detected in less than 65 min (including RCA and microchip electrophoresis) by this platform. Stable dsDNA C2CA product of genomic DNA for V. cholerae can be detected with the introduced integrated platform. Furthermore, the usefulness of this technique for the monitoring of RCA was demonstrated. This integrated platform provides a sensitive, fast, high-throughput, and reproducible method for signal amplification and detection of the padlock probes in the same microchip and is a promising tool for highly specific gene detection strategies.     

Detection of membrane-binding proteins by surface plasmon resonance with an all-aqueous amplification scheme

We report here a surface plasmon resonance (SPR) method for detection of cell membrane binding proteins with high degree signal amplification carried out in an all-aqueous condition. Ultrahigh detection sensitivity was achieved for a membrane-based biosensing interface through the use of functional gold nanoparticles (AuNP) in combination with in situ atom transfer radical polymerization (ATRP) reaction. Fusion of phosphatidylcholine vesicles on a calcinated SPR gold chip established a supported bilayer membrane in which cell receptor monosialoganglioside GM1 was embedded for capture of bacterial cholera toxin (CT). The surface-bound CT was recognized with biotinylated anti-CT, which was linked to the biotin-AuNP through an avidin bridge. The biotin-AuNP surface was functionalized with ATRP initiator that triggers localized growth of poly(hydroxyl-ethyl methacrylate) (PHEMA) brush, contributing to marked SPR signal enhancement and quantitative measurement of CT at very low concentrations. The resulting polymer film has been characterized by optical and atomic force microscopy. A calibration curve for CT detection has been obtained displaying a response range from 6.3 × 10(-16) to 6.3 × 10(-8) M with a detection limit of 160 aM (equivalent to ~9500 molecules in 100 μL sample solution). Sensitive detection of biomolecules in complex medium has been conducted with CT-spiked serum, and the detection limit can be effectively improved by 6 orders of magnitude compared to direct measurement in serum. The combined AuNP/ATRP method reported here opens new avenues for ultrasensitive detection of proteins on delicate sensor interfaces constructed by lipid membranes or cell membrane mimics.     

Triggered polycatenated DNA scaffolds for DNA sensors and aptasensors by a combination of rolling circle amplification and DNAzyme amplification

The concept of triggered polycatenated DNA scaffolds has been elegantly introduced into ultrasensitive biosensing applications by a combination of rolling circle amplification (RCA) and DNAzyme amplification. As compared to traditional methods in which one target could only initiate the formation of one circular template for RCA reaction, in the present study two species of linear single-stranded DNA (ssDNA) monomers are self-assembled into mechanically interlocked polycatenated nanostructures on capture probe-tagged magnetic nanoparticles (MNPs) only upon the introduction of one base mutant DNA sequence as initiator for single-nucleotide polymorphisms (SNPs) analysis. The resultant topologically polycatenated DNA ladder is further available for RCA process by using the serially ligated circular DNA as template for the synthesis of hemin/G-quadruplex HRP-mimicking DNAzyme chains, which act as biocatalytic labels for the luminol-H(2)O(2) chemiluminescence (CL) system. Notably, the problem of high background induced by excess hemin itself is circumvented by immobilizing the biotinylated RCA products on streptavidin-modified MNPs via biotin-streptavidin interaction. Similarly, a universal strategy is contrived by substitutedly employing aptamer as initiator for the construction of polycatenated DNA scaffolds to accomplish ultrasensitive detection of proteins based on structure-switching of aptamer upon target binding, which is demonstrated by using thrombin as a model analyte in this study. Overall, with two successive amplification steps and one magnetic separation procedure, this flexible biosensing system exhibits not only high sensitivity and specificity with the detection limits of SNPs and thrombin as low as 71 aM and 6.6 pM, respectively, but also excellent performance in real human serum assay with no PCR preamplification for SNPs assay. Given the unique and attractive characteristics, this study illustrates the potential of DNA nanotechnology in bioanalytical applications for both fundamental and practical research.     

Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled ddNTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.     

DNA sensor with a dipyridophenazine complex of osmium(lI) as an electrochemical probe

Application of a dipyrido[3,2-a:2',3'-c]phenazine (DPPZ)-type metal complex as an DNA electrochemical probe was studied. The introduction of electron-donating groups (NH2) was effective for controlling the redox potential and binding affinities of the DPPZ-type osmium complex. The [Os(DA-bpy)2DPPZ]2+ complex (DA-bpy; 4,4'-diamino-2,2'-bipyridine) had a lower half-wave potential (E 1/2) of 147 mV (vs Ag/AgCl) and higher binding affinity with DNA (binding constant, K = 3.1 x 10(7) M(-1)) than those of other complexes. With a single-stranded DNA immobilized gold electrode, the hybridization signal (deltaI) of the [Os(DA-bpy)2DPPZ]2+ complex was linear in the concentration range of 1.0 pg mL(-1) - 0.12 microg mL(-1) for the targeted DNA with a regression coefficient of 0.999. The detection limit was 0. 1 pg mL(-1). The 400-bp yAL3 gene was also detected with good sensitivity and selectivity using the [Os(DA-bpy)2DPPZ]2+ complex.     

Detection of approximately 10(3) copies of DNA by an electrochemical enzyme-amplified sandwich assay with ambient O(2) as the substrate

The electrochemical sandwich-type, enzyme-amplified assay of Zhang, Kim, and Heller (Anal. Chem. 2003, 75, 3267-3269) was simplified by replacing the amplifying horseradish peroxidase with bilirubin oxidase (BOD). BOD catalyzes the reduction of ambient O(2) to water and obviates the need for adding H(2)O(2). Femtomolar (10(-)(15) M) concentrations of DNA were detected at a 10-microm-diameter tip of a carbon fiber electrode. Correspondingly, a few thousand copies of DNA were detected in approximately 5-microL samples. The sandwich is formed in an electron-conducting redox hydrogel, to the polymer of which a DNA capture sequence is bound. Capture of the analyte DNA and its hybridization with a BOD-labeled complementary DNA sequence, electrically connects the BOD label to the electron-conducting redox polymer, which is in electrical contact with the electrode. Placing the BOD in contact with the redox polymer thus converts the noncatalytic base layer into a catalyst for the electroreduction of O(2) to water at +0.12 V (vs Ag/AgCl) (Figure 1). In an exemplary assay, approximately 3000 copies of the iron transporting sequence of the sit gene of Shigella flexneri were detected without PCR amplification.     

Detection and measurement of crack closure and opening by an ultrasonic method

In order to assess fatigue crack propagation, one of the most-used laws is due to Elber. This involves, however, accurate measurement of the opening load of the crack which is closed at its tip. We propose a new ultrasonic method based on wave diffraction by the crack tip and a record of the echodynamic. It accurately detects and measures both closure and opening of cracks (corresponding lengths and loads). It is able to do that both near the lateral faces and in the bulk of the specimen. It is well suited to thick CT specimens.     

Formation of bone-like apatite on titanium filaments incubated in a simulated body fluid by using an electrochemical method

Apatite (HA) layer can be formed on the surface of titanium using the electrochemical deposit method. In the present study, we found the current and loading time strongly affected the granule size and quantity of HA. When a low current was applied, needle-like HA was formed and irregular granules were seen at a higher current. We also found the main components of both the HA structures were Ca and P, and the percentage Ca/P was 1.69, which is similar to that of a natural bone.     

Impact of beta-cypermethrin on soil microbial community associated with its bioavailability: a combined study by isothermal microcalorimetry and enzyme assay techniques

In this study, an isothermal microcalorimetric technique has been used to show that beta-cypermethrin (CYP) had no significant effect (p > 0.05) on soil microbial activity at 80 μg g(-1) soil. Our soil enzyme data indicated that beta-CYP ranging 10-80 μg g(-1) soil had no significant effect (p > 0.05) on soil enzyme activities such as β-glucosidase, urease, acid-phosphatase, and dehydrogenase. Therefore, our results infer that beta-CYP would not pose severe toxicity to soil microbial community, but its toxic level may vary greatly with environment that associates with its increase in bioavailability: the level in soil (at μg g(-1)) < the level in sediment (varying from μg g(-1) to μg L(-1)) 0.05). These results suggest that the heavy application of beta-CYP may not cause damage to soil microbial community which is very different from its high toxicity to the aquatic organism.     

Synthesis of calcium zincate powders by a chemical Co-precipitation method and their electrochemical performances

Calcium zincate powders used as active materials for a secondary Zn electrode were prepared by a chemical precipitation (CP) method. The characteristic properties of calcium zincate powders were examined by thermal gravimetric analysis (TGA), X-ray diffraction (XRD) analysis, Brunauer-Emmett-Teller (BET) measurement, Transmission electron microscope (TEM) and micro-Raman spectroscopy. For comparison, the secondary Zn electrodes using CP-calcium zincate powders, so-called the CP-ZnCa, were obtained and examined. The electrochemical performances of the secondary Zn electrodes were investigated by galvanostatic charge/discharge measurements. As a result, the best performance of the CP-ZnCa powders were synthesized at pH 12 with a mole ratio of Zn:Ca = 2.5:1. The experimental results indicated that the secondary Zn electrode based on the CP-ZnCa powders exhibited better charge/discharge reversibility and longer cycle-life performance.     

Development of a protein chip: a MS-based method for quantitation of protein expression and modification levels using an immunoaffinity approach

Protein chip technology permits analysis of the expression and modification status of numerous targeted proteins within a single experiment, mainly through the use of antibody-based microarrays. Despite recent improvements in these protein chips, their applications are still limited for a variety of reasons, which include technical challenges in fabrication of the antibody chips as well as the very low specificity achieved by current detection methods. We have developed a unique approach for relative and/or absolute quantitation of protein expression and modification based on the capture of epitope peptides on affinity beads, which can be used to develop a mass-spectrometry-based protein chip technology. This new method, which utilizes antibodies immobilized on beads for the capture of target peptides, instead of proteins, eliminates many of the problems previously associated with protein chips. We present here several proof-of-principle experiments examining model peptides by this technique. These experiments show that the method is capable of (i). detecting peptides bound to a single antibody bead, (ii). detecting peptides at low (fmol) levels, (iii). producing MS/MS data of suitable quality for protein identification via database searching or de novo sequencing, (iv). quantitating peptides affinity-bound to antibody beads, (v). specifically detecting target peptides in complex mixtures over wide dynamic ranges, and (vi) is compatible with a microarray format for high-throughput analysis. Because our novel method uses antibody beads instead of a derivatized capture surface, and peptides instead of proteins for affinity capture, it can overcome many of the pitfalls of previous protein chip fabrications. Therefore, this method offers an improved approach to protein chip technology that should prove useful for diagnostics and drug development applications.     

Multiple and simultaneous detection of specific bacteria in enriched bacterial communities using a DNA microarray chip with randomly generated genomic DNA probes

A DNA microarray chip for detecting the presence of specific bacterial strains was developed using random genomic probes derived from genomic DNA, i.e., without any sequence information. Thirteen bacteria from different genuses were selected as targets. For the fabrication of the random genomic probes, genomic DNA from pure cultures of each bacterium was fractionated using several pairs of restriction endonucleases. After size fractionation of the genomic DNA fragments, random genomic libraries for each bacterium were constructed. From the library, specific probes were amplified by PCR and the probes were affixed to a slide glass to fabricate the DNA microarray chip. The results from tests with pure and mixed cultures of the bacteria used in the fabrication of the chips showed specific responses and only a small portion of cross-hybridization. This DNA microarray chip was also tested to detect the presence of specific bacteria in mixed populations. In these tests, it was demonstrated that this system provided a fast and specific response to the presence of bacterial species in mixed samples, even in activated sludge samples. This indicates that any DNA microarray chip for the detection of specific bacteria can be fabricated using the same protocols as presented in this study without requiring any genus level sequence information from pure isolates.