A molecular beacon design for a colorimetric loop-mediated isothermal amplification assay.

In this study, a molecular beacon (MB) was designed for colorimetric loop-mediated isothermal amplification (cLAMP). The length of complementary bases on the MB, guanine and cytosine content (GC content), and hybridization sites of complementary bases were investigated as key factors affecting the design of the MB. We designed MBs consisting of 10, 15, and 20 complementary bases located at both ends of the HRPzyme. In the case of the long dumbbell DNA structure amplified from the hlyA gene of Listeria monocytogenes, possessing a flat region (F1c-B1) of 61 base pairs (bp), an MB was designed to intercalate into the flat region between the F1c and B1 regions of the LAMP amplicons. In the case of the short dumbbell DNA structure amplified from the bcfD gene of Salmonella species possessing a flat region (F1c-B1) length of 6 bp, another MB was designed to intercalate into the LoopF or LoopB regions of the LAMP amplicons. The results revealed that the hybridization site of the MB on the LAMP amplicons was not crucial in designing the MB, but the GC content was an important factor. The highest hybridization efficiencies for LAMP amplicons were obtained from hlyA gene-specific and bcfD gene-specific MBs containing 20- and 15-base complementary sequences, respectively, which exhibited the highest GC content. Therefore, designing MBs with a high GC content is an effective solution to overcome the low hybridization efficiency of cLAMP assays. The results obtained can be used as primary data for designing MBs to improve cLAMP accessibility.

Colorimetric detection of norovirus by helicase-dependent amplification method based on specific primers integrated with HRPzyme.

Noroviruses (NoVs) are the most common causes of epidemic gastroenteritis, responsible for at least 50% of all gastroenteritis outbreaks worldwide and significant causes of foodborne illness. In the USA, approximately 21 million illnesses attributable to NoVs have annually occurred. Therefore, there is a great demand to develop a rapid, low-cost, and accurate detection method for NoVs. This study first reported colorimetric helicase-dependent amplification (HDA) methods based on specific primers integrated with HRPzyme for the rapid and sensitive detection of NoV GI and GII. The colorimetric HDA methods exhibited a detection limit of 10 copies mL-1 of each NoV GI and GII and were confirmed to be specific to each NoV GI and GII. The period required to complete the HDA method was 2 h, including a step of RNA extraction and cDNA synthesis without expensive instruments such as a thermal cycler and detector. The cutoff value of the method for the oyster artificially inoculated with a known amount of NoV was all 102 copies g-1 for NoV GI and GII. Therefore, the HDA method developed in this study can be useful tool for the on-site detection of NoVs in food samples.

A colorimetric Loop-mediated isothermal amplification (LAMP) assay based on HRP-mimicking molecular beacon for the rapid detection of Vibrio parahaemolyticus.

In the world wide, food poisoning accidents related to Vibrio spp. are on the rise, even numbers of food poisoning by other foodborne pathogens are decreasing. Therefore, the requirement of the rapid, sensitive and convenient detection method for V. parahaemolyticus has been grown. The objective of this study is to develop a colorimetric loop-mediated isothermal amplification (LAMP) assay using a molecular beacon (HRPzyme connected with complementary oligonucleotides at the 5' and 3' ends) for the rapid, sensitive, and convenient detection of V. parahaemolyticus. The colorimetric LAMP assay optimized at 58.8°C showed a detection limit of 1 × 100 CFU/mL and was confirmed to be specific to V. parahaemolyticus. The colorimetric LAMP assay can be finished within 1 h including DNA extraction step. The method was successfully applied to flatfish samples artificially inoculated with known amount of V. parahaemolyticus, and its cut-off value for the flatfish samples was 1 × 101 CFU/g. In addition, the colorimetric LAMP assay developed in the study was found to be able to correct false-positive results, which are known to be a disadvantage of conventional LAMP assays. Therefore, these results indicated that the colorimetric LAMP method is a useful tool for the rapid, sensitive and convenient detection of V. parahaemolyticus in fishes and can also be used as a point-of-care molecular diagnostic technique since it does not require any expensive equipment such as a thermocycler and detectors.

Adenosine Triphosphate Bioluminescence-Based Bacteria Detection Using Targeted Photothermal Lysis by Gold Nanorods.

Bacterial infections are common causes of morbidity and mortality worldwide; therefore, environmental contamination by bacterial pathogens represents a global public health concern. Consequently, a selective, rapid, sensitive, and in-field detection platform for detecting significant bacterial contamination is required to ensure hygiene and protect public health. Here, we developed a fast and simple platform for the selective and sensitive detection of bacteria by measuring adenosine triphosphate (ATP) bioluminescence following targeted photothermal lysis mediated by antibody-conjugated gold nanorods. This method employed both targeted photothermal lysis of bacteria by near-infrared (NIR) irradiation and highly selective detection of the lysed bacteria via ATP bioluminescence within 36 min (incubation, 30 min; NIR irradiation, 6 min). The use of the proposed method allowed limits of detection in pure solution of 12.7, 70.7, and 5.9 CFU for Escherichia coli O157:H7, Salmonella typhimurium, and Listeria monocytogenes, respectively. Additionally, bacteria were successfully detected on artificially inoculated plastic cutting boards. Furthermore, this method was highly specific, without cross-reaction among pathogenic bacteria. We believe that the proposed method has significant potential as an on-site diagnostic tool for applications associated with public health and environmental pollution monitoring.

Ultrasensitive Detection of Escherichia coli O157:H7 by Immunomagnetic Separation and Selective Filtration with Nitroblue Tetrazolium/5-Bromo-4-chloro-3-indolyl Phosphate Signal Amplification.

Here, we report an enhanced colorimetric method using enzymatic amplification with nitroblue tetrazolium (NBT)/5-bromo-4-chloro-3-indolyl phosphate (BCIP) precipitation for the ultrasensitive detection of Escherichia coli O157:H7 through immunomagnetic separation-selective filtration. Biotinylated anti- E. coli O157:H7 antibody and streptavidin-alkaline phosphatase were conjugated to the surface of magnetic nanoparticles, and E. coli O157:H7-conjugates complexes remained on the membrane filter surface. The resultant light brown spots on the membrane filter were amplified with NBT/BCIP solution to yield enzyme-catalyzed precipitation, which increased with an increasing E. coli O157:H7 concentration. E. coli O157:H7 was detected in pure samples with limits of detection of 10 and 6.998 colony-forming units (CFU)/mL through visual observation and measurement of optical density, respectively. The proposed method was applied to a lettuce sample inoculated with selective E. coli O157:H7, which was detected within 55 min without cross-reactivity to non-target bacteria. This enhanced colorimetric method has potential for on-site detection of food contaminants and environmental pollutants.

Quantitative analysis of lard in animal fat mixture using visible Raman spectroscopy.

Food adulteration is a serious issue that requires verification and strict management due to healthcare, morality, and social value problems. In the context of fat, food manufacturers blend lard with vegetable oils or animal fats for convenience and gaining economic benefits. Thus, we herein report the classification of 4 animal fats, e.g., beef tallow, pork lard, chicken fat, duck oil, using Raman spectroscopy combined with simple calculation of intensity ratios of Raman signal at vibrational modes corresponding to unsaturated fatty acids and total fatty acids. Various calculated values of the species were compared to find a feature that is able to classify each fats using Raman peak ratio. As a result, we suggested "Oil gauge (OG)" as a standard feature for classification of the fats in Raman analysis field. Furthermore, a quantification of the lard in other fat was accomplished with good linear correlation using the OG values.

Colorimetric molecular diagnosis of the HIV gag gene using DNAzyme and a complementary DNA-extended primer.

We have developed a novel strategy for the colorimetric detection of PCR products by utilizing a target-specific primer modified at the 5'-end with an anti-DNAzyme sequence. A single-stranded DNAzyme sequence folds into a G-quadruplex structure with hemin and shows strong peroxidase activity. When the complementary strand binds to the DNAzyme sequence, it blocks the formation of the G-quadraduplex structure and loses its peroxidase activity. In the presence of the target gene, PCR amplification proceeds, and anti-DNAzyme sequence modified primers present in the reaction mixture form a double strand through primer extension. Therefore, it does not block the DNAzyme sequence. Further, a colorimetric signal is generated by the addition of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) and H2O2 at the end of the reaction. We have successfully detected a single copy of the HIV type 1 gag gene in buffer and 10 copies in human serum. The strategy developed could be used to detect DNA and RNA in complex biological samples by simple primer designing that includes DNAzyme and a DNA extended primer.

Colorimetric Detection of Norovirus in Oyster Samples through DNAzyme as a Signaling Probe.

Worldwide, norovirus is one of the most associated causes of acute gastroenteritis, which leads to nearly 50 000 child deaths every year in developing countries. Therefore, there is great demand to develop a rapid, low-cost, and accurate detection assay for the foodborne norovirus infection to reduce mortality caused by norovirus. Considering the importance of norovirus, we have demonstrated a highly sensitive and specific colorimetric detection method for analysis of human norovirus genogroups I and II (HuNoV GI and GII) in oyster samples. This is the first report to employ colorimetric HRPzyme-integrated polymerase chain reaction (PCR) for direct norovirus detection from the real shellfish samples. We found that the HRPzyme-integrated PCR method is more sensitive than the gel electrophoresis approach and could detect the HuNoV GI and GII genome up to 1 copy/mL. The specificity of the proposed method was successfully demonstrated for HuNoV GI and GII. Further, we performed testing HuNoVs in the spiked oyster samples, and the HRPzyme-integrated PCR method proved to be an ultrasensitive and selective method for detecting HuNoVs in the real samples. By integration of the proposed method with the portable PCR machine, it would be more reliable to improve food safety by detecting HuNoVs in the different types of shellfish, such as oyster and mussel, at the production field.

Single-Step LRET Aptasensor for Rapid Mycotoxin Detection.

Contamination of foods by mycotoxins is a common yet serious problem. Owing to the increase in consumption of fresh produce, consumers have become aware of food safety issues caused by mycotoxins. Therefore, rapid and sensitive mycotoxin detection is in great demand in fields such as food safety and public health. Here we report a single-step luminescence resonance energy transfer (LRET) aptasensor for mycotoxin detection. To accomplish the single-step sensor, our sensor was constructed by linking a quencher-labeled aptamer through a linker to the surface of upconversion nanoparticles (UCNPs). Our LRET aptasensor is composed of Mn2+-doped NaYF4:Yb3+,Er3+ UCNPs as the LRET donor, and black hole quencher 3 (BHQ3) as the acceptor. The maximum quenching efficiency is obtained by modulating the linker length, which controls the distance between the quencher and the UCNPs. Our distinctive design of LRET aptasensor allows detection of mycotoxins selectively in colored food samples within 10 min without multiple bioassay steps. We believe our single-step aptasensor has a significant potential for on-site detection of food contaminants, environmental pollutants, and biological metabolites.

Homogeneous and selective detection of cadmium ions by forming fluorescent cadmium-protein nanoclusters.

We synthesized fluorescent Cd nanoclusters (CdNCs) through a protein-directed method, and the synthesis method was utilized for a homogeneous, ultrasensitive, and selective detection of cadmium ion (Cd2+). CdNCs were synthesized using a modified protein-directed method for developing a rapid Cd2+ detection system. For rapid Cd2+ detection, the reaction time was reduced by optimizing the reaction conditions such as temperature, reducing agent concentration, and protein concentration. The synthesized CdNCs had ca. 2 nm diameter and showed strong fluorescence at 485 nm under 365 nm UV light. The fluorescence of the CdNCs increased with increasing Cd2+ concentrations, and the limit of detection in deionized water was 15.68 fM. This method enables the detection of Cd2+ through the Cd concentration-dependent formation of fluorescent CdNCs in tap, fountain, and pond water samples with detection limits of 0.75, 7.65, and 48.2 fM, respectively. The sensitivity and specificity of our method are comparable to those of several existing methods for Cd2+ detection. Furthermore, the system enables the homogeneous detection of Cd2+ without separation and washing, thereby broadening its application in analytical chemistry.

Homogeneous Immunosensor Based on Luminescence Resonance Energy Transfer for Glycated Hemoglobin Detection Using Upconversion Nanoparticles.

We report an immunosensor based on luminescence resonance energy transfer (LRET) to detect homogeneous glycated hemoglobin (HbA1c). This system uses near-infrared (NIR)-to-visible rare-earth upconversion nanoparticles (UCNPs), such as NaYF4:Yb(3+), Er(3+), as the donor and HbA1c as the acceptor. The HbA1c used as target molecules showed absorption at 541 nm, which corresponded with the emission of the UCNPs. When HbA1c was added, LRET occurred between the donor and acceptor under laser irradiation of 980 nm because of the specific recognition between the anti-HbA1c monocolonal antibody-functionalized UCNPs and HbA1c. In the absence of HbA1c, there was strong upconversion luminescence intensity; however, in its presence, the distance between the donor and acceptor decreased to enable energy transfer, consequently quenching the luminescence of the UCNPs. The proposed method was successfully applied to HbA1c detection in blood samples. Our results indicate that the LRET-based immunosensor allows for specific and sensitive detection of HbA1c in a homogeneous manner.

Detection of ochratoxin A (OTA) in coffee using chemiluminescence resonance energy transfer (CRET) aptasensor.

We report a chemiluminescence resonance energy transfer (CRET) aptasensor for the detection of ochratoxin A (OTA) in roasted coffee beans. The aptamer sequences used in this study are 5'-DNAzyme-Linker-OTA aptamer-3'-dabcyl. Dabcyl at the end of the OTA aptamer region plays as a quencher in CRET aptasensor. When hemin and OTA are added, the dabcyl-labeled OTA aptamer approaches to the G-quadruplex-hemin complex by formation of the G-quadruplex-OTA complex. The G-quadruplex-hemin complexes possess horseradish peroxidase (HRP)-like activity, and therefore, the HRP-mimicking DNAzyme (HRPzyme) catalyzes peroxidation in the presence of luminol and H2O2. Resonance energy transfer between luminol (donor) and dabcyl (acceptor) enables quenching of chemiluminescence signals. The signal decreases with increasing the concentration of OTA within the range of 0.1-100ngmL(-1) (limit of detection 0.22ngmL(-1)), and the level of recovery of the respective 1ngmL(-1) and 10ngmL(-1) spiked coffee samples was 71.5% and 93.3%. These results demonstrated the potential of the proposed method for OTA analysis in diverse foods.

An aptamer-based dipstick assay for the rapid and simple detection of aflatoxin B1.

A rapid and simple dipstick assay based on an aptamer has been developed for the determination of aflatoxin B1 (AFB1). The dipstick assay format was based on a competitive reaction of the biotin-modified aptamer specific to AFB1 between target and cy5-modified DNA probes. Streptavidin and anti-cy5 antibody as capture reagents were immobilized at test and control lines on a membrane of the dipstick assay. After optimization, the limit of detection for the dipstick assay was 0.1 ng/ml AFB1 in buffer. The method was confirmed to be specific to AFB1, and the entire process of the assay can be completed within 30 min. Aqueous methanol (20%) provided a good extraction efficiency, and the matrix influence from corn extracts was successfully reduced through 2-fold dilution. The results of AFB1 analysis for corn samples spiked with known concentration of AFB1 by the dipstick assay and ELISA showed good agreement. The cut-off value of the dipstick assay for corn samples was 0.3 ng/g AFB1. Therefore, the dipstick assay is first reported and considered as a rapid, simple, on-site and inexpensive screening tool for AFB1 determination in grains as well as a corn.

A regeneratable, label-free, localized surface plasmon resonance (LSPR) aptasensor for the detection of ochratoxin A.

Binding of an analyte on the surface of a nanoparticle typically promotes a change in the local refractive index, which gives rise to a shift in the wavelength of the localized surface plasmon resonance (LSPR) absorption band. The magnitude of the LSPR wavelength change is dependent on both the location of the analyte relative to the surface of the nanoparticle and the degree of alteration of the refractive index. We have employed this phenomenon as the basis for designing a new, label-free approach for the detection of the toxic mold mycotoxin, ochratoxin A (OTA) that employs a gold nanorod (GNR) and an aptamer target binding mechanism. In this system, binding of OTA causes an accumulation of OTA and G-quadruplex structure of the aptamer. This process results in a longitudinal wavelength shift of the LSPR peak associated with a change in the local refractive index near the GNR surface. By using this method, OTA can be quantitatively detected at concentrations lower than 1 nM. In addition, the results of this effort show that aptamer functionalized GNR substrate is robust in that it can be regenerated for reuse over seven times by heating in methanol at 70 °C to remove OTA. Moreover, the proposed biosensor system exhibits high selectivity for OTA over other mycotoxins. Finally, the sensor can be employed to detect OTA in ground corn samples with excellent recovery levels.

Homogeneous assay of target molecules based on chemiluminescence resonance energy transfer (CRET) using DNAzyme-linked aptamers.

We have designed a single-stranded DNAzyme-aptamer sensor for homogeneous target molecular detection based on chemiluminescence resonance energy transfer (CRET). The structure of the engineered single-stranded DNA (ssDNA) includes the horseradish peroxidase (HRP)-like DNAzyme, optimum-length linker (10-mer-length DNA), and target-specific aptamer sequences. A quencher dye was modified at the 3' end of the aptamer sequence. The incorporation of hemin into the G-quadruplex structure of DNAzyme yields an active HRP-like activity that catalyzes luminol to generate a chemiluminescence (CL) signal. In the presence of target molecules, such as ochratoxin A (OTA), adenosine triphosphate (ATP), or thrombin, the aptamer sequence was folded due to the formation of the aptamer/analyte complex, which induced the quencher dye close to the DNAzyme structure. Consequently, the CRET occurred between a DNAzyme-catalyzed chemiluminescence reaction and the quencher dye. Our results showed that CRET-based DNAzyme-aptamer biosensing enabled specific OTA analysis with a limit of detection of 0.27ng/mL. The CRET platform needs no external light source and avoids autofluorescence and photobleaching, and target molecules can be detected specifically and sensitively in a homogeneous manner.

Rapid colorimetric detection of Salmonella typhimuriumusing a selective filtration technique combined with antibody-magnetic nanoparticle nanocomposites.

Detection of pathogenic bacteria that pose a great risk to human health requires a rapid, convenient, reliable, and sensitive detection method. In this study, we developed a selective filtration method using monoclonal antibody (MAb)-magnetic nanoparticle (MNP) nanocomposites for the rapid and sensitive colorimetric detection of Salmonella typhimurium. The method contains two key steps: the immunomagnetic separation of the bacteria using MAb-MNP nanocomposites and the filtration of the nanocomposite-bound bacteria. Color signals from the nanocomposites remaining on the membrane were measured, which reflected the amount of bacteria in test samples. Immunomagnetic capture efficiencies of 8 to 90 % for various concentrations of the pathogen (2 × 10(4)-2 × 10(1) cells) were obtained. After optimization of the method, 2 × 10(1) cells of S. typhimurium in pure culture solution was detectable as well as in artificially inoculated vegetables (100 cells/g). The method was confirmed to be highly specific to S. typhimurium without cross-reaction to other pathogenic bacteria and could be concluded within 45 min, yielding results in a shorter or similar time period as compared with recently reported antibody immobilized on magnetic-particle-based methods. This study also demonstrated direct application of MAb-MNP nanocomposites without a dissociation step of bacteria from magnetic beads in colorimetric assays in practice.