Bio-barcode Assay Research Articles

A broad-spectrum antibody based bio-barcode fluorescence immunosensor for simultaneous detection of eight heterocyclic aromatic amines (HAAs) in heat processed meat

• A broad-spectrum specific antibody prepared can equivalently recognize 8 HAAs. • This immunosensor has achieved detecting total amount of 8 HAAs in one test process. • This immunosensor is simple, convenient, and effective for detection of 8 HAAs. • The bio-barcode assay has been introduced to achieve signal amplification detection. • This immunosensor has good reliability and practicability for detection of 8 HAAs. Heterocyclic aromatic amines (HAAs) as carcinogenic and mutagenic substance are naturally produced in heat processed meat. In this work, we have proposed a novel and sensitive fluorescence immunosensor for simultaneous detecting eight HAAs in heat processed meat samples. Herein, a broad-spectrum antibody simultaneously recognizing eight HAAs, amino modified ssDNA and Alexa Flour 488 labeled ssDNA are connected to silica nanoparticles for preparing the bio-barcode immune signal probe. Coating antigens are linked to AuNPs to form the coupling complex as fluorescent quencher. Based on the competition between quencher and analyte for binding to antibody of signal probe, as the analyte increases, the amount of quenchers combined to the signal probe decreases, and the fluorescence intensity increases. With MeIQx as the analyte, the immunosensor has a wide linear range from 0.1–200 μg L −1 with low limit of detection of 0.01 μg L −1 . The applicability of the fluorescence immunosensor is evaluated by measuring total amount of eight HAAs in real heat processed meat. The measured results of this fluorescence immunosensor are in good agreement with that of UPLC-MS/MS and ELISA. This fluorescence immunosensor provides an effective detection tool for the simultaneous detection of multiple HAAs in heat processed food samples.

Dynamic Bio-Barcode Assay Enables Electrochemical Detection of a Cancer Biomarker in Undiluted Human Plasma: A Sample-In-Answer-Out Approach.

There is a need for biosensing systems that can be operated at the point-of-care (POC) for disease screening and diagnostics and health monitoring. In spite of this, simple to operate systems with the required analytical sensitivity and specificity in clinical samples, using a sample-in-answer-out approach, remain elusive. Reported here is an electrochemical bio-barcode assay (e-biobarcode assay) that integrates biorecognition with signal transduction using molecular (DNA/protein) machines and signal readout using nanostructured electrodes. The e-biobarcode assay eliminates multistep processing and uses a single step for analysis following sample collection into the reagent tube. A clinically relevant performance for the analysis of prostate specific antigen (PSA) in undiluted and unprocessed human plasma: a log-linear range of 1 ng mL-1 -200 ng mL-1 and a LOD of 0.4 ng mL-1 , was achieved. The e-biobarcode assay offers a realistic solution for biomarker analysis at the POC.

A Spellbinding Interplay Between Biological Barcoding and Nanotechnology

Great scientific research with improved potential in probing biological locales has remained a giant stride. The use of bio-barcodes with the potential use of nanotechnology is a hallmark being developed among recent advanced techniques. Biobarcoding is a novel method used for screening biomolecules to identify and divulge ragbag biodiversity. It establishes successful barcoding projects in the field of nanomedical technology for massively testing disease diagnosis and treatment. Biobarcoding and nanotechnology are recently developed technologies that provide unique opportunities and challenges for multiplex detection such as DNAs, proteins and nucleic acids of animals, plants, viruses, and various other species. These technologies also clump drug delivery, gene delivery, and DNA sequencing. Bio-barcode amplification assay (BCA) is used at large for the detection and identification of proteins and DNAs. DNA barcoding combined with nanotechnology has been proven highly sensitive rendering fast uniplex and multiplex detection of pathogens in food, blood, and other specimens. This review takes a panoramic view of current advances in nano bio-barcodes which have been summarized to explore additional applications such as detection of cytokines, neurotransmitters, cancer markers, prostate-specific antigens, and allergens. In the future, it will also be possible to detect some fungi, algae, protozoa, and other pollutants in food, agriculture, and clinical samples. Using these technologies, specific and efficient sensors would possibly be developed that can perform swift detections of antigens, allergens, and other specimens.

Bio-barcode technology for detection of Staphylococcus aureus protein A based on gold and iron nanoparticles

S. aureus is one of important causes of disease, food poisoning in humans and animals. The generally methods for detection of S. aureus is time consuming. Therefore, a new method is necessary for rapid, sensitive and specific diagnosis of S. aureus. In the present study, two probes and a Bio-barcode DNA were designed for detection of S. aureus (Protein A). Firstly, magnetic nanoparticle (MNPs) and gold nanoparticle (AuNPs) were synthesized at 80 °C and 100 °C, respectively. The AuNPs and the MNPs were functionalized with probe1, Bio-barcode DNA and probe2, respectively. Target DNA was added into the nanomaterial's system containing bio-barcode DNA-AuNPs-probe1 and probe2-MNPs to formed bio-barcode DNA-AuNPs-probe1-target DNA-probe2-MNPs complex. The bio-barcode DNA-AuNPs-probe1-target DNA-probe2-MNPs complex was separated with magnetic field. Finally, the bio-barcode DNA was released from surface of complex using DTT (0.8 M) and there was isolated of nanoparticles by magnetic field and centrifuge. The fluorescence intensity of bio-barcode DNA was measured in different concentrations of S. aureus (101 to 108 CFU mL−1) by fluorescence spectrophotometry. The results showed that standard curve was linearly from 102 to 107 CFU mL−1. Limit of detection of bio-barcode assay for both PBS and real samples was 86 CFU mL−1.

Establishment of fluorescence-based quantitative real-time polymerase chain reaction for the detection of barcode DNA in the novel bio-barcode assay

Establishment of fluorescence-based quantitative real-time polymerase chain reaction for the detection of barcode DNA in the novel bio-barcode assay

Nanoparticle based bio-bar code technology for trace analysis of aflatoxin B1 in Chinese herbs

A novel and sensitive assay for aflatoxin B1 (AFB1) detection has been developed by using bio-bar code assay (BCA). The method that relies on polyclonal antibodies encoded with DNA modified gold nanoparticle (NP) and monoclonal antibodies modified magnetic microparticle (MMP), and subsequent detection of amplified target in the form of bio-bar code using a fluorescent quantitative polymerase chain reaction (FQ-PCR) detection method. First, NP probes encoded with DNA that was unique to AFB1, MMP probes with monoclonal antibodies that bind AFB1 specifically were prepared. Then, the MMP-AFB1-NP sandwich compounds were acquired, dehybridization of the oligonucleotides on the nanoparticle surface allows the determination of the presence of AFB1 by identifying the oligonucleotide sequence released from the NP through FQ-PCR detection. The bio-bar code techniques system for detecting AFB1 was established, and the sensitivity limit was about 10−8 ng/mL, comparable ELISA assays for detecting the same target, it showed that we can detect AFB1 at low attomolar levels with the bio-bar-code amplification approach. This is also the first demonstration of a bio-bar code type assay for the detection of AFB1 in Chinese herbs.

Sandwich NP-based biobarcode assay for quantification C-reactive protein in plasma samples

A NP-based biobarcode for C-reactive protein (CRP) quantification in plasma samples is reported for the first time. The assay uses capture antibody functionalized magnetic beads (pAbCRP2-MP), multifunctional oligonucleotide encoded probes modified with a detection antibody (pAbCRP1-ePSP), and a fluorescent DNA microarray. Thus, magnetic beads are added to the sample to form immunocomplexes that will be isolated, to then add the codified particles to form a sandwich complex with both particles and the target protein, subsequently the complexes are treated to release the oligonucleotide codes, which are finally hybridized in a fluorescent DNA microarray. The assay has been implemented to the analysis of plasma samples being able to quantify this biomarker within 900 ng mL−1 to 12500 ng mL−1 with an excellent accuracy (mean of recovery of 99.5 ± 4.2%, N = 3). The CRP biobarcode has been used on a small pilot clinical study in which plasma samples from patients suffering different pathologies, most of them related to cardiovascular diseases (CVDs). The samples have been analyzed and the results compared to a reference method demonstrating that the assay can be useful for monitoring this biomarker on patients being suspicious to be under risk of suffering CVDs or other diseases involving inflammatory processes.

Biobarcode assay for the oral anticoagulant acenocoumarol

A novel approach for therapeutic drug monitoring of oral anticoagulants (OA) in clinical samples is reported, based on a NP-based biobarcode assay. The proposed strategy uses specific antibodies for acenocumarol (ACL) covalently bound to magnetic particles (pAb236-MP) and a bioconjugate competitor (hACL-BSA) linked to encoded polystyrene probes (hACL-BSA-ePSP) on a classical competitive immunochemical format. By using this scheme ACL can be detected in low nM range (LOD, 0.96 ± 0.26, N = 3, in buffer) even in complex samples such as serum or plasma (LOD 4 ± 1). The assay shows a high reproducibility (%CV 1.1 day-to-day) and is robust, as it is demonstrated by the fact that ACL can be quantified in complex biological samples with a very good accuracy (slope = 0.97 and R2 = 0.91, of the linear regression obtained when analyzing spiked vs measured values). Moreover, we have demonstrated that the biobarcode approach has the potential to overcome one of the main challenges of the multiplexed diagnostic, which is the possibility to measure in a single run biomarker targets present at different concentration ranges. Thus, it has been proven that the signal and the detectability can be modulated by just modifying the oligonucleotide load of the encoded probes. This fact opens the door for combining in the same assay encoded probes with the necessary oligonucleotide load to achieve the detectability required for each biomarker target.

High throughput differential identification of TMPRSS2-ERG fusion genes in prostate cancer patient urine.

Identifying genetic diversity is important for studies in cancer as it can provide insights on disease progression and treatment. Although clinical outcome and major symptom of cancer might be same in all patients, the type of overexpressed gene could be different. Even though prostate-specific antigen assay is a good tool widely used for prostate cancer diagnosis, it is not capable of providing information on genetic differences. Therefore, screening method that can differentiate genetic differences is necessary. Here we detected different types of TMPRSS2-ERG, prostate cancer specific fusion genes, to verify the genetic diversity between the patients using high throughput screening method, bio-barcode assay. Prostate cancer patients with different types of fusion gene were successfully differentiated directly from untreated patients' urine, while traditional PSA assay could not. This non-invasive assay, when used with PSA assay, can be a strong secondary screening method which can offer new insights on disease progression and clinical outcome.

Nanozyme-based bio-barcode assay for high sensitive and logic-controlled specific detection of multiple DNAs

Since HCV and HIV share a common transmission path, high sensitive detection of HIV and HCV gene is of significant importance to improve diagnosis accuracy and cure rate at early stage for HIV virus-infected patients. In our investigation, a novel nanozyme-based bio-barcode fluorescence amplified assay is successfully developed for simultaneous detection of HIV and HCV DNAs with excellent sensitivity in an enzyme-free and label-free condition. Here, bimetallic nanoparticles, PtAuNPs, present outstanding peroxidase-like activity and act as barcode to catalyze oxidation of nonfluorescent substrate of amplex red (AR) into fluorescent resorufin generating stable and sensitive "Turn On" fluorescent output signal, which is for the first time to be integrated with bio-barcode strategy for fluorescence detection DNA. Furthermore, the provided strategy presents excellent specificity and can distinguish single-base mismatched mutant from target DNA. What interesting is that cascaded INHIBIT-OR logic gate is integrated with biosensors for the first time to distinguish individual target DNA from each other under logic function control, which presents great application in development of rapid and intelligent detection.

An Aptamer Bio-barCode (ABC) assay using SPR, RNase H, and probes with RNA and gold-nanorods for anti-cancer drug screening.

With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer]). After washing and melting, our aptamers, acting as a DNA bio-barcode, are released from the sandwiches and hybridized with the probes specially designed for RNase H for surface plasmon resonance (SPR) sensing. In an aptamer-probe duplex, RNase H digests the RNA in the probe and releases the intact aptamer for another round of hybridization and digestion. With signal enhancement effects from gold-nanorods (Au-NRs) on probes for SPR sensing, the detection limit was found to be 1 nM for the aptamer and 80 pM for Cyto-c. Without the time-consuming DNA amplification steps by PCR, the detection process of this new ABC assay can be completed within three hours. As a proof-of-concept, phenylarsine oxide was found to be a potent agent to kill liver cancer cells with multi-drug resistance at the nano-molar level. This approach thus provides a fast, sensitive and robust tool for anti-cancer drug screening.

A Competitive Bio-Barcode Amplification Immunoassay for Small Molecules Based on Nanoparticles.

A novel detection method of small molecules, competitive bio-barcode amplification immunoassay, was developed and described in this report. Through the gold nanoparticles (AuNPs) probe and magnetic nanoparticles (MNPs) probe we prepared, only one monoclonal antibody can be used to detect small molecules. The competitive bio-barcode amplification immunoassay overcomes the obstacle that the bio-barcode assay cannot be used in small molecular detection, as two antibodies are unable to combine to one small molecule due to its small molecular structure. The small molecular compounds, triazophos, were selected as targets for the competitive bio-barcode amplification immunoassay. The linear range of detection was from 0.04 ng mL−1 to 10 ng mL−1, and the limit of detection (LOD) was 0.02 ng mL−1, which was 10–20 folds lower than ELISA (Enzyme Linked Immunosorbent Assay). A practical application of the proposed immunoassay was evaluated by detecting triazophos in real samples. The recovery rate ranged from 72.5% to 110.5%, and the RSD was less than 20%. These results were validated by GC-MS, which indicated that this convenient and sensitive method has great potential for small molecular in real samples.

Fluorescence bio-barcode DNA assay based on gold and magnetic nanoparticles for detection of Exotoxin A gene sequence

Bio-barcode DNA based on gold nanoparticle (bDNA-GNPs) as a new generation of biosensor based detection tools, holds promise for biological science studies. They are of enormous importance in the emergence of rapid and sensitive procedures for detecting toxins of microorganisms. Exotoxin A (ETA) is the most toxic virulence factor of Pseudomonas aeruginosa. ETA has ADP-ribosylation activity and decisively affects the protein synthesis of the host cells. In the present study, we developed a fluorescence bio-barcode technology to trace P. aeruginosa ETA. The GNPs were coated with the first target-specific DNA probe 1 (1pDNA) and bio-barcode DNA, which acted as a signal reporter. The magnetic nanoparticles (MNPs) were coated with the second target-specific DNA probe 2 (2pDNA) that was able to recognize the other end of the target DNA. After binding the nanoparticles with the target DNA, the following sandwich structure was formed: MNP 2pDNA/tDNA/1pDNA-GNP-bDNA. After isolating the sandwiches by a magnetic field, the DNAs of the probes which have been hybridized to their complementary DNA, GNPs and MNPs, via the hydrogen, electrostatic and covalently bonds, were released from the sandwiches after dissolving in dithiothreitol solution (DTT 0.8M). This bio-barcode DNA with known DNA sequence was then detected by fluorescence spectrophotometry. The findings showed that the new method has the advantages of fast, high sensitivity (the detection limit was 1.2ng/ml), good selectivity, and wide linear range of 5–200ng/ml. The regression analysis also showed that there was a good linear relationship (∆F=0.57 [target DNA]+21.31, R2=0.9984) between the fluorescent intensity and the target DNA concentration in the samples.

Gold Nanoparticles-Based Barcode Analysis for Detection of Norepinephrine.

Nanotechnology-based bio-barcode amplification analysis offers an innovative approach for detecting neurotransmitters. We evaluated the efficacy of this method for detecting norepinephrine in normal and oxidative-stress damaged dopaminergic cells. Our approach use a combination of DNA barcodes and bead-based immunoassays for detecting neurotransmitters with surface-enhanced Raman spectroscopy (SERS), and provides polymerase chain reaction (PCR)-like sensitivity. This method relies on magnetic Dynabeads containing antibodies and nanoparticles that are loaded both with DNA barcords and with antibodies that can sandwich the target protein captured by the Dynabead-bound antibodies. The aggregate sandwich structures are magnetically separated from the solution and treated to remove the conjugated barcode DNA. The DNA barcodes are then identified by SERS and PCR analysis. The concentration of norepinephrine in dopaminergic cells can be readily detected using the bio-barcode assay, which is a rapid, high-throughput screening tool for detecting neurotransmitters.

A gold nanoparticle based immunosorbent bio-barcode assay combined with real-time immuno-PCR for the detection of polychlorinated biphenyls

A gold nanoparticle based bio-barcode assay combined with real-time immuno- polymerase chain reaction (PCR) was developed for the determination of polychlorinated biphenyls (PCBs). Gold nanoparticles modified with thiol-capped DNA and antibody for affixing probes were used to replace antibody-DNA conjugates in immuno-PCR. The modified gold nanoparticles were fixed on the PCR tube wall through a competitive immune reaction. Signal-DNA could be released from the gold nanoparticle surface into the tubes and used as template DNA. Real-time PCR was subsequently performed to directly quantify DNA signal. A detection limit of 2.55pgL−1 was obtained under optimized conditions. This method was successfully used to detect Aroclor 1248 in Hairtail samples collected from the East China Sea near Zhejiang Province. Recovery values ranged from 84% to 104%, and the coefficient of variation (CV) was acceptable. Results were validated by GC-ECD, indicating that this convenient and sensitive method has great potential for trace PCBs screening in real environmental samples.

Nanomaterial-based biosensors using dual transducing elements for solution phase detection.

Biosensors incorporating nanomaterials have demonstrated superior performance compared to their conventional counterparts. Most reported sensors use nanomaterials as a single transducer of signals, while biosensor designs using dual transducing elements have emerged as new approaches to further improve overall sensing performance. This review focuses on recent developments in nanomaterial-based biosensors using dual transducing elements for solution phase detection. The review begins with a brief introduction of the commonly used nanomaterial transducers suitable for designing dual element sensors, including quantum dots, metal nanoparticles, upconversion nanoparticles, graphene, graphene oxide, carbon nanotubes, and carbon nanodots. This is followed by the presentation of the four basic design principles, namely Förster Resonance Energy Transfer (FRET), Amplified Fluorescence Polarization (AFP), Bio-barcode Assay (BCA) and Chemiluminescence (CL), involving either two kinds of nanomaterials, or one nanomaterial and an organic luminescent agent (e.g. organic dyes, luminescent polymers) as dual transducers. Biomolecular and chemical analytes or biological interactions are detected by their control of the assembly and disassembly of the two transducing elements that change the distance between them, the size of the fluorophore-containing composite, or the catalytic properties of the nanomaterial transducers, among other property changes. Comparative discussions on their respective design rules and overall performances are presented afterwards. Compared with the single transducer biosensor design, such a dual-transducer configuration exhibits much enhanced flexibility and design versatility, allowing biosensors to be more specifically devised for various purposes. The review ends by highlighting some of the further development opportunities in this field.

A fully integrated microdevice for biobarcode assay based biological agent detection.

An integrated microdevice, consisting of a micropump, a passive mixer, a magnetic separation chamber, and a microcapillary electrophoretic channel, was constructed for biobarcode assay based multiplex biological agent detection in a sample-to-answer-out manner within 30 min with high sensitivity.

Surface-enhanced Raman spectroscopy detection of dopamine by DNA Targeting amplification assay in Parkisons's model.

Dopamine is a potent neuromodulator in the brain that influences a variety of motivated behaviors and is involved in several neurologic diseases. We evaluated a bio-barcode amplification assay for its ability to detect dopamine in a mouse model with and without prior administration of the neurotoxin 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP). Our approach uses a combination of DNA barcodes and bead-based immunoassays for detecting neurotransmitters with surface-enhanced Raman spectroscopy (SERS). This method relies on a gold nanoplate with adsorbed antibodies and gold nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. C57BL/6 mice were infused intranasally with MPTP (25mg/kg/day) over 7 consecutive days. At 7 and 21 days after the last administration of MPTP, dopamine was found by western blot analysis to have decreased in the midbrain by 37.44% and 92.95%, respectively. Furthermore, the Raman intensity of dopamine in the midbrains of MPTP-treated mice decreased by 56.77% and 61.12% on days 7 and 21, respectively. Our results demonstrate that the concentration of dopamine in midbrain and striatum of MPTP-treated mice can be easily detected using the bio-barcode assay, which is a rapid, high-throughput screening tool for detecting neurotransmitters.

Potential applications of magnetic particles to detect and treat Alzheimer's disease.

Nanotechnology is an exciting and promising scientific discipline. At the nanoscale, a material displays novel physical properties that offer many new and beneficial products and applications. In particular, magnetic nanoparticles - a core/shell nanoparticle - present considerable diagnostic and therapeutic potentials, and superparamagnetic iron oxide nanoparticles (SPIONs) are considered promising theranostic tools. Alzheimer's disease (AD) is a neurodegenerative disorder that predominantly affects people over 65 years of age. The disease is characterized by the presence of extracellular plaques in the brain which are formed by interwoven fibrils composed of variants of the β-amyloid peptide. Medication can temporarily retard worsening of symptoms, but only in the first stages of the disease; early detection is thus of crucial importance. This minireview covers the progress made in research on the use of magnetic nanoparticles for ex vivo and/or in vivo detection and diagnosis of AD by means of magnetic resonance imaging (MRI), or to label peptides and fibrils. Of particular importance is the use of these nanoparticles to detect AD biomarkers in biological fluids. A description is given of the bio-barcode amplification assay using functionalized magnetic particles, as well as the use of such nanoparticles as a system for inhibiting or delaying the assembly of peptide monomers into oligomers and fibrils. Lastly, a brief overview is given of possible future lines of research in this.

A dual amplification strategy for DNA detection combining bio-barcode assay and metal-enhanced fluorescence modality.

Silver-enhanced fluorescence was coupled with a bio-barcode assay to facilitate a dual amplification assay to demonstrate a non-enzymatic approach for simple and sensitive detection of DNA. In the assay design, magnetic nanoparticles seeded with silver nanoparticles were modified with the capture DNA, and silver nanoparticles were modified with the binding of ssDNA and the fluorescently labeled barcode dsDNA. Upon introduction of the target DNA, a sandwich structure was formed because of the hybridization reaction. By simple magnetic separation, silver-enhanced fluorescence of barcode DNAs could be readily measured without the need of a further step to liberate barcode DNAs from silver nanoparticles, endowing the method with simplicity and high sensitivity with a detection limit of 1 pM.