Rapid detection of Staphylococcus aureus via a sensitive DNA hybridization assay based on a long-lifetime luminescent europium marker

A two-probe tandem nucleic acid hybridization assay for detection of Staphylococcus aureus is presented. It is based on a europium(III) complex as a marker that has a long fluorescence lifetime, high quantum yield and can be easily conjugated to an oligonucleotide signaling probe. The amino-modified capture probe was associated with the signaling probe to form a two-probe tandem DNA pattern that is complementary to the target DNA. The method was optimized in terms of hybridization temperature, hybridization time and washing time. This resulted in good specificity and sensitivity when detecting such bacteria in food samples.

CdS quantum dots as a fluorescent sensing platform for nucleic acid detection

We demonstrate that CdS quantum dots (QDs) can be applied to fluorescence-enhanced detection of nucleic acids in a two-step protocol. In step one, a fluorescently labeled single-stranded DNA probe is adsorbed on the QDs to quench its luminescence. In step two, the hybridization of the probe with its target ssDNA produces a double-stranded DNA which detaches from the QD. This, in turn, leads to the recovery of the fluorescence of the label. The lower detection limit of the assay is as low as 1?nM. The scheme (that was applied to detect a target DNA related to the HIV) is simple and can differentiate between perfectly complementary targets and mismatches.

Fluorescence energy transfer-based multiplexed hybridization assay using gold nanoparticles and quantum dot conjugates on photonic crystal beads

A multiplexed assay strategy was developed for the detection of nucleic acid hybridization. It is based on fluorescence resonance energy transfer (FRET) between gold nanoparticles (AuNPs) and multi-sized quantum dots (QDs) deposited on the surface of silica photonic crystal beads (SPCBs). The SPCBs were first coated with a three-layer primer film formed by the alternating adsorption of poly(allylamine hydrochloride) and poly(sodium 4-styrensulfonate). Probe DNA sequences were then covalently attached to the carboxy groups at the surface of the QD-coated SPCBs. On addition of DNA-AuNPs and hybridization, the fluorescence of the donor QDs is quenched because of the close proximity of the AuNPs. However, the addition of target DNA causes a recovery of the fluorescence of the QD-coated SPCBs, thus enabling the quantitative assay of hybridized DNA. Compared to fluorescent dyes acting as acceptors, the use of AuNPs results in much higher quenching efficiency. The multiplexed assay displays a wide linear range, high sensitivity, and very little cross-reactivity. This work, where such SPCBs are used for the first time in a FRET assay, is deemed to present a new and viable approach towards high-throughput multiplexed gene assays.

Aptamer-based molecular recognition for biosensor development

Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.

A real-time characterization method to rapidly optimize molecular beacon signal for sensitive nucleic acids analysis

This research demonstrates an integrated microfluidic titration assay to characterize the cation concentrations in working buffer to rapidly optimize the signal-to-noise ratio (SNR) of molecular beacons (MBs). The “Microfluidic Droplet Array Titration Assay" (MiDATA) integrated the functions of sample dilution, sample loading, sample mixing, fluorescence analysis, and re-confirmation functions all together in a one-step process. It allows experimentalists to arbitrarily change sample concentration and acquire SNR measurements instantaneously. MiDATA greatly reduces sample dilution time, number of samples needed, sample consumption, and the total titration time. The maximum SNR of molecular beacons is achieved by optimizing the concentrations of the monovalent and divalent cation (i.e., Mg²⁺ and K⁺) of the working buffer. MiDATA platform is able to reduce the total consumed reagents to less than 50 μL, and decrease the assay time to less than 30 min. The SNR of the designated MB is increased from 20 to 126 (i.e., enhanced the signal 630 %) using the optimal concentration of MgCl₂ and KCl determined by MiDATA. This novel microfluidics-based titration method is not only useful for SNR optimization of molecular beacons but it also can be a general method for a wide range of fluorescence resonance energy transfer (FRET)-based molecular probes.

Polymer-based devices for the label-free detection of DNA in solution: low DNA concentrations yield large signals

Poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons) have been shown to change their optical properties in the presence of single-stranded DNA. We hypothesize that this is due to the negatively charged DNA penetrating through the Au overlayer of the etalon, resulting in cross-linking and collapse of the positively charged microgels. We have shown that this technology is capable of detecting micromolar concentrations of target DNA in solutions containing two and four base pair mismatch sequences without the use of labels. Furthermore, the device’s response increases as the concentration of DNA decreases, which is unique for sensing strategies. We point out that coupling this transduction mechanism to DNA amplification strategies could result in extremely low detection limits.

Multi-channel PMMA microfluidic biosensor with integrated IDUAs for electrochemical detection

A novel multi-channel poly(methyl methacrylate) (PMMA) microfluidic biosensor with interdigitated ultramicroelectrode arrays (IDUAs) for electrochemical detection was developed. The focus of the development was a simple fabrication procedure and the realization of a reliable large IDUA that can provide detection simultaneously to several microchannels. As proof of concept, five microchannels are positioned over a large single IDUA where the channels are parallel with the length of the electrode finger. The IDUAs were fabricated on the PMMA cover piece and bonded to a PMMA substrate containing the microfluidic channels using UV/ozone-assisted thermal bonding. Conditions of device fabrication were optimized realizing a rugged large IDUA within a bonded PMMA device. Gold adhesion to the PMMA, protective coatings, and pressure during bonding were optimized. Its electrochemical performance was studied using amperometric detection of potassium ferri and ferro hexacyanide. Cumulative signals within the same chip showed very good linearity over a range of 0–38 μM (R ²?=?0.98) and a limit of detection of 3.48 μM. The bonding of the device was optimized so that no cross talk between the channels was observed which otherwise would have resulted in unreliable electrochemical responses. The highly reproducible signals achieved were comparable to those obtained with separate single-channel devices. Subsequently, the multi-channel microfluidic chip was applied to a model bioanalytical detection strategy, i.e., the quantification of specific nucleic acid sequences using a sandwich approach. Here, probe-coated paramagnetic beads and probe-tagged liposomes entrapping ferri/ferro hexacyanide as the redox marker were used to bind to a single-stranded DNA sequence. Flow rates of the non-ionic detergent n-octyl-β-d-glucopyranoside for liposome lysis were optimized, and the detection of the target sequences was carried out coulometrically within 250 s and with a limit of detection of 12.5 μM. The robustness of the design and the reliability of the results obtained in comparison to previously published single-channel designs suggest that the multi-channel device offers an excellent opportunity for bioanalytical applications that require multianalyte detection and high-throughput assays.

Magnetic particles–based biosensor for biogenic amines using an optical oxygen sensor as a transducer

We have developed a fibre optic biosensor with incorporated magnetic microparticles for the determination of biogenic amines. The enzyme diamine oxidase from Pisum sativum was immobilized either on chitosan-coated magnetic microparticles or on commercial microbeads modified with a ferrofluid. Both the immobilized enzyme and the ruthenium complex were incorporated into a UV-cured inorganic–organic polymer composite and deposited on a lens that was connected, by optical fibres, to an electro-optical detector. The enzyme catalyzes the oxidation of amines under consumption of oxygen. The latter was determined by measuring the quenched fluorescence lifetime of the ruthenium complex. The limits of detection for the biogenic amines putrescine and cadaverine are 25–30 μmol?L^?1, and responses are linear up to a concentration of 1 mmol L^?1.

Development of chemiluminescent assays for the quantitative detection and imaging of 5-bromo-2′deoxyuridine-labeled DNA in parvovirus B19-infected cells

Incorporation of exogenous analogues is a widely used method to evaluate DNA synthesis in cultured cells exposed to exogenous factors such as infectious agents. Herein, two new quantitative methodologies exploiting ultrasensitive chemiluminescence (CL) detection of 5-bromo-2′-deoxyuridine (BrdU) have been developed: a CL microscope imaging assay to evaluate BrdU labelling at single-cell level and a CL dot-blot assay to measure the amounts of DNA produced in the course of an in vitro infection of proliferating cells. The assays have been optimized on UT7/EpoS1 cells cultured in presence of different concentrations of BrdU (from 3 to 100 μM) and used to monitor parvovirus B19 (B19) life cycle in infected cells. The CL microscope imaging assay provided a detailed localization of BrdU-labelled nuclei allowing to count positive cells and measure their related CL intensity signals. The CL dot-blot assay, coupled with a B19 capture procedure performed with a specific peptide nucleic acid probe, has been designed to discriminate and selectively quantify cellular and viral BrdU-labelled genomes. Quantitative evaluation of BrdU-labelled B19 DNA has been achieved by means of a CL calibration curve. The high detectability, down to 2?×?10⁶ B19 genome copies, and the linear range extending up to 5?×?10⁸ copies make the method suitable to evaluate the amounts of B19 DNA produced throughout a replicative viral cycle.

Detection of Helicobacter pylori with a nanobiosensor based on fluorescence resonance energy transfer using CdTe quantum dots

We report on a method for the sensitive determination of Helicobacter that is based on fluorescence resonance energy transfer using two oligonucleotide probes labeled with CdTe quantum dots (QDs) and 5-carboxytetramethylrhodamine (Tamra) respectively. QDs labeled with an amino-modified first oligonucleotide, and a Tamra-labeled second oligonucleotide were added to the DNA targets upon which hybridization occurred. The resulting assembly brings the Tamra fluorophore (the acceptor) and the QDs (the donor) into close proximity and causes fluorescence resonance energy transfer (FRET) to occur upon photoexcitation of the donor. In the absence of target DNA, on the other hand, the probes are not ligated, and no emission by the Tamra fluorophore is produced due to the lack of FRET. The feasibility of the method was demonstrated by the detection of a synthetic 210-mer nucleotide derived from Helicobacter on a nanomolar level. This homogeneous DNA detection scheme is simple, rapid and efficient, does not require excessive washing and separation steps, and is likely to be useful for the construction of a nanobiosensor for Helicobacter species.

Simultaneous detection of Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes using oscillatory-flow multiplex PCR

An oscillatory-flow multiplex PCR method in a capillary microfluidic channel has been developed for the simultaneous determination of pre-purified DNA of multiple foodborne bacterial pathogens. The PCR solution passes three temperature zones in an oscillatory manner. The thermal stability and sample evaporation of the microfluidic device were investigated. Under controlled conditions, a highly efficient multiplex PCR was accomplished as demonstrated for the simultaneous amplifications of 278 bp, 168 bp, and 106 bp DNA fragments within 35 min after 35 cycles for simultaneous detection of Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes. This is much shorter than that of a conventional PCR machine. The detection limits of bacterial genome DNA for the three species are about 399, 314, and 626 copies per μL, respectively. This is comparable to those obtained with the conventional multiplex PCR. Consequently, the oscillatory-flow multiplex PCR technology holds good potential for rapid amplification and detection of nucleic acids of microbial foodborne pathogens.

Fluorometric sensing of DNA using curcumin encapsulated in nanoparticle-assembled microcapsules prepared from poly(diallylammonium chloride-co-sulfur dioxide)

We report on the synthesis of microcapsules (MCs) containing self-assembled nanoparticles formed from poly[diallylammonium chloride-co-(sulfur dioxide)] in the presence of citrate and silica sol nanoparticles. The MCs are spherical, and SEM and optical microscopy reveal them to have micrometer size. The fluorescent probe curcumin was encapsulated in the MCs and found to be located in the shell. The fluorescence of curcumin in the MCs is altered depending on their microenvironment. Effects of pH and ammonia on the fluorescence of curcumin in the MCs also were studied. The brightness of the probe in the MCs increases on addition of DNA. The effect was used to determine DNA from fish sperm by fluorometry. The association constant (K) is 4?000 mL.g^?1, and the number of binding sites is ~1.0.

Detection of thrombin using an excimer aptamer switch labeled with dual pyrene molecules

We constructed an excimer aptamer probe containing one pyrene molecule at each end of a DNA aptamer to achieve the detection of thrombin, which binds to the heparin-binding site of thrombin with high binding affinity. The specific binding of thrombin to the excimer aptamer probe brought the two pyrene molecules at the termini of the duplex of the aptamer into close proximity, generating an excimer. The excimer emitted a distinct fluorescence peak, and fluorometric measurement of excimer allowed the sensitive detection of thrombin. The effects of experimental conditions like pH, ionic strength, and cations were investigated and optimized. The detection limit for thrombin was about 42 pM. This aptamer switch has potential in the study of molecular interactions and protein sensing with other switch-based detection strategy.

A lanthanide nanoparticle-based luminescent probe for folic acid

We report on a novel luminescent method for the detection of folic acid (FA), a member of the vitamin B family. Y₂O₃ nanoparticles were doped with europium(III) ions and surface-modified with captopril. Their fluorescence is quenched by FA, and intensity is a function of folic acid concentration in the 0.1 – 40 μM concentration range. The detection limit is 83 nM of FA at pH 7 and room temperature.

Detection of mismatched caspase-3 DNA oligonucleotides with an SPR biosensor following amplification by Taq polymerase

We demonstrate that base mismatches of caspase-3 DNA sequences can be detected by surface plasmon resonance (SPR) following signal amplification by polymerase from Thermus aquaticus (Taq). The concentration of magnesium ions and the respective dNTPs for polymerase binding to the oligonucleotides on the sensing surface were optimized. Taq polymerase binds to double-stranded DNA that is self-assembled on the gold surface of the biosensor to induce an SPR signal. Experiments are presented on the effect of Mg(II) and dNTP concentrations on the activity of the polymerase on the sensing surface. The detection limits are 50 pM, 0.1 nM, 0.7 nM, 7 nM, and 20 nM for correctly matched, single-base mismatched, two-base mismatched, three-base mismatched and four-base mismatched DNA of caspase-3, respectively. This is attributed to the optimized experimental conditions, with samples containing 2 μM of Mg(II) and 0.3 mM of dNTP.

A duplex–triplex nucleic acid nanomachine that probes pH changes inside living cells during apoptosis

A duplex–triplex switchable DNA nanomachine was fabricated and has been applied for the demonstration of intracellular acidification and apoptosis of Ramos cells, with graphene oxide (GO) not only as transporter but also as fluorescence quencher. The machine constructed with triplex-forming oligonucleotide exhibited duplex–triplex transition at different pH conditions. By virtue of the remarkable difference in affinity of GO with single-stranded DNA and triplex DNA, and the super fluorescence quenching efficiency of GO, the nanomachine functions as a pH sensor based on fluorescence resonance energy transfer. Moreover, taking advantage of the excellent transporter property of GO, the duplex–triplex/GO nanomachine was used to sense pH changes inside Ramos cells during apoptosis. Fluorescence images showed different results between living and apoptotic cells, illustrating the potential of DNA scaffolds responsive to more complex pH triggers in living systems.

Rapid separation of four probiotic bacteria in mixed samples using microchip electrophoresis with laser-induced fluorescence detection

Microchip electrophoresis (MCE) coupled to laser-induced fluorescence detection was applied to the rapid separation of Bifidobacterium, Lactobacillus casei, Lactobacillus acidophilus, and Enterococccus faecalis. All bacteria were quickly separated within 150?s using a running buffer of pH 8.5 containing Tris, borate, EDTA, and poly(ethylene oxide). The latter was crucial to reduce the bacterial adsorption on the walls of the microchannels. The pH of 8.5 warrants that bacteria carry a negative charge at their surface and thus display good electrophoretic performance. The method was used to analyze medical samples containing these probiotics, and the results showed that the identification and detection of bacteria by MCE is advantageous in terms of sample consumption, waste production, time of analysis, and instrumental effort.

Fluorescent detection of silver(I) and cysteine using SYBR Green I and a silver(I)-specific oligonucleotide

We report on a novel method for the determination of silver ion (Ag⁺) and cysteine (Cys) by using the probe SYBR Green I (SGI) and an Ag+-specific cytosine-rich oligonucleotide (C-DNA). The fluorescence of SGI is very weak in the absence or presence of randomly coiled C-DNA. If, however, C-DNA interacts with Ag⁺ through the formation of cytosine-Ag⁺-cytosine (C-Ag⁺-C) base pairs, the randomly coiled C-DNA undergoes a structural changes to form a hairpin-like structure, thereby increasing the fluorescence of SGI. This fluorescence turn-on process allows the detection of Ag⁺ in the 10–600?nM concentration range, with a detection limit of 4.3?nM. Upon the reaction of Ag⁺ with Cys, Cys specifically removes Ag⁺ from the C-Ag⁺-C base pairs and destroys the hairpin-like structure. This, in turn, results in a decrease in fluorescence intensity. This fluorescence turn-off process enables the determination of Cys in the 8–550?nM concentration range, with a detection limit of 4.5?nM. The method reported here for the determination of either Ag⁺ or Cys is simple, sensitive, and affordable, and may be applied to other detection systems if appropriately selected DNA sequences are available.