Nucleic acid quantification using nicking–displacement,rolling circle amplification and bio-bar-code mediated triple-amplification

In the present study, an inductively-coupled plasma-mass spectrometry (ICP-MS)-based triple-amplification system, by combination of nicking–displacement, rolling circle amplification (RCA) and bio-bar-code probes, was fabricated for the detection of DNA target. By using this system, hepatitis B virus (HBV) DNA target down to 3.2 × 10⁻¹⁷ M was detected by DNA probes labeled with Au nanoparticles (AuNPs). Single nucleotide polymorphisms in genes can also be effectively discriminated. In addition, we proved that this strategy is capable of detecting the target in complicated biological samples and holds great potential application in biomedical research.     

Electrochemical and Electrochemiluminescence Determination of Cancer Cells Based on Aptamers and Magnetic Beads

The electrochemical and electrochemiluminescence (ECL) detection of cell lines of Burkitt’s lymphoma (Ramos) by using magnetic beads as the separation tool and high‐affinity DNA aptamers for signal recognition is reported. Au nanoparticles (NPs) bifunctionalized with aptamers and CdS NPs were used for electrochemical signal amplification. The anodic stripping voltammetry technology employed for the analysis of cadmium ions dissolved from CdS NPs on the aggregates provided a means to quantify the amount of the target cells. This electrochemical method could respond down to 67 cancer cells per mL with a linear calibration range from 1.0×10² to 1.0×10⁵ cells mL^?1, which shows very high sensitivity. In addition, the assay was able to differentiate between target and control cells based on the aptamer used in the assay, indicating the wide applicability of the assay for diseased cell detection. ECL detection was also performed by functionalizing the signal DNA, which was complementary to the aptamer of the Ramos cells, with tris(2,2‐bipyridyl) ruthenium. The ECL intensity of the signal DNA, replaced by the target cells from the ECL probes, directly reflected the quantity of the amount of the cells. With the use of the developed ECL probe, a limit of detection as low as 89 Ramos cells per mL could be achieved. The proposed methods based on electrochemical and ECL should have wide applications in the diagnosis of cancers due to their high sensitivity, simplicity, and low cost.     

阳离子荧光共轭聚合物结合纳米颗粒用于DNA检测

利用纳米颗粒对目标DNA的富集、分离作用以及阳离子荧光共轭聚合物良好的荧光特性,建立了一种特异性检测DNA的新方法.首先将标记有猝灭基团的DNA捕获探针修饰到纳米颗粒上,捕获互补的DNA分子;然后加入S1核酸酶,除去未捕获到互补DNA的捕获探针;最后用Dnase Ⅰ将颗粒上的双链切断,使猝灭基团从纳米颗粒上解离下来,与阳离子荧光共轭聚合物结合并猝灭其荧光.结果表明,目标核酸的浓度与该聚合物的荧光猝灭程度正相关,且具有良好的特异性,线性响应范围为5.0～40 nmol/L; 检出限为3.7 nmol/L(S/N=3).     

The complete replacement of antibodies by protein-imprinted poly(ethylene-co-vinyl alcohol) in sandwich fluoroimmunoassays

The replacement of antibodies by molecularly imprinted polymers (MIPs) has been investigated for many decades. However, indirect protocols (including natural primary and secondary antibodies) are still utilized to evaluate the ability of MIP thin films to recognize target molecules. MIPs can be prepared as either a thin film or as particles, and cavities that are complementary to the template can be generated on their surfaces. We have prepared thin film MIPs and particle MIPs prepared by solvent evaporation and phase inversion, respectively, from solutions of poly(ethylene-co-vinyl alcohol) (pEVAL) in the presence of the target analytes amylase, lysozyme, and lipase. These were first adsorbed on MIP thin films and by MIP particles that contain fluorescent quantum dots. Sandwich fluoroimmunoassays were then conducted to quantify them in MIP-coated 96-well microplates. The method was applied to determine amylase in saliva, and results were compared with a commercial analytical system.

Biocompatible core-shell nanoparticle-based surface-enhanced Raman scattering probes for detection of DNA related to HIV gene using silica-coated magnetic nanoparticles as separation tools

A novel, highly selective DNA hybridization assay has been developed based on surface-enhanced Raman scattering (SERS) for DNA sequences related to HIV. This strategy employs the Ag/SiO₂ core-shell nanoparticle-based Raman tags and the amino group modified silica-coated magnetic nanoparticles as immobilization matrix and separation tool. The hybridization reaction was performed between Raman tags functionalized with 3′-amino-labeled oligonucleotides as detection probes and the amino group modified silica-coated magnetic nanoparticles functionalized with 5′-amino-labeled oligonucleotides as capture probes. The Raman spectra of Raman tags can be used to monitor the presence of target oligonucleotides. The utilization of silica-coated magnetic nanoparticles not only avoided time-consuming washing, but also amplified the signal of hybridization assay. Additionally, the results of control experiments show that no or very low signal would be obtained if the hybridization assay is conducted in the presence of DNA sequences other than complementary oligonucleotides related to HIV gene such as non-complementary oligonucleotides, four bases mismatch oligonucleotides, two bases mismatch oligonucleotides and even single base mismatch oligonucleotides. It was demonstrated that the method developed in this work has high selectivity and sensitivity for DNA detection related to HIV gene.     

Heterogeneous immunoassay for soy protein determination using nile blue-doped silica nanoparticles as labels and front-surface long-wavelength fluorimetry

A long-wavelength fluoroimmunoassay for the determination of soy protein is reported for the first time using a conjugate composed of anti-soy protein antibodies bound to nile blue-doped silica nanoparticles (NPs). These NPs have been synthesized by a reverse-micelle microemulsion method and functionalized by using 3-(aminopropyl)triethoxysilane (APS) and 3-(trihydroxysilyl)propyl methylphosphonate (THPMP) to avoid NP aggregation. The tracer has been obtained by linking the functionalized NPs with anti-soy protein antibodies previously oxidised with sodium periodate. The immunoassay has been developed in 96-well microplates using a heterogeneous competitive format with antibody capture. Soy proteins are immobilised onto the wells and bovine serum albumin is added to block the surface, thus minimising non-specific binding. After washing, the microplates can be stored ready to use. At the analysis time, soy protein standards or sample and tracer are added and incubated and, after the corresponding washing and drying steps, the fluorescence is measured onto the solid surface at λ_ex 620 and λ_em 680 nm. The method features a dynamic range of 0.1–10 mg L⁻¹ and a detection limit of 0.05 mg L⁻¹. The precision of the method has been assayed at 0.5 and 5 mg L⁻¹ protein concentrations, obtaining the values of relative standard deviation of 9.6% and 6.1%, respectively. This new immunoassay has been applied to the analysis of food containing soy protein and the results obtained have been compared to those provided by a commercial ELISA kit with no statistically differing results. Also, a recovery study has been performed, providing percentages in the range of 81.5–111.0%.     

Surface‐Bound Cucurbit[8]uril Catenanes on Magnetic Nanoparticles Exhibiting Molecular Recognition

We demonstrate the preparation of surface‐bound cucurbit[8]uril (CB[8]) catenanes on silica nanoparticles (NPs), where CB[8] was employed as a tethered supramolecular “handcuff” to selectively capture target guest molecules. In this catenane, CB[8] was threaded onto a methyl viologen (MV²⁺) axle and immobilized onto silica NPs. The formation of CB[8] catenanes on NPs were confirmed by UV/Vis titration experiments and lithographic characterization, demonstrating a high density of CB[8] on the silica NPs surface, 0.56 nm^?2. This CB[8] catenane system exhibits specific molecular recognition towards certain aromatic molecules such as perylene bis(diimide), naphthol and aromatic amino acids, and thus it can act as a nanoscale molecular receptor for target guests. Furthermore, we also demonstrate its use as an efficient and recyclable nano‐platform for peptide separation. By embedding magnetic NPs inside silica NPs, separation could be achieved by simply applying an external magnetic field. Moreover, the peptides captured by the catenanes could be released by reversible single‐electron reduction of MV²⁺. The entire process demonstrated high recoverability.     

Amplification free detection of herpes simplex virus DNA

Amplification-free detection of nucleic acids in complex biological samples is an important technology for clinical diagnostics, especially in the case where the detection is quantitative and highly sensitive. Here we present the detection of a synthetic DNA sequence from Herpes Simplex Virus-1 within swine cerebrospinal fluid (CSF), using a sandwich-like, magnetic nanoparticle pull-down assay. Magnetic nanoparticles and fluorescent polystyrene nanoparticles were both modified with DNA probes, able to hybridise either end of the target DNA, forming the sandwich-like complex which can be captured magnetically and detected by fluorescence. The concentration of the target DNA was determined by counting individual and aggregated fluorescent nanoparticles on a planar glass surface within a fluidic chamber. DNA probe coupling for both nanoparticles was optimized. Polystyrene reporter nanoparticles that had been modified with amine terminated DNA probes were also treated with amine terminated polyethylene glycol, in order to reduce non-specific aggregation and target independent adhesion to the magnetic particles. This way, a limit of detection for the target DNA of 0.8 pM and 1 pM could be achieved for hybridisation buffer and CSF respectively, corresponding to 0.072 and 0.090 femtomoles of target DNA, in a volume of 0.090 mL.     

Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures

G4-FID (G-quadruplex fluorescent intercalator displacement) is a simple and fast method that allows to evaluate the affinity of a compound for G-quadruplex DNA and its selectivity towards duplex DNA. This assay is based on the loss of fluorescence of thiazole orange (TO) upon competitive displacement from DNA by a putative ligand. We describe here the development of a high-throughput version of this assay performed in 96-well microplates, and fully transposable to 384-well microplates. The test was calibrated with a set of G-quadruplex ligands characterized for their ability to bind quadruplex within a large range of affinity. The comparison of the results obtained in microplates and in cuvettes was conducted indicating a full agreement. Additionally, the spectral range of the test was enlarged using two other fluorescent on/off probes whose absorption are red-shifted (TO-PRO-3) and blue-shifted (Hoechst 33258) as compared to that of TO. These labels enable to screen a large diversity of compounds with various optical properties, which was exemplified by evaluation of affinity and selectivity of the porphyrin TMPyP4 that could not be evaluated previously. Altogether, our study demonstrates that the HT-G4-FID assay offers the possibility to label a large variety of G-quadruplexes of biological interest and should enable screening of collections of putative G4-ligands of high structural diversity. It thus represents a powerful tool to bring into light new ligands able to discriminate between quadruplexes of different structures.     

Colloidal gold-polystyrene bead hybrid for chemiluminescent detection of sequence-specific DNA

A sensitive chemiluminescent (CL) detection of sequence-specific DNA has been developed by taking advantage of a magnetic separation/mixing process and the amplification feature of colloidal gold labels. In this protocol, the target oligonucleotides are hybridized with magnetic bead-linked capture probes, followed by the hybridization of the biotin-terminated amplifying DNA probes and the binding of streptavidin-coated gold nanoparticles; the nanometer-sized gold tags are then dissolved and quantified by a simple and sensitive luminol CL reaction. The proposed CL protocol is evaluated for a 30-base model DNA sequence, and the amount as low as 0.01 pmol of DNA is determined, which exhibits a 150 x enhancement in sensitivity over previous gold dissolution-based electrochemical formats and an enhancement of 20 x over the ICPMS detection. Further signal amplification is achieved by the assembly of biotinylated colloidal gold onto the surface of streptavidin-coated polystyrene beads. Such amplified CL transduction allows detection of DNA targets down to the 100 amol level, and offers great promise for ultrasensitive detection of other biorecognition events.     

Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization

A novel multiplexed method for short RNA detection is reported that employs a design strategy in which capture and reporter probes anneal to each other in the presence of a short RNA target via the formation of a stable three-component complex. Quantum dots (QDs) functionalized with reporter DNA are thus specifically bound onto a capture probe-modified 96-well plate by one-step hybridization for simple RNA detection. In comparison with conventional organic dye-modified reporter probes, the use of reporter DNA-modified QD conjugates increase the melting temperature and lead to the detection of short RNA without the need for a ligation reaction. Moreover, QD properties allow multiple short RNA sequences to be simultaneously determined via rapid and simple one-step hybridization, as exemplified herein. The present results clearly demonstrate that this new strategy can be used to detect dual-short RNA sequence at concentrations of 10 pM in 100 μL.     

Simultaneous electrochemical determination of two analytes based on nuclease-assisted target recycling amplification

In the present study, a method for simultaneous determination of two different DNAs is developed based on nuclease-assisted target recycling and nanoparticle amplification. The target recycling process is accomplished by taking advantage of the cleavage property of nicking endonuclease (NEase) for specific nucleotide sequences in duplex. In the presence of target DNA, the linker DNA in our detection system can hybridize with the target and be cleaved to form short fragments. Thus the target DNA is released and recognized by another linker DNA, activating the next round of cleavage reaction. On the other hand, two bio-barcode probes, a PbS nanoparticles (NPs)-DNA probe and a CdS NPs-DNA probe, are used for tracing two target DNAs to further amplify the detection signals. Based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Pb²⁺ and Cd²⁺ obtained by dissolving two probes, two different target DNAs are determined with high sensitivity and single-base mismatch selectivity.     

A one-step highly sensitive method for DNA detection using dynamic light scattering

A one-step homogeneous DNA detection method with high sensitivity was developed using gold nanoparticles (AuNPs) coupled with dynamic light scattering (DLS) measurement. Citrate-protected AuNPs with a diameter of 30 nm were first functionalized with two sets of single-stranded DNA probes and then used as optical probes for DNA detection. In the presence of target DNA, the hybridization between target DNA and the two nanoparticle probes caused the formation of nanoparticle dimers, trimers, and oligomers. As a result, the nanoparticle aggregation increased the average diameter of the whole nanoparticle population, which can be monitored simply by DLS measurement. A quantitative correlation can be established between the average diameter of the nanoparticles and the target DNA concentration. This DLS-based assay is extremely easy to conduct and requires no additional separation and amplification steps. The detection limit is around 1 pM, which is 4 orders of magnitude better than that of light-absorption-based methods. Single base pair mismatched DNAs can be readily discriminated from perfectly matched target DNAs using this assay.     

A novel technology for the detection, enrichment, and separation of trace amounts of target DNA based on amino-modified fluorescent magnetic composite nanoparticles

A novel, highly sensitive technology for the detection, enrichment, and separation of trace amounts of target DNA was developed on the basis of amino-modified fluorescent magnetic composite nanoparticles (AFMN). In this study, the positively charged amino-modified composite nanoparticles conjugate with the negatively charged capture DNA through electrostatic binding. The optimal combination of AFMN and capture DNA was measured by dynamic light scattering (DLS) and UV–vis absorption spectroscopy. The highly sensitive detection of trace amounts of target DNA was achieved through enrichment by means of AFMN. The detection limit for target DNA is 0.4 pM, which could be further improved by using a more powerful magnet. Because of their different melting temperatures, single-base mismatched target DNA could be separated from perfectly complementary target DNA. In addition, the photoluminescence (PL) signals of perfectly complementary target DNA and single-base mismatched DNA as well as the hybridization kinetics of different concentrations of target DNA at different reaction times have also been studied. Most importantly, the detection, enrichment, and separation ability of AFMN was further verified with milk. Simple and satisfactory results were obtained, which show the great potential in the fields of mutation identification and clinical diagnosis.     

基于双纳米金探针杂交法检测HBV DNA

利用双纳米金探针结合基因芯片平台建立了一种检测乙肝病毒基因(HBV DNA)的新方法. 根据HBV DNA的保守序列设计捕获探针和信号报告探针, 通过一对互补的纳米金检测探针的双杂交法对HBV DNA进行信号放大, 最后进行银染, 达到对HBV DNA的可视化检测. 该方法的灵敏度高, 可检测10 fmol/L的HBV DNA, 且能在1.5 h内完成检测. 其具有的快速、 高灵敏度及低成本等优势使其有望发展成为一种检测HBV DNA的新方法.     

Control over surface DNA density on gold nanoparticles allows selective and sensitive detection of mercury(II)

We have developed a new highly selective and sensitive technique for the detection of Hg(2+) using DNA-functionalized gold nanoparticles (Au NPs) and OliGreen. This system is the first that allows the detection of Hg(2+) based on the release of DNA molecules, induced by conformational changes on Au NP surfaces, and its sensitivity is highly dependent upon surface DNA density. When Hg(2+) ions interact with the thymidine units of the DNA molecules bound to the Au NPs through Au-S bonds, the conformations of these DNA derivatives change from linear to hairpin structures, causing the release of some of the DNA molecules from the surface of the Au NPs into the bulk solution to react with OliGreen. The fluorescence of OliGreen-DNA complexes increased with increasing concentration of Hg(2+), and Hg(2+) could be detected at concentrations as low as 25 nM. A linear correlation existed between the fluorescence intensity and the concentration of Hg(2+) over the range 0.05-2.5 microM (R(2) = 0.98). This simple and cost-effective probe was applied to determine the spiked Hg(2+) in the pond samples; the recoveries (96-102%) suggested low matrix interference and high sensitivity.     

Iron oxide/tantalum oxide core–shell magnetic nanoparticle-based microwave-assisted extraction for phosphopeptide enrichment from complex samples for MALDI MS analysis

A new type of metal-oxide-coated magnetic nanoparticles (NPs)—tantalum-oxide-coated magnetic iron oxide (Fe₃O₄@Ta₂O₅) NPs—which are used as affinity probes for selectively trapping phosphopeptides from complex samples, is demonstrated in this study. In this approach, phosphopeptide enrichment was achieved by incubating the NPs with sample solutions under microwave heating within 1 min. The NP–target species conjugates were readily isolated from samples by magnetic separation followed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometric analysis. When using human serum as the sample, phosphorylated fibrinopeptide-A-derived ions are the only ions observed in the MALDI mass spectra after enrichment by the Fe₃O₄@Ta₂O₅ NPs. Furthermore, only phosphopeptides appear in the MALDI mass spectra after using the affinity probes to selectively trap target species from the tryptic digest of a cell lysate and milk sample. The results demonstrated that the Fe₃O₄@Ta₂O₅ NPs have the capability of selectively trapping phosphorylated peptides from complex samples. The detection limit of this approach for a phosphopeptide (FQpSEEQQQTEDELQDK) was ~10 fmol. Figure For the first time, tantalum oxide-coated magnetic iron oxide (Fe₃O₄@Ta₂O₅) NPs were demonstrated as suitable affinity-probes for selectively trapping phosphopeptides from complex samples. To shorten the analysis time, phosphopeptide enrichment was achieved by incubating the NPs with sample solutions under microwave-heating within 1 min. MALDI MS was employed for characterization of the species trapped by the NPs.     

Adhesive microarrays for multipurpose diagnostic tools

We are reporting here a new technology for the straightforward production of integrated microarrays. The approach is based on the use of adhesive supports enabling (i) the immobilization of biomolecules as microarrays (up to 2500 spots per cm(2)) and (ii) the easy assembly of these microarrays with complex 3D structures such as 96-well bottomless microplates or polymer and glass microfluidic networks. The analytical performances of the system were demonstrated for sandwich protein detection (C-reactive protein) and hybridization assays, both in classical 96-well microplate format and microfluidic environment.     

Enzyme-free surface plasmon resonance aptasensor for amplified detection of adenosine via target-triggering strand displacement cycle and Au nanoparticles

Herein, we combine the advantage of aptamer technique with the amplifying effect of an enzyme-free signal-amplification and Au nanoparticles (NPs) to design a sensitive surface plasmon resonance (SPR) aptasensor for detecting small molecules. This detection system consists of aptamer, detection probe (c-DNA1) partially hybridizing to the aptamer strand, Au NPs-linked hairpin DNA (Au-H-DNA1), and thiolated hairpin DNA (H-DNA2) previously immobilized on SPR gold chip. In the absence of target, the H-DNA1 possessing hairpin structure cannot hybridize with H-DNA2 and thereby Au NPs will not be captured on the SPR gold chip surface. Upon addition of target, the detection probe c-DNA1 is forced to dissociate from the c-DNA1/aptamer duplex by the specific recognition of the target to its aptamer. The released c-DNA1 hybridizes with Au-H-DNA1 and opens the hairpin structure, which accelerate the hybridization between Au-H-DNA1 and H-DNA2, leading to the displacement of the c-DNA1 through a branch migration process. The released c-DNA1 then hybridizes with another Au-H-DNA1 probe, and the cycle starts anew, resulting in the continuous immobilization of Au-H-DNA1 probes on the SPR chip, generating a significant change of SPR signal due to the electronic coupling interaction between the localized surface plasma of the Au NPs and the surface plasma wave. With the use of adenosine as a proof-of-principle analyte, this sensing platform can detect adenosine specifically with a detection limit as low as 0.21 pM, providing a simple, sensitive and selective protocol for small target molecules detection.     

A highly efficient and versatile microchip capillary electrophoresis method for DNA separation using gold nanoparticle as a tag

A highly efficient and versatile method for DNA separation using Au nanoparticles (Au NPs) as a tag based on microchip capillary electrophoresis (MCE) was developed. The thiol-modified DNA-binding Au NPs were utilized as a tag. Target DNA was sandwiched between Au NPs and probe DNA labeled with horseradish peroxidase (HRP). In electrophoresis separation, the difference in electrophoretic mobility between free probe and probe-target complex was magnified by Au NPs, which enabled the resulting mixture to be separated with high efficiency by microchip capillary electrophoresis. Horseradish peroxidase was used as a catalytic label to achieve sensitive electrochemical DNA detection via fast catalytic reactions. With this protocol, 27-mer DNA fragments with different sequences were separated with high speed and high resolution. The proposed method was critical to achieve improved DNA separations in hybridization analyses.