Ultrahighly Sensitive Homogeneous Detection of DNA and MicroRNA by Using Single‐Silver‐Nanoparticle Counting

DNA and RNA analysis is of high importance for clinical diagnoses, forensic analysis, and basic studies in the biological and biomedical fields. In this paper, we report the ultrahighly sensitive homogeneous detection of DNA and microRNA by using a novel single‐silver‐nanoparticle counting (SSNPC) technique. The principle of SSNPC is based on the photon‐burst counting of single silver nanoparticles (Ag NPs) in a highly focused laser beam (about 0.5 fL detection volume) due to Brownian motion and the strong resonance Rayleigh scattering of single Ag NPs. We first investigated the performance of the SSNPC system and then developed an ultrasensitive homogeneous detection method for DNA and microRNA based on this single‐nanoparticle technique. Sandwich nucleic acid hybridization models were utilized in the assays. In the hybridization process, when two Ag‐NP–oligonucleotide conjugates were mixed in a sample containing DNA (or microRNA) targets, the binding of the targets caused the Ag NPs to form dimers (or oligomers), which led to a reduction in the photon‐burst counts. The SSNPC method was used to measure the change in the photon‐burst counts. The relationship between the change of the photon‐burst counts and the target concentration showed a good linearity. This method was used for the assay of sequence‐specific DNA fragments and microRNAs. The detection limits were at about the 1 fM level, which is 2–5 orders of magnitude more sensitive than current homogeneous methods.     

Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins

In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis.     

Immunoassays using capillary electrophoresis laser induced fluorescence detection for DNA adducts

Human DNA is exposed to a variety of endogenous and environmental agents that may induce a wide range of damage. The critical role of DNA damage in cancer development makes it essential to develop highly sensitive and specific assays for DNA lesions. We describe here ultrasensitive assays for DNA damage, which incorporate immuno-affinity with capillary electrophoresis (CE) separation and laser induced fluorescence (LIF) detection. Both competitive and non-competitive assays using CE/LIF were developed for the determination of DNA adducts of benzo[a]pyrene diol epoxide (BPDE). A fluorescently labeled oligonucleotide containing a single BPDE adduct was synthesized and used as a fluorescent probe for competitive assay. Binding between this synthetic oligonucleotide and a monoclonal antibody (MAb) showed both 1:1 and 1:2 complexes between the MAb and the oligonucleotide. The 1:1 and 1:2 complexes were separated by CE and detected with LIF, revealing binding stoichiometry information consistent with the bidentate nature of the immunoglobulin G antibody. For non-competitive assay, a fluorescently labeled secondary antibody fragment F(ab′)₂ was used as an affinity probe to recognize a primary antibody that was specific for the BPDE-DNA adducts. The ternary complex of BPDE-DNA adducts with the bound antibodies was separated from the unbound antibodies using CE and detected with LIF for quantitation of the DNA adducts. The assay was used for the determination of trace levels of BPDE-DNA adducts in human cells. Analysis of cellular DNA from A549 human lung carcinoma cells that were incubated with low doses of BPDE (32 nM–1 μM) showed a clear dose–response relationship. BPDE is a potent environmental carcinogen, and the ultrasensitive assays for BPDE-DNA adducts are potentially useful for monitoring human exposure to this carcinogen and for studying cellular repair of DNA damage.     

Electrochemical DNA sensor by the assembly of graphene and DNA-conjugated gold nanoparticles with silver enhancement strategy

Sensitive and selective detection of DNA is in urgent need due to its important role in human bodies. Many disorders, such as Alzheimer's disease and various cancers, are closely related with DNA damage. In this work, a novel electrochemical DNA biosensor was constructed on a DNA-assembling graphene platform which provided a robust, simple and biocompatible platform with large surface area for DNA immobilization. The as-designed DNA sensor was fabricated by directly assembling captured ssDNA on a graphene-modified electrode through the π-π stacking interaction between graphene and ssDNA bases. Then, the target DNA sequence and oligonucleotide probes-labeled AuNPs were able to hybridize in a sandwich assay format, following the AuNPs-catalyzed silver deposition. The deposited silver was further detected by differential pulse voltammetry. Owing to the high DNA loading ability of graphene and the distinct signal amplification by AuNPs-catalyzed silver staining, the resulting biosensor exhibited a good analytical performance with a wide detection linear range from 200 pM to 500 nM, and a low detection limit of 72 pM. Additionally, the biosensor was proved to be able to discriminate the complementary sequence from the single-base mismatch sequence. The simple biosensor is promising in developing electronic, on-chip assays in clinical diagnosis, environmental control, and drug discovery.     

Detection of transgenes in soybean via a polymerase chain reaction and a simple bioluminometric assay based on a universal aequorin-labeled oligonucleotide probe

The recombinant photoprotein aequorin was used as a reporter in highly sensitive and automatable hybridization assays for the analysis of transgenic sequences in genetically modified organisms (GMO). The terminator of the nopaline synthase gene (NOS) from Agrobacterium tumefaciens and the 35S promoter sequence were detected in genetically modified soybean. The endogenous, soybean-specific, lectin gene was also detected for confirmation of the integrity of extracted DNA. A universal detection reagent was produced through conjugation of aequorin to the oligonucleotide (dA)₃₀. Biotinylated (through PCR) products for the three target sequences were captured onto streptavidin-coated wells, and one strand was removed by NaOH treatment. The immobilized single-stranded DNAs were then hybridized with oligonucleotide probes consisting of a target-specific segment and a poly(dT) tail. This allowed the subsequent determination of all hybrids through the use of the (dA)₃₀-aequorin conjugate as a universal reagent. The bound aequorin was measured by adding Ca²⁺ and integrating the light emission for 3 s. As low as 2 pM (100 amol per well) of amplified DNA was detectable for all three targets, with a signal-to-background ratio of about 2. The analytical range extended up to 2000 pM. As low as 0.05% GMO content in soybean can be detected with a signal-to-background ratio of 8.2. The overall repeatability of the proposed assay, including DNA extraction, PCR, and hybridization assay, ranged from 7.5–19.8%. The use of a (dA)₃₀-aequorin conjugate renders the assay configuration general for any target DNA, provided that the specific probe carries a poly(dT) tail.     

Conjugated polyelectrolyte amplified fluorescent assays with probe functionalized silica nanoparticles for chemical and biological sensing

Low-cost sensors with high sensitivity and selectivity for chemical and biological detection are of high scientific and economic importance. Silica nanoparticles (NPs) have shown vast promise in sensor applications by virtue of their controllable surface modification, good chemical stability, and biocompatibility. This mini-review summarizes our recent development of silica NP-based assays for chemical and biological detection, where silica NPs serve as the substrate for probe immobilization, target recognition, and separation. The assay performance is further improved through the introduction of conjugated polyelectrolyte to amplify the detection signal. The assays have been demonstrated to be successful for the detection of DNA, small molecules, and proteins. They could be generalized for other targets based on specific interactions, such as DNA hybridization, antibody-antigen recognition, and target-aptamer binding.     

Electrochemical biosensors for detection of point mutation based on surface ligation reaction and oligonucleotides modified gold nanoparticles

An electrochemical method for point mutation detection based on surface ligation reaction and oligonucleotides (ODNs) modified gold nanoparticles (AuNPs) was demonstrated. Point mutation identification was achieved using Escherichia coli DNA ligase. This system for point mutation detection relied on a sandwich assay comprising capture ODN immobilized on Au electrodes, target ODN and ligation ODN. Because of the sequence-specific surface reactions of E. coli DNA ligase, the ligation ODN covalently linked to the capture ODN only in the presence of a perfectly complementary target ODN. The presence of ligation products on Au electrode was detected using chronocoulometry through hybridization with reporter ODN modified AuNPs. The use of AuNPs improved the sensitivity of chronocoulometry in this approach, a detection limit of 0.9 pM complementary ODN was obtained. For single base mismatched ODN (smODN), a negligible signal was observed. Even if the concentration ratio of complementary ODN to smODN was decreased to 1:1000, a detectable signal was observed. This work may provide a specific, sensitive and cost-efficient approach for point mutant detection.     

Electrochemical sensing of silver tags labelled DNA immobilized onto disposable graphite electrodes

An electrochemical approach for the improved electrochemical sensing of DNA was developed in this study based on the oxidation signals of silver and DNA base, guanine by using disposable pencil graphite electrode (PGE) electrodes. The easy surface modification of disposable electrodes PGEs with nucleic acids was performed by passive adsorption using amino linked DNA oligonucleotide attached onto the surface of silver nanoparticles (Ag-NPs). Firstly, the microscopic characterization of silver nanoparticles was investigated by transmission electron microscopy (TEM) and scanning electron microscopy (SEM), and the electrochemical behaviour of these NPs was studied by using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques. Then, the overall performance of this novel electrochemical DNA sensing method based on these nanoparticles is studied and discussed in terms of optimum analytical conditions, such as; the effect of DNA concentration, NPs concentration and different buffer solutions, etc. in order to obtain silver and guanine oxidation signals in higher sensitivity and selectivity. The main features related with this electrochemical assay based on silver nanoparticles are discussed and compared with other assays reported in the literatures.     

Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric QD-FRET transduction method. The selectivity of the hybridization assays was demonstrated by the detection of single nucleotide polymorphism.     

Time-resolved fluorescence based DNA detection using novel europium ternary complex doped silica nanoparticles

A two-probe tandem DNA hybridization assay including capture DNA₁, probe DNA₂, and target DNA₃ was prepared. The long-lived luminescent europium complex doped nanoparticles (NPs) were used as the biomarker. The complex included in the particle was Eu(TTA)₃(5-NH₂-phen)-IgG (ETN-IgG), the europium complex Eu(TTA)₃(5-NH₂-phen) linking an IgG molecule. Silica NPs containing ETN-IgG were prepared by the reverse microemulsion method, and were easy to label oligonucleotide for time-resolved fluorescence assays. The luminophores were well-protected from the environmental interference when they were doped inside the silica network. The sequences of Staphylococcus aureus and Escherichia coli genes were designed using software Primer Premier 5.0. Amino-modified capture DNA₁ was covalently immobilized on the common glass slides surface. The detection was done by monitoring the fluorescence intensity from the glass surface after the hybridization reaction with the NPs labeled probe DNA₂ and complementary target DNA₃. The sensing system presented short hybridization time, satisfactory stability, sensitivity, and selectivity. This approach was successfully employed for preliminary application in the detection of pure cultured E. coli, it might be an effective tool for pathogen DNA monitoring.     

Streptavidin-enhanced assay for sensitive and specific detection of single nucleotide polymorphism in TP53

This paper reports an approach to detection of single nucleotide polymorphism based on special amplification assay and surface plasmon resonance biosensor technology. In this assay, a part of the target DNA is recognized by a probe (probe A) coupled with streptavidin–oligonucleotide (SON) complexes ex situ, and when the mixture is injected in the sensor, another part of the target DNA is recognized by a DNA probe (probe B) immobilized on the sensor surface. To achieve high sensitivity and specificity, the assay is optimized in terms of composition of SON complexes, probe design, and assay temperature. It is demonstrated that this approach provides high specificity (no response to targets containing single-mismatched bases) and sensitivity (improves sensor response to perfectly matched oligonucleotides by one order of magnitude compared to the direct detection method). The assay is applied to detection of a short synthetic analogue of TP53 containing a “hot spot”—single nucleotide mismatch frequently mutated in germ line cancer—at levels down to 40 pM.     

Anti-fouling characteristics of surface-confined oligonucleotide strands bioconjugated on streptavidin platforms in the presence of nanomaterials

This work describes our studies on the molecular design of interfacial architectures suitable for DNA sensing which could resist non-specific binding of nanomaterials commonly used as labels for amplifying biorecognition events. We observed that the non-specific binding of bio-nanomaterials to surface-confined oligonucleotide strands is highly dependent on the characteristics of the interfacial architecture. Thiolated double stranded oligonucleotide arrays assembled on Au surfaces evidence significant fouling in the presence of nanoparticles (NPs) at the nanomolar level. The non-specific interaction between the oligonucleotide strands and the nanomaterials can be sensitively minimized by introducing streptavidin (SAv) as an underlayer conjugated to the DNA arrays. The role of the SAv layer was attributed to the significant hydrophilic repulsion between the SAv-modified surface and the nanomaterials in close proximity to the interface, thus conferring outstanding anti-fouling characteristics to the interfacial architecture. These results provide a simple and straightforward strategy to overcome the limitations introduced by the non-specific binding of labels to achieve reliable detection of DNA-based biorecognition events.     

DNA interaction probed by evanescent wave cavity ring-down absorption spectroscopy via functionalized gold nanoparticles

Evanescent wave cavity ring-down absorption spectroscopy (EW-CRDS) is employed to study interaction and binding kinetics of DNA strands by using gold nanoparticles (Au NPs) as sensitive reporters. These Au NPs are connected to target DNA of study that hybridizes with the complementary DNA fixed on the silica surface. By the absorbance of Au NPs, the interaction between two DNA strands may be examined to yield an adsorption equilibrium constant of 2.2 × 10¹⁰ M⁻¹ using Langmuir fit. The binding efficiency that is affected by ion concentration, buffer pH and temperature is also examined. This approach is then applied to the label-free detection of the DNA mutation diseases using the sandwich hybridization assay. For monitoring a gene associated with sickle-cell anemia, the detection limit and the adsorption equilibrium constant is determined to be 1.2 pM and (3.7 ± 0.8) × 10¹⁰ M⁻¹, distinct difference from the perfectly matched DNA sequence that yields the corresponding 0.5 pM and (1.1 ± 0.2) × 10¹¹ M⁻¹. The EW-CRDS method appears to have great potential for the investigation of the kinetics of a wide range of biological reactions.     

Magnetic field induced aggregation of nanoparticles for sensitive molecular detection

A molecular detection method utilizing the magnetically induced aggregation of silver nanoparticle (NP)-embedded silica NPs for SERS activation is described. Here, silver embedded magnetic NPs (Ag-M-dots) composed of a magnetic core and silica shells, on whose surface silver NPs were formed, were used. Because the magnetic field induced aggregated Ag-M-dots exhibit a strong SERS signal compared to the dispersed Ag-M-dots, the system allows for the detection of adsorbed Raman label compound even at the 100 fM level. Adenine was tested as a model biocompound and its Raman spectrum could be observed at concentrations as low as 1 pM. The experimental results were supported by the theoretical calculations.     

Nanoparticle-based electrochemical immunosensor for the detection of phosphorylated acetylcholinesterase: an exposure biomarker of organophosphate pesticides and nerve agents

A nanoparticle-based electrochemical immunosensor has been developed for the detection of phosphorylated acetylcholinesterase (AChE), which is a potential biomarker of exposure to organophosphate (OP) pesticides and chemical warfare nerve agents. Zirconia nanoparticles (ZrO(2) NPs) were used as selective sorbents to capture the phosphorylated AChE adduct, and quantum dots (ZnS@CdS, QDs) were used as tags to label monoclonal anti-AChE antibody to quantify the immunorecognition events. The sandwich-like immunoreactions were performed among the ZrO(2) NPs, which were pre-coated on a screen printed electrode (SPE) by electrodeposition, phosphorylated AChE and QD-anti-AChE. The captured QD tags were determined on the SPE by electrochemical stripping analysis of its metallic component (cadmium) after an acid-dissolution step. Paraoxon was used as the model OP insecticide to prepare the phosphorylated AChE adducts to demonstrate proof of principle for the sensor. The phosphorylated AChE adduct was characterized by Fourier transform infrared spectroscopy (FTIR) and mass spectroscopy. The binding affinity of anti-AChE to the phosphorylated AChE was validated with an enzyme-linked immunosorbent assay. The parameters (e.g., amount of ZrO(2) NP, QD-anti-AChE concentration,) that govern the electrochemical response of immunosensors were optimized. The voltammetric response of the immunosensor is highly linear over the range of 10 pM to 4 nM phosphorylated AChE, and the limit of detection is estimated to be 8.0 pM. The immunosensor also successfully detected phosphorylated AChE in human plasma. This new nanoparticle-based electrochemical immunosensor provides an opportunity to develop field-deployable, sensitive, and quantitative biosensors for monitoring exposure to a variety of OP pesticides and nerve agents.     

Enzyme-amplified electrochemical hybridization assay based on PNA, LNA and DNA probe-modified micro-magnetic beads

In the present study, we investigated the properties of PNA and LNA capture probes in the development of an electrochemical hybridization assay. Streptavidin-coated paramagnetic micro-beads were used as a solid phase to immobilize biotinylated DNA, PNA and LNA capture probes, respectively. The target sequence was then recognized via hybridization with the capture probe. After labeling the biotinylated hybrid with a streptavidin–enzyme conjugate, the electrochemical detection of the enzymatic product was performed onto the surface of a disposable electrode. The assay was applied to the analytical detection of biotinylated DNA as well as RNA sequences. Detection limits, calculated considering the slope of the linear portion of the calibration curve in the range 0–2 nM were found to be 152, 118 and 91 pM, coupled with a reproducibility of the analysis equal to 5, 9 and 6%, calculated as RSD%, for DNA, PNA and LNA probes respectively, using the DNA target. In the case of the RNA target, the detection limits were found to be 51, 60 and 78 pM for DNA, PNA and LNA probes respectively.     

Ultrasensitive optical detection of trinitrotoluene by ethylenediamine-capped gold nanoparticles

This study found that 1,2-ethylenediamine (EDA) as a primary amine could be modified onto the surface of citrate-stabilized gold nanoparticles (Au NPs), and the EDA-capped Au NPs were successfully used as an ultrasensitive optical probe for TNT detection. The strong donor–acceptor (D–A) interactions between EDA and trinitrotoluene (TNT) at the Au NP/solution interface induced significant aggregation of the EDA-capped Au NPs, and enabled to easily realize the direct colorimetric detection of ultratrace TNT. The results showed that such a color change was readily seen by the naked eye, and the colorimetric detection could be down to 400 pM level of TNT with excellent discrimination against other nitro compounds. UV–vis absorption spectroscopy was used to examine the TNT-induced changes in local surface plasmon resonance (LSPR) of EDA-capped Au NPs, and a new LSPR band at ca. 630 nm arose along with the addition of TNT, which produced a detection limit of TNT down to ca. 40 pM. Furthermore, dynamic light scattering measurements evidenced the ultratrace TNT-induced small changes in the size of the EDA-capped Au NPs, and realized the quick and accurate detection of TNT in 0.4 pM level. These results demonstrated the ultrahigh sensitivity of this optical probe for TNT detection. Moreover, this optical probe is sample, stable, low-cost, and these excellent properties make it quite promising for infield and rapid detection of TNT.     

Chemiluminescent Determination of MicroRNA-141 Using Target-Dependent Activation of the Peroxidase-Mimicking DNAzyme

A chemiluminescent method was developed for microRNA-141 (miRNA-141) detection based on the target-dependent activation of peroxidase-mimicking DNAzyme. The structure of the probes was optimized which allowed the development of a sensitive method for miRNA-141. Under the optimized conditions, the detection limit and the linear range were 100?pM and 0.1–50?nM, respectively. The sensitivity of the assay was 270,000?nM^?1. The values of coefficient of variation measured within the working range varied less than 2%, which indicates excellent precision for the proposed method.     

A Simple Structure-Switch Aptasensor Using Label-Free Aptamer for Fluorescence Detection of Aflatoxin B1

Aflatoxin B1 (AFB1) is one of the mycotoxins produced by Aspergillus flavus and Aspergillus parasiticus, and it causes contamination in foods and great risk to human health. Simple sensitive detection of AFB1 is important and demanded for food safety and quality control. Aptamers can specifically bind to targets with high affinity, showing advantages in affinity assays and biosensors. We reported an aptamer structure-switch for fluorescent detection of aflatoxin B1 (AFB1), using a label-free aptamer, a fluorescein (FAM)-labeled complementary strand (FDNA), and a quencher (BHQ1)-labeled complementary strand (QDNA). When AFB1 is absent, these three strands assemble into a duplex DNA structure through DNA hybridization, making FAM close to BHQ1, and fluorescence quenching occurs. In the presence of AFB1, the aptamer binds with AFB1, instead of hybridizing with QDNA. Thus, FAM is apart from BHQ1, and fluorescence increases with the addition of AFB1. This assay allowed detection of AFB1 with a detection limit of 61 pM AFB1 and a dynamic concentration range of 61 pM to 4 μM. This aptamer-based method enabled detection of AFB1 in complex sample matrix (e.g., beer and corn flour samples).