Detection Of Multiple DNA Targets Research Articles

Surface Functionalization and Reversible Disassembly of DNA-Assembly Nanoparticles for Sensitive and Multiplexed Detection of DNA Targets Without Enzymatic and Catalytic Amplification.

Recently, DNA-assembly nanoparticles based on DNA-metal ion interactions are emerging as new building blocks for drug delivery and metal nanostructure synthesis. However, the surface modification of DNA-assembly nanoparticles using functional biomolecules that can identify specific targets has rarely been explored. In this study, we developed a new immobilization chemical strategy to efficiently functionalize the barcode DNA-assembly nanoparticles (bcDNA NPs) with thiolated probe DNA (pDNA) for synthesizing pDNA-functionalized bcDNA NPs (pDNA-bcDNA NPs). We used them as nanoprobes to successfully demonstrate the sensitive and selective detection of multiple DNA targets. Importantly, Au ions played an essential role as anchoring sites via their conjugation with both thiolated pDNA and bcDNA NPs. In addition, we could reversibly and rapidly disassemble the pDNA-bcDNA NPs into the initial bcDNA strands with a recovery rate of 91%; this process significantly amplified the signal by releasing a million bcDNA strands, which enabled DNA quantification from a single pDNA-bcDNA NP. The Au3+ concentration, pH, and surface passivation conditions were carefully investigated to maximize the pDNA loading to 8500 strands/bcDNA NP. The limit of detection was determined to be 221 fM, which is the most sensitive among the absorbance-based methods without polymerase chain reaction, hybridization chain reactions, catalytic hairpin assembly, and other reactions involving enzymes and catalysts. The reversible disassembly of DNA strands and Au ion-mediated conjugation chemistry could be extended for the detection of other types of targets, such as proteins, metal ions, and small molecules, using other organic functionalities that are or can be thiolated, including polypeptides, aptamers, and antibodies.

Dual-color graphene quantum dots and carbon nanoparticles biosensing platform combined with Exonuclease III-assisted signal amplification for simultaneous detection of multiple DNA targets

Sensitive and simultaneous detection of multiple biomarkers such as target DNA or proteins using biocompatible materials with good analysis performance remains an important challenge. Herein, we successfully developed a signal “off-on” highly sensitive multiplex detection platform based on the combination of dual-color graphene quantum dots (blue GQDs and green GQDs) modified DNA probes with carbon nanoparticles (CNPs), which is a cheap, effective nonfluorescent quencher to simultaneously quench the fluorescence of both GQDs-DNA probes. The Exo III-assisted sequence-independent target recycling and signal amplification strategy was integrated into this sensing platform, which endows it with high sensitivity towards the multiplex detection of targets DNA. The detection limits of 6.6 pM for HIV and 9.5 pM for HBV were achieved respectively, which is about 60-fold lower than that of traditional unamplified homogeneous fluorescent assay methods. Our proposed multiplex detecting platform is advantageous in both respective and simultaneous detection of multiple targets and can also discriminate perfectly matched targets from mismatched targets in both PBS buffer and 1% human serum samples, demonstrating its potential to be a reliable strategy for highly sensitive simultaneous detection of multiple target genes in practical diagnosis applications.

A novel emulsion PCR method coupled with fluorescence spectrophotometry for simultaneous qualitative, quantitative and high-throughput detection of multiple DNA targets

We constructed and validated a novel emulsion PCR method combined with fluorescence spectrophotometry (EPFS) for simultaneous qualitative, quantitative and high-throughput detection of multiple DNA targets. In a single reaction set, each pair of primers was labeled with a specific fluorophore. Through emulsion PCR, a target DNA was amplified in droplets that functioned as micro-reactors. After product purification, different fluorescent-labeled DNA products were qualitatively analyzed by the fluorescent intensity determination. The sensitivity and specificity of the system was examined using four kinds of genetically modified (GM) maize. The qualitative results revealed high specificity and sensitivity of 0.5% (w/w). In addition, the quantitative results revealed that the absolute limit of detection was 103 copies, showing good repeatability. Moreover, the reproducibility assays were further performed using four foodborne pathogenic bacteria to further evaluate the applicability of the system. Consequently, the same qualitative, quantitative and high-throughput results were confirmed with the four GM maize. To sum up, the new EPFS system is the first analytical technology of this kind that enables simultaneous qualitative, quantitative and high-throughput analysis of multiple genes.

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples.

Sensitive, probe-based detection of multiple DNA targets is limited by the competitive reannealing of the antiparallel duplex DNA helix with the complementary DNA strand. To address this, we developed Cliffhanger primers, which create single-stranded DNA overhangs on PCR amplicons while simultaneously increasing the multiplex PCR efficacy and allowing PCR amplification using crude lysates of human faecal samples. A multiplex PCR that targeted eight genes from diarrhoeagenic Escherichia coli plus an internal control was performed and compared to a routine method that consisted of culture followed by multiplex PCR with fragment length separation. A total of 2515 clinical faecal samples from patients with diarrhoea were tested using both methods, and there was a significant increase in clinical sensitivity and negative predictive value with the Cliffhanger method for seven out of eight genes. All Cliffhanger-only positive samples were confirmed by Sanger sequencing of the PCR amplicon. Notably, the Cliffhanger method reduced the total sample turn-around time in the laboratory from 20 hours to 6 hours. Hence, use of Cliffhanger primers increased assay robustness, decreased turn-around time and increased PCR efficacy. This increased the overall clinical sensitivity without the loss of specificity for a heavily multiplexed PCR assay.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets.

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 102-105 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing.

Loading of silicon nanoparticle labels with redox mediators for detection of multiple DNA targets within a single voltammetric sweep

We have constructed electrochemical labels by loading four different redox mediators into silica nanoparticles (SiNPs) through electrostatic attraction. The mediators were methylene blue, ferrocinium tetrafluoroborate, tris (2,2-bipyridyl) dichlororuthenium (II) hexahydrate and acridine orange. The SiNPs were coated with avidin, which enabled attachment to biotin-tagged DNA sequences, forming signal probes. The immobilisation of four different capture probes onto screen printed electrodes enabled a simple qualitative and semi-quantitative detection of four different target probes within a single voltammetric sweep using differential pulse voltammetry. This was illustrated by detecting sequences found in four forms of the influenza virus, the influenza A sub-types H1N1, H3N2, H5N1 and influenza B. The limits of detection were 1.6pM, 1.6pM, 4.7pM and 2.9pM, respectively.

Multiplex Strand Invasion Based Amplification (mSIBA) assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

Nucleic acid amplification tests have become a common method for diagnosis of STIs due to their improved sensitivity over immunoassays and traditional culture-based methods. Isothermal nucleic acid amplification methods offer significant advantages over polymerase chain reaction (PCR) because they do not require sophisticated instruments needed for thermal cycling of PCR. We recently reported a novel isothermal nucleic acid amplification method, Strand Invasion-Based Amplification (SIBA), which exhibited high analytical sensitivity and specificity for amplification of DNA. However, because the reactions were detected using an intercalating dye, this method was only suitable for amplifying a single genomic target. Here, we report the development of multiplexed SIBA (mSIBA) that allows simultaneous detection of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and an internal control in the same reaction tube. SIBA is compatible with probes, allowing the detection of multiple DNA targets in the same reaction tube. The IC was developed to assess the quality of the isolated DNA and the integrity of the enzyme system, as well as to test oligonucleotides. The mSIBA assay retained high analytical sensitivity and specificity for the detection of CT and NG. The development of mSIBA enables rapid screening for CT and NG within point-of-care or central laboratory settings.

Parallel solid-phase isothermal amplification and detection of multiple DNA targets in microliter-sized wells of a digital versatile disc

An integrated method for the parallelized detection of multiple DNA target sequences is presented by using microstructures in a digital versatile disc (DVD). Samples and reagents were managed by using both the capillary and centrifugal forces induced by disc rotation. Recombinase polymerase amplification (RPA), in a bridge solid phase format, took place in separate wells, which thereby modified their optical properties. Then the DVD drive reader recorded the modifications of the transmitted laser beam. The strategy allowed tens of genetic determinations to be made simultaneously within <2 h, with small sample volumes (3 μL), low manipulation and at low cost. The method was applied to high-throughput screening of relevant safety threats (allergens, GMOs and pathogenic bacteria) in food samples. Satisfactory results were obtained in terms of sensitivity (48.7 fg of DNA) and reproducibility (below 18 %). This scheme warrants cost-effective multiplex amplification and detection and is perceived to represent a viable tool for screening of nucleic acid targets.

Ultrathin 2D Metal–Organic Framework Nanosheets

A facile surfactant-assisted bottom-up synthetic method to prepare a series of freestanding ultrathin 2D M-TCPP (M = Zn, Cu, Cd or Co, TCPP = tetrakis(4-carboxyphenyl)porphyrin) nanosheets with a thickness of sub-10 nm is developed. As a proof-of-concept application, some of them are successfully used as new platforms for DNA detection. The Cu-TCPP nanosheet-based sensor shows excellent fluorescent sensing performance and is used for the simultaneous detection of multiple DNA targets.

Ultrasensitive photoelectrochemical biosensing of multiple biomarkers on a single electrode by a light addressing strategy.

Ultrasensitive multiplexed detection of biomarkers on a single electrode is usually a great challenge for electrochemical sensors. Here, a light addressable photoelectrochemical sensor (LAPECS) for the sensitive detection of multiple DNA biomarkers on a single electrode was reported. The sensor was constructed through four steps: (1) immobilization of capture DNA (C-DNA) of different targets on different areas of a single large-sized gold film electrode, (2) recognition of each target DNA (T-DNA) and the corresponding biotin-labeled probe DNA (P-DNA) through hybridization, (3) reaction of the biotin-labeled probe DNA with a streptavidin-labeled all-carbon PEC bioprobe, and (4) PEC detection of multiple DNA targets one by one via a light addressing strategy. Through this principle, the LAPECS can achieve ultrasensitive detection of three DNA sequences related to hepatitis B (HBV), hepatitis C (HCV) and human immunodeficiency (HIV) viruses with a similar wide calibration range of 1.0 pM ∼ 0.01 μM and a low detection limit of 0.7 pM by using one kind of PEC bioprobe. Moreover, the detection throughput of LAPECS may be conveniently expanded by simply enlarging the size of the substrate electrode or reducing the size of the sensing arrays and the light beam. The present work thus demonstrates the promising applications of LAPECS in developing portable, sensitive, high-throughput, and cost-effective biosensing systems.

The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor.

By using an acoustic wave methodology that allows direct sensing of biomolecular conformations, we achieved the detection of multiple target DNAs using a single probe, exploiting the fact that each bound target results in a hybridized product of a different shape.

Graphitic carbon nitride nanosheet-based multicolour fluorescent nanoprobe for multiplexed analysis of DNA

We demonstrate that nanosheets composed of graphitic carbon nitride (g-C3N4) can serve as a low-cost and efficient fluorescent nanoprobe for the multiplexed detection of DNA in solution. The strategy is based on the finding that g-C3N4 is capable of binding dye-labeled single-stranded DNA (ssDNA) which results in quenching of the fluorescence of the dye. If target DNA hybridizes with dye-labeled ssDNA, the interaction between dye-labeled ssDNA and g-C3N4 is weakened, and this results in desorption of the dsDNA from the surface of the g-C3N4 and in recovery of fluorescence. The large surface area of g-C3N4 nanosheets allows for simultaneous quenching of multicolor DNA probes labeled with different dyes, leading to the development of multiplexed DNA sensors for the detection of multiple DNA targets in a single solution. By using one 15-mer DNA fragment and one 18-mer DNA fragment as proof-of-principle analytes, the method displayed good analytical performance. The limits of detection are 75 and 62 pM, respectively. The method is simple and sensitive, and was used to detect DNA in serum samples. We perceive that this method represents a new approach towards multiplexed assays for applications in DNA monitoring, clinical diagnosis, and in the detection of genetic disorders.

Simultaneous Detection of Multiple DNA Targets by Integrating Dual‐Color Graphene Quantum Dot Nanoprobes and Carbon Nanotubes

Simultaneous detection of multiple DNA targets was achieved based on a biocompatible graphene quantum dots (GQDs) and carbon nanotubes (CNTs) platform through spontaneous assembly between dual-color GQD-based probes and CNTs and subsequently self-recognition between DNA probes and targets.

The Use of Cycleave PCR for the Differentiation of the Rejuvenating Herb Species Pueraria candollei (White Kwao Khruea), Butea superba (Red Kwao Khruea), and Mucuna macrocarpa (Black Kwao Khruea), and the Simultaneous Detection of Multiple DNA Targets in a DNA Admixture

Kwao Khruea, the tuberous roots of Pueraria candollei Graham ex Benth. (White Kwao Khruea), Butea superba Roxb. (Red Kwao Khruea), and Mucuna macrocarpa Wall. (Black Kwao Khruea), are used as rejuvenating herbs in traditional medicine in many tropical countries. Although Kwao Khruea has attracted strong interest because of its rejuvenation properties, each species is used for specific purposes and effects. P. candollei shows estrogenic effects in females. In contrast, B. superba and M. macrocarpa show androgenic effects in males. The potential misidentification of dried tuberous roots of various Kwao Khruea species might cause problems in the drug market, especially when they are reduced into powders. A cycleave PCR, which is based on the sequence of chloroplast matK gene, was developed to differentiate P. candollei, B. superba, and M. macrocarpa. The results showed that cycleave PCR is able to identify specific Kwao Khruea species. A multiplex cycleave PCR was optimized for the simultaneous detection of two different DNA targets in a DNA admixture. The specificity of this technique was confirmed by its ability to distinguish M. macrocarpa from five related Mucuna species. Cycleave PCR can be a specific, sensitive, and rapid method for the identification of medicinal plants and crude plant samples.

Simultaneous detection of multiple DNA targets based on encoding metal ions

We present a novel strategy for simultaneous electrochemical detection of multiple DNA targets based on the use of different encoding metal ions as tags. The principle of this scheme is that metal ions bound to metallothionein (MT) molecules can be released down after hybridization with DNA targets and then be detected by stripping voltammetry. The novel detection probes, ssDNA/MT conjugates, covered with different metal ions were synthesized for the first time, then three encoding metal ions (Zn2+, Cd2+, and Pb2+) were used to differentiate the signals of three virus DNA due to their well-defined anodic stripping peaks at −1.13V (Zn), −0.78V (Cd), and −0.52V (Pb) at BiFE, respectively. The anodic peak currents increased linearly with the concentrations of DNA targets in the range from 0.1nM to 10nM with a detection limit of 33pM. In addition, the one-base mismatched target was effectively discriminated from the complementary target. The described results demonstrated that this method possesses high sensitivity and selectivity for multi-target DNA assay and has great potential in applications for detection of even more targets in biological assays, particularly immunoassays.

Liposome–Quantum Dot Complexes Enable Multiplexed Detection of Attomolar DNAs without Target Amplification

Sensitive detection of DNA usually relies on target amplification approaches such as polymerase chain reaction and rolling circle amplification. Here we describe a new approach for sensitive detection of low-abundance DNA using liposome-quantum dot (QD) complexes and single-particle detection techniques. This assay allows for detection of single-stranded DNA at attomolar concentrations without the involvement of target amplification. Importantly, this strategy can be employed for simultaneous detection of multiple DNA targets.

Radio Frequency Identification Sensor Chips with Anticollision Algorithm for Simultaneous Detection of Multiple DNA Targets

A newly developed DNA measurement method for multiple single nucleotide polymorphism (SNP) typing using a radio-frequency identification (RFID) sensor chip was demonstrated. The RFID sensor chip monolithically integrates a sensor, amplifier, analog-to-digital converter (ADC), and a passive wireless communication interface for receiving commands and transmitting data on a 2.5×2.5 mm2 silicon chip. For the simultaneous multitarget measurement, anticollision control and peak-power suppression are essential. To assign a unique identification number (UID) for the identification of multiple sensor chips, a reproducible random number generator circuit (RRG) was designed and installed on the chip. Peak-power consumption was reduced to 1018 µW by a clock gating of functional circuit blocks. Multiple SNP typing was carried out by simultaneously operating five RFID sensor chips (four with photosensors and one with a temperature sensor). The target DNA was captured on the sensor chips, and SNPs were detected by observing bioluminescence. Finally, the observed data were wirelessly transmitted to the reader.

A Graphene Nanoprobe for Rapid, Sensitive, and Multicolor Fluorescent DNA Analysis

AbstractCoupling nanomaterials with biomolecular recognition events represents a new direction in nanotechnology toward the development of novel molecular diagnostic tools. Here a graphene oxide (GO)‐based multicolor fluorescent DNA nanoprobe that allows rapid, sensitive, and selective detection of DNA targets in homogeneous solution by exploiting interactions between GO and DNA molecules is reported. Because of the extraordinarily high quenching efficiency of GO, the fluorescent ssDNA probe exhibits minimal background fluorescence, while strong emission is observed when it forms a double helix with the specific targets, leading to a high signal‐to‐background ratio. Importantly, the large planar surface of GO allows simultaneous quenching of multiple DNA probes labeled with different dyes, leading to a multicolor sensor for the detection of multiple DNA targets in the same solution. It is also demonstrated that this GO‐based sensing platform is suitable for the detection of a range of analytes when complemented with the use of functional DNA structures.

Instantaneous Derivatization Technology for Simultaneous and Homogeneous Determination of Multiple DNA Targets

There are potential advantages, in terms of simplicity and speed, for detecting DNA hybridization steps directly without using any external labels, especially for the multiplexed assays. In the current paper, we describe the use of a carrier-resolved label-free multiplexed assay for the simultaneous detection of multiple DNA targets. Herein we demonstrate that this protocol, using three homogeneous carriers thermosensitive poly(N-isopropylacrylamide), polystyrene beads, and magnetic beads, respectively, for simultaneous determination of three short DNA fragments specific to hepatitis B virus. Briefly, one hybridization occurs between a mixture of three different capture probe DNAs immobilized onto three carriers and three targets in a single vessel, and then chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotide-rich regions within the target DNA. An excellent linearity is found within the range between 0.1 and 6.0 pmol with the lowest detection limit of 100 fmol. In contrast to current encoding strategies, every hybridization signal for the corresponding DNA target in our protocol is uniquely immobilized onto one carrier vehicle with a unique and intrinsic physical-chemical signature. Moreover, an instantaneous derivatization reaction is employed for the label-free determination of three targets in a single vessel. In addition, a simple CL setup is employed to read the carrier code instead of an expensive and complicated flow cytometer or imaging system commonly used for multiplexed assays. Further signal amplification is achieved by employing three amplified DNAs for second hybridization, which include a guanine nucleobase-rich sequence domain for the generation of light and an additional tethered nucleic acid domain complementary with one of the target DNA as an amplification platform. Such simple amplified CL transduction allows detection of DNA targets down to the 15-fmol level. This new protocol also provided a good capability in discriminating perfectly complementary DNA from single-base mismatches and noncomplementary sequences. Overall, the protocol described here may have value in a variety of clinical, environmental, and biodefense applications for which the accurate quantitative analysis of multiple DNA targets is desired.

Multiplexed DNA Detection with Biobarcoded Nanoparticle Probes

Sorting the mail: A highly selective assay for the detection of multiple DNA targets in solution was developed based on gold nanoparticles with oligonucleotide reporters. Four DNA targets associated with infectious viruses were detected simultaneously without enzymatic amplification at mid-femtomolar concentrations.