Detection Of DNA Hybridization Research Articles

Nitrogen doped chiral carbonaceous nanotube for ultrasensitive DNA direct electrochemistry, DNA hybridization and damage study

In the interest of developing novel electrocatalyst for high performance DNA biosensing, with distinctive chiral double helix nanostructure, nitrogen doped chiral carbonaceous nanotube (Chiral-CNT) was employed for ultrasensitive label-free DNA biosensing research. Chiral-CNT can quantitative detection of four DNA bases with high sensitivity and selectivity. Without any prehydrolysis and labeling process, direct electrochemistry of single-stranded DNA and double-stranded DNA, qualitative and quantitative detection of DNA hybridization (low detection limit: 0.0268 g L−1) were realized. Moreover, sensitive detection of DNA damage induced by fenton reagent was also realized with low detection limit of 0.0350 mg mL−1 and high sensitivity of 7.42 μA mg−1 mL. The high biosensing performance attributes to the unique chiral structure of Chiral-CNT, leads to efficient interreaction between Chiral-CNT and DNA molecule.

Label-free detection of live cancer cells and DNA hybridization using 3D multilayered plasmonic biosensor

Three-dimensional (3D) multilayered plasmonic nanostructures consisting of Au nanosquares on top of SU-8 nanopillars, Au asymmetrical nanostructures in the middle, and Au asymmetrical nanoholes at the bottom were fabricated through reversal nanoimprint technology. Compared with two-dimensional and quasi-3D plasmonic nanostructures, the 3D multilayered plasmonic nanostructures showed higher electromagnetic field intensity, longer plasmon decay length and larger plasmon sensing area, which are desirable for highly sensitive localized surface plasmonic resonance biosensors. The sensitivity and resonance peak wavelength of the 3D multilayered plasmonic nanostructures could be adjusted by varying the offset between the top and bottom SU-8 nanopillars from 31% to 56%, and the highest sensitivity of 382 and 442 nm/refractive index unit were observed for resonance peaks at 581 and 805 nm, respectively. Live lung cancer A549 cells with a low concentration of 5 × 103 cells ml−1 and a low sample volume of 2 μl could be detected by the 3D multilayered plasmonic nanostructures integrated in a microfluidic system. The 3D plasmonic biosensors also had the advantages of detecting DNA hybridization by capturing the complementary target DNA in the low concentration range of 10−14–10−7 M, and providing a large peak shift of 82 nm for capturing 10−7 M complementary target DNA without additional signal amplification.

Poly-L-lysine Coated Surfaces for Ultrasensitive Nucleic Acid Detection.

Poly‐L‐lysine is one of the biocompatible polymers having amino and carboxyl groups in its structure. This attractive feature of poly‐L‐lysine makes it very convenient for bioactive molecule attachment. This study details the preparation of poly‐L‐lysine‐based pencil graphite electrodes (PLL/PGEs) and use of the coated electrodes for direct ultrasensitive DNA hybridization detection. In the first part of this study, poly‐L‐lysine coated electrodes were prepared using L‐lysine as the monomer by cyclic voltammetry (CV) with different cyclic scans. The effect of these cyclic scans during the electropolymerization was investigated. Coated electrodes were characterized by cyclic voltammetry, electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). Then, one‐pot preparation of poly‐L‐lysine composites with graphene (GN) and multi‐walled carbon nanotubes (MWCNTs) onto the pencil graphite electrodes were achieved. Electrochemical responses of these 3 electrodes were compared. After all, electrochemical DNA hybridization was performed using the poly‐L‐lysine‐based electrodes prepared at optimum polymerization condition. The PLL/PGE coated electrode presented a good linear response in the target concentration range of 1.0×10−13 to 1.0×10−6 with a detection limit of 2.25×10−14 using differential pulse voltammetry as the detection method. We believe that poly‐L‐lysine‐based surfaces will be useful for further clinical applications.

In-situ ultrasensitive label-free DNA hybridization detection using optical fiber specklegram

In this work, we present a compact and ultrasensitive bio-molecule sensor based on fiber specklegram, achieving a DNA detection sensitivity of 10−16 M. To our knowledge, the new device is the most sensitive fiber-optic DNA sensor reported to date. Importantly, the well-known temperature cross-sensitivity issue in many fiber-optic devices has been entirely removed by the introduction of a reference fiber-optic channel embedded in microfluidic channels. In the experiment, we demonstrate label-free DNA hybridization detection at different concentrations, where normalized intensity inner product of the collected specklegrams are calculated and used for determining the DNA concentration. The result shows the exact ssDNA concentration can be precisely determined with a single experiment in 60 min. The new fiber sensor presents distinctive advantages over traditional bio-sensors in terms of sensitivity, precision and cost, which may find many practical applications in health and medicine, e.g., point-of-care testing and disease diagnosis.

Detection of DNA hybridization using graphene-coated black phosphorus surface plasmon resonance sensor

In this paper, graphene-coated black phosphorus at the metal surface for the detection of DNA hybridization event is numerically demonstrated. The strategy consists of placing the sensing medium on top of black phosphorus–graphene-coated SPR which interfaces with phosphate-buffered saline solution carrying single-stranded DNA. Upon hybridization with its complementary DNA, desorption of the nanostructures takes place and thus enables the sensitive detection of the DNA hybridization event. The proposed sensor exhibits a sensitivity (125 ο/RIU), detection accuracy (0.95) and quality factor (13.62 RIU−1) for complementary DNA. In comparison with other reported papers, our suggested sensor provides much better performance. Thus, this label-free DNA detection platform should spur off new interest towards the use of black phosphorus–graphene-coated SPR interfaces.

Nanocarbon-Based Field-Effect Transistor Biosensors (bioFETs) for Real-Time Detection of DNA Sequences

Field-effect transistor devices based on functionalized nanocarbon materials (2-D graphene thin layers and 1-D carbon nanotubes) are a promising technology for biomolecular sensing applications. In particular, this type of devices allows for label-free detection of DNA hybridization with the advantage of an easy and direct electrical readout in comparison with most routine techniques. In this work, we report on the design and fabrication of nanocarbon-based bioFETs for DNA hybridization detection. Employing a combination of microfluidics and real-time electrical measurements, we investigated the response of bioFETs to single-stranded DNA (ssDNA) probe tethering and hybridization with complementary target ssDNA in saline buffer solution. The bioFETs were assembled from individual carbon nanotubes or graphene nanoribbons connected by pairs of metallic electrodes using photolithography techniques. Transfer curves of bioFETs in saline buffer were measured using an immersed pseudo-reference electrode. We obtained transfer curves showing current modulation with high OFF-current at the charge-neutrality point. Probe and target ssDNA were chosen as 22-nucleotide-long complementary sequences. Probe tethering on nanocarbon was obtained using diazonium chemistry followed by EDC/NHS coupling of an amine moiety placed at the extremity of the DNA probe [1]. Transfer characteristics were measured before/after probe and target injection. Moreover, to further characterize the bioFETs response, probe immobilization and probe-target hybridization were recorded in real-time using electrical readout. The development of highly selective and ultra-sensitive sensors for DNA will open novel technological avenues to improve the detection of genetic biomarkers for various diseases. [1] Bouilly, D. et al. Nano Letters 16, 4679–4685 (2016)

Voltammetric Application of Polypyrrole-Modified Microelectrode Array for the Characterization of DNA Methylation in Glutathione S-Transferase Pi 1

ABSTRACTDirect and efficient label-free voltammetric detection of glutathione S-transferase Pi 1 (GSTP1) hypermethylation is reported using a custom-developed 16-channel microelectrode array chip. The microelectrode array chip is used in a dipstick configuration allowing detection of DNA hybridization in a solution volume of only 0.35 mL. Platinum microelectrode disks (n = 16) 30 µm in diameter have been modified with a polypyrrole bilayer before any contact with the oligonucleotides. The attachment of 15-mer Probe DNA to the bilayer is random but controlled by the presence of aliphatic tether groups allowing it to form a bidentate complex with the probe DNA. The voltammetric detection procedure of methylated GSTP1-specific target DNA is combined with bisulfite treatment of target DNA. Changes at the interface of the modified microelectrodes in an array configuration are used to record simultaneously cyclic voltammetry on all of the devices. The detection of hybridization is evaluated statistically by a yes or no event by comparing the changes in recorded cyclic voltammograms before and after exposure to the target DNA. All cyclic voltammograms of the methylated target show a greater percentage change than those with the nonmethylated target exposure and show a greater change in cyclic voltammogram area after methylated target exposure. We observe an average percentage difference of 25.6 ± 4.9% with a variation of 19.1%. These results demonstrate that the fast sensing strategy possesses sensitivity and good specificity. Furthermore, this technology can potentially support rapid, accurate diagnosis and risk assessment of patients with prostate cancer.

Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes.

In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs) and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs). Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.

Silver-dendrimer nanocomposites as oligonucleotide labels for electrochemical stripping detection of DNA hybridization

Silver-dendrimer nanocomposites were synthesized and used as oligonucleotide labels for electrochemical stripping detection of DNA hybridization. The synthesized silver-dendrimer nanocomposites were characterized by UV–vis spectrophotometry, X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). Ratios of silver/dendrimer were optimized in order to obtain stable nanocomposites with maximal silver loading in the interior of a polymeric shell. The silver-dendrimer nanocomposites were attached to sequence-known DNA probes specific to colitoxin, and used to detect probe hybridization by dissolution of the silver nanoparticles in the interior of dendrimer in a diluted nitric acid, followed by measurement of Ag+ ions by anodic stripping voltammetry (ASV). Use of differential pulse voltammetry for the stripping step, along with optimization of the ASV conditions, enabled a detection limit of 0.78 pM. The present strategy, in combination with dendrimer-encapsulated copper labeled oligonucleotides probe reported previously, could potentially be used to detect single or multiple DNA targets in one sample.

Substrate Optimization of Carbon Nanomaterial Based DNA Hybridization Detection System

Substrate Optimization of Carbon Nanomaterial Based DNA Hybridization Detection System

Spiky gold shells on magnetic particles for DNA biosensors

Combined separation and detection of biomolecules has the potential to speed up and improve the sensitivity of disease detection, environmental testing, and biomolecular analysis. In this work, we synthesized magnetic particles coated with spiky nanostructured gold shells and used them to magnetically separate out and detect oligonucleotides using SERS. The distance dependence of the SERS signal was then harnessed to detect DNA hybridization using a Raman label bound to a hairpin probe. The distance of the Raman label from the surface increased upon complementary DNA hybridization, leading to a decrease in signal intensity. This work demonstrates the use of the particles for combined separation and detection of oligonucleotides without the use of an extrinsic tag or secondary hybridization step.

Graphene solution-gated field effect transistor DNA sensor fabricated by liquid exfoliation and double glutaraldehyde cross-linking

Graphene based solution-gated field effect transistors (G-SgFETs) have been extensively investigated as potential biosensors for various analytes. Liquid exfoliated graphene (LEG) is a recently developed economic and efficient carbon material, in comparison with graphene materials produced by other methods like Hummers, mechanical exfoliation and epitaxy. However, bio-sensitive and LEG based SgFETs (bioLEG-SgFETs) have not been demonstrated because of the deficiency in oxygen containing groups on LEG nano-sheets which are believed to be able to graft bio-sensing probes. Here, we describe a method for fabricating bioLEG-SgFETs and demonstrate their bio-application in single-strand DNA (ssDNA) detection, for the first time. The as-prepared LEG supernatant, deposited and functionalized films are thoroughly characterized by scanning electron microscopy, atom force microscopy, Raman and X-ray photoelectron spectroscopy. Furthermore, the feasibility of the proposed method is testified by the typical ambipolar transferring features possessed by G-SgFETs, as well as the ionic screening effect exhibited by the bio-modified G-SgFETs. BioLEG-SgFETs' performance acting as a sensor is evaluated by the detection of DNA hybridization, as proof-of-concept, which include target complementary ssDNA (csDNA), mismatched and half-matched ssDNA. The limit-of-detection for csDNA is about 10 fM. Accordingly, LEG would be a promising alternative for the traditional graphene materials used in G-SgFETs.

Label free detection for DNA hybridization using surface plasmon photonic crystal fiber biosensor

In this paper, a novel design of a highly sensitive surface plasmon (SP) photonic crystal fiber (PCF) biosensor for DNA hybridization detection is presented and analyzed. Through this study, the coupling between the core guided modes in a silica core D-shaped PCF and the SP modes around the gold nano-wires is studied and verified. Further, the structural geometrical parameters of the proposed biosensors are adjusted to achieve the highest sensitivity for DNA hybridization detection. The analysis is carried out using full vectorial finite element method. The proposed biosensor achieves a high sensitivity of 94.59 nm/RIU. To the best of the author’s knowledge, it is the first time to introduce a label free SP PCF DNA biosensor with high sensitivity. Moreover, the structure of the suggested sensor is easy for fabrication with standard PCF fabrication technologies. Furthermore, the suggested biosensor has a great potential for DNA classification based applications.

One-step coelectrodeposition-assisted layer-by-layer assembly of gold nanoparticles and reduced graphene oxide and its self-healing three-dimensional nanohybrid for an ultrasensitive DNA sensor.

A layer-by-layer (LBL) assembly was employed for preparing multilayer thin films with a controlled architecture and composition. In this study, we report the one-step coelectrodeposition-assisted LBL assembly of both gold nanoparticles (AuNPs) and reduced graphene oxide (rGO) on the surface of a glassy carbon electrode (GCE) for the ultrasensitive electrochemical impedance sensing of DNA hybridization. A self-healable nanohybrid thin film with a three-dimensional (3D) alternate-layered nanoarchitecture was obtained by the one-step simultaneous electro-reduction of both graphene oxide and gold chloride in a high acidic medium of H2SO4 using cyclic voltammetry and was confirmed by different characterization techniques. The DNA bioelectrode was prepared by immobilizing the capture DNA onto the surface of the as-obtained self-healable AuNP/rGO/AuNP/GCE with a 3D LBL nanoarchitecture via gold-thiol interactions, which then served as an impedance sensing platform for the label-free ultrasensitive electrochemical detection of DNA hybridization over a wide range from 1.0 × 10-9 to 1.0 × 10-13 g ml-1, a low limit of detection of 3.9 × 10-14 g ml-1 (S/N = 3), ultrahigh sensitivity, and excellent selectivity. This study presents a promising electrochemical sensing platform for the label-free ultrasensitive detection of DNA hybridization with potential application in cancer diagnostics and the preparation of a self-healable nanohybrid thin film with a 3D alternate-layered nanoarchitecture via a one-step coelectrodeposition-assisted LBL assembly.

Structural design of porous photonic crystal fibres

Researchers at the University of Adelaide, Australia, and the Islamic University of Technology, Bangladesh, report the optimum design for a porous photonic crystal fibre capable of terahertz frequency transmission. Photonic crystal fibres (PCFs), also known as micro-structured optical fibres (MOFs), are a new class of optical fibre. The significance of PCFs is their remarkable optical properties, such as providing single mode operation, high birefringence, and controllable chromatic dispersion characteristics, which are not obtainable using conventional optical fibres. As a result, PCFs are used extensively in different medical imaging applications, for example, in Optical Coherence Tomography (OCT). OCT is an imaging technology that allows non-invasive cross-sectional imaging of biological tissue. Bringing such techniques into the terahertz domain will be assisted by the development of PCFs that operate in the terahertz regime. There are different types of PCFs, including solid core PCF, hollow core PCF and porous core PCF. A solid core PCF experiences large material loss, which is a property that makes these PCFs unsuitable for terahertz signal transmission. In a hollow core PCF, the loss is greatly reduced, but such fibres operate over a narrow frequency range. To overcome the described disadvantages of solid core and hollow core fibres, porous core fibres were introduced. A porous core fibre contains a number of micro-structured air holes in the core. The advantage of the porous structure is that the fibre global parameters, including air hole size, pitch distance (centre-to-centre distance between air holes), core diameter and shape of air holes can be tuned as required for different applications. Thus, for porous fibre PCFs, the effective material loss, birefringence, dispersion, confinement loss, numerical aperture and other modal properties can be obtained by design. Nowadays, PCFs are used in the field of sensing, biomedical imaging, time domain spectroscopy, security, detecting DNA hybridisation and bio-sensing, skin cancer and breast cancer detection, and in communication applications. However, there are no previously reported articles on terahertz PCFs with sufficient numerical aperture (NA) to be used for OCT applications. In this issue of Electronics Letters, Saiful Islam and colleagues propose a terahertz PCF with high birefringence, high NA, and near zero dispersion variation. The measured high birefringence is reported to be due to the elliptical-shaped asymmetrical structure of the air holes inside the core. The asymmetrical structure of air holes created a refractive index difference between the polarisation modes, thus generating birefringence. The observation of high NA is reported to be due to the high birefringence and high modal effective area. Moreover, flattened dispersion is reported due to the waveguide structure and chosen materials that the waveguide was formed of. The kagome-based PCF has the advantage that it has a significantly lower confinement loss than other PCF structures. Terahertz time-domain spectroscopy set-up in the National T-Ray lab at the University of Adelaide. Saiful Islam at the University of Adelaide. The reported simulations in this Letter have allowed for rapid design optimisation that can now be experimentally tested. The major challenge of a PCF design is to anticipate difficulties in fabrication. Thus, the fabrication possibilities of a PCF must be addressed. For accuracy, obtaining correct parameters to describe the structural and optical properties of the fibre, such as refractive index, material absorption loss, relative permittivity and relative permeability, is of great importance. S. Islam states that ‘‘Our PCF design was produced with ease of fabrication in mind, allowing future realisation. Thus, applications in THz-OCT, chemical sensing, and multichannel communications are envisaged.’’ S. Islam and colleagues are currently using photonic crystal fibres to design chemical sensors for skin cancer detection. Non-invasive breast cancer detection is possible via detecting the presence of certain protein markers in human saliva. The authors are also designing sensors to detect hazardous chemicals for security applications. ‘‘We are planning to extend our PCF designs with the use of graphene or gold coasting to exploit surface plasmons for enhanced sensing’’, explains S. Islam. In practice, PCFs are limited to reasonably simple geometries due to difficulties in fabrication. However, emerging techniques exploiting developments in 3D printing are promising methods to overcome current limitations. S. Islam predicts that ‘‘It is possible that in the next decade will we begin to see more sophisticated PCFs with remarkable properties that are not deemed practical in today's technology.’’

Copper nanocluster as a fluorescent indicator for label-free and sensitive detection of DNA hybridization assisted with a cascade isothermal exponential amplification reaction

A copper nanocluster (CuNCs)-based fluorescence biosensing platform was developed for label-free DNA detection through a cascade isothermal exponential amplification reaction (EXPAR).

Wafer scale fabrication of graphene microelectrode arrays for the detection of DNA hybridization

Since the discovery of graphene, and due to its unique properties, we have witnessed a growing interest in the use of graphene-based devices for applications in the most diverse areas, namely in biosensing, particularly in the detection of genetic material. DNA can bind directly to graphene without the need of a linker and that makes this platform highly interesting for biosensor development.Here, electrochemical chips consisting of 6 independent gold microelectrode arrays as working electrode, and platinum reference and counter electrodes were fabricated at the wafer scale and, after graphene transfer and patterning, were used in the detection of DNA hybridization. Combining the sensitivity of electrochemical impedance spectroscopy and the selectivity of DNA beacons, we were able to detect DNA hybridization in a linear range between 5pM and 5nM, which is in the relevant clinical range for many diseases, with sensitivity to single nucleotide polymorphism.

Photonic crystals on copolymer film for label-free detection of DNA hybridization

The presence of a single-nucleotide polymorphism in Apolipoprotein E4 gene is implicated with the increased risk of developing Alzheimer's disease (AD). In this study, detection of AD-related DNA oligonucleotide sequence associated with Apolipoprotein E4 gene sequence was achieved using localized-surface plasmon resonance (LSPR) on 2D-Photonic crystal (2D-PC) and Au-coated 2D-PC surfaces. 2D-PC surfaces were fabricated on a flexible copolymer film using nano-imprint lithography (NIL). The film surface was then coated with a dual-functionalized polymer to react with surface immobilized DNA probe. DNA hybridization was detected by monitoring the optical responses of either a Fresnel decrease in reflectance on 2D-PC surfaces or an increase in LSPR on Au-coated 2D-PC surfaces. The change in response due to DNA hybridization on the modified surfaces was also investigated using mismatched and non-complementary oligonucleotides sequences. The proof-of-concept results are promising towards the development of 2D-PC on copolymer film surfaces as miniaturized and wearable biosensors for various diagnostic and defense applications.

A novel biosensor based on DNA hybridization for ultrasensitive detection of NOS terminator gene sequences

In this work, we have successfully designed a novel biosensor based on DNA hybridization for ultrasensitive detection of NOS terminator gene sequences (NOSt). This biosensor was synthesized by connecting single-stranded capture DNA (sDNA)-labeled graphene oxide quantum dots (GOQDs) (QDs-sDNA) as fluorescent probe and graphene oxide (GO) as quencher. The detection principle based on hybridization combinations can occur between QDs-sDNA and complementary target DNA; moreover, QDs-sDNA can bind to GO with significantly higher affinity than QDs-dsDNA. In the absence of complementary target DNA, QDs-sDNA was absorbed onto the surface of GO, and the fluorescence of QDs-sDNA was quenched due to fluorescent resonant energy transfer. In the presence of a complementary target DNA, its hybridization with QDs-sDNA formed QDs-dsDNA, which cannot be adsorbed to the GO surface and this leads to reduced quenching. By comparing the fluorescence intensity of QDs-sDNA and QDs-dsDNA in the presence of GO, we can achieve target DNA detection. Thus, rapid, simple, sensitive, efficient, and eco-friendly detection of NOSt was realized. This biosensor had a detection limit of 0.008nM and a linear range of 0.05–50nM. Moreover, this sensor can selectivity detect target DNA compared with random and single-base-mismatched sequences, and was successfully applied to the determination target DNA sequences in biological fluids directly. This sensor can be applied to detect other target DNA sequences by simply changing the types of sDNA coupled to the GOQDs.

Evolution of Surface Plasmon Supermodes in Metal-Clad Microwire and Its Potential for Biosensing

A finite-element method based on the vector H-field formulation in conjunction with perturbation techniques is used to study metal-clad microwire waveguides for bio-sensing applications. Sensors are designed to detect DNA hybridization through the change of the effective index and attenuation constant of the waveguide structure. The key parameters, such as effective index, loss coefficient, and spot sizes, are presented and potential sensor applications are discussed.