Detection Of DNA Hybridization Research Articles

Highly Sensitive Refractive Index-Based Sensor for DNA Hybridization Using Subwavelength Grating Waveguide

A biosensor for detecting DNA hybridization via refractive index sensing has been demonstrated using a subwavelength grating (SWG) waveguide. Waveguide dimensions are selected by parametric optimizations to increase the mode-analyte overlap with considerations of typical silicon-on-insulator fabrications technology. DNA layer is added with a linker layer on silicon pillars of the SWG waveguide to optimize and detect the DNA hybridization. Some essential characteristics such as mode overlap factor, change in effective refractive index, waveguide sensitivity, and shift in resonance wavelength are computed for the different dimensional parameters of the SWG waveguide in DNA hybridization along with mode field intensity and normalized power using the finite element method. The DNA hybridization is shown by variation in normalized power of interacting light in cladding region of the waveguide for 0% to 100% fractional change of dsDNA and ssDNA. Waveguide sensitivity, shift in resonance wavelength, device sensitivity, and intrinsic limit of detection are obtained to ∼ 0.157, 7.01, 605 nm/RIU, and 1.30 × 10−4 RIU, respectively, for the optimized structure of SWG waveguide in sensing of DNA hybridization, which could be suitable aspects for detecting DNA hybridization.

Optimum Functionalization of Si Nanowire FET for Electrical Detection of DNA Hybridization

In this work, we demonstrate a wafer-scale fabrication of biologically sensitive Si nanowire FET for pH sensing and electrical detection of deoxyribonucleic acid (DNA) hybridization. Based on conventional “top-down” CMOS compatible technology, our bioFETs explore a wide range of design (nanowires (NW), nanoribbons (NR), and honeycomb (HC) structures) with opening access scaled down to only 120 nm. After device fabrication, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BG</sub> transfer and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> output characteristics show a conventional n-type FET behavior with an I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> value higher than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> , as well as an increase of threshold voltage as the NW width is reduced. Then, using a capacitive coupling in our dually-gated Si bioFETs, the pH sensitivity is enhanced with a pH response up to 600 mV/pH. Finally, we successfully detected an increase of threshold voltage of n-type silicon nanowires (SiNWs) due to hybridized target DNA molecules.

Plug-in label-free optical fiber DNA hybridization sensor based on C-type fiber Vernier effect

A reflective Fabry-Perot interference (FPI) label-free biosensor based on Vernier effect is designed and implemented for in situ real-time DNA hybridization detection. The sensor is made by splicing single-mode fiber (SMF), a segment of C-type fiber and SMF. The Vernier effect occurs between the solid cavity FPI and the air cavity FPI. In our experiment, a high sensitivity of 10791.12 nm/RIU is obtained in the refractive index (RI) range of 1.3311–1.3450. On this basis, we immobilized probe DNA (pDNA) on the surface of SMF to detect the complementary DNA (cDNA), demonstrating use for label-free sensing of DNA hybridization. The experimental results show that the sensor can detect 1 µM cDNA with high specificity. The paper demonstrates the first research of optical fiber DNA biosensor based on the open microcavity FPI Vernier effect. In addition, the sensor has the advantages of high sensitivity, strong stability, simple structure and simple fabrication. It can also be applied to other biomolecule detection based on probe-target biological binding events, which has great application potential in medical diagnostics, food science, genetic engineering and other biological fields.

Real-time label-free detection of DNA hybridization using a functionalized graphene field effect transistor: a theoretical study.

Detection of DNA hybridization with high sensitivity and accuracy plays a major role in clinical diagnosis and treatment. Despite intense experimental studies of graphene field effect transistor as DNA hybridization detector, the mechanism of detection and changes in the electrical properties of the device is not investigated in detail. To this end, we have investigated an armchair graphene nanoribbon (AGNR) interconnected between gold electrodes as a detector of DNA hybridization. Using non-equilibrium Green’s function method and density functional theory, the effect of 1-pyrenebutanoic acid succinimidyl ester (PBASE) linker, probe, and target DNA on the electrical properties of the device has been investigated at zero bias voltage. The results show that, after functionalization of AGNR with PBASE, the conductance of the device increases while functionalization with probe and target DNA leads to a decrease in conductance. The changes in the projected density of states on the AGNR and transmission around Fermi energy are the reason for the change in conductance of the system. In all cases, both charge transfer and electrostatic gating are responsible for the change in the electrical properties of the system. The results show that our device detects DNA hybridization with a sensitivity of 10% at zero bias voltage, and by applying a suitable gate voltage, it can show higher sensitivity.Graphical abstract

In Situ Temperature-Compensated DNA Hybridization Detection Using a Dual-Channel Optical Fiber Sensor

A multifunction, high-sensitivity, and temperature-compensated optical fiber DNA hybridization sensor combining surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) has been designed and implemented. We demonstrate, for the first time to our knowledge, the dual-parameter measurement of temperature and refractive index (RI) by simultaneously using SPR and MZI in a simple single-mode fiber (SMF)-no-core fiber (NCF)-SMF structure. The experimental results show RI sensitivities of 930 and 1899 nm/RIU and temperature sensitivities of 0.4 and -1.4 nm/°C for the MZI and SPR, respectively. We demonstrate a sensitivity matrix used to simultaneously detect both parameters, solving the problem of temperature interference of RI variation-based biosensors. In addition, the sensor can also distinguish biological binding events by detecting the localized RI changes at the fiber's surface. We realize label-free sensing of DNA hybridization detection by immobilizing probe DNA (pDNA) onto the fiber as the probe to capture complementary DNA (cDNA). The experimental results show that the sensor can qualitatively detect cDNA after temperature compensation, and the limit of detection (LOD) of the sensor reaches 80 nM. The proposed sensor has advantages of high sensitivity, real time, low cost, temperature compensation, and low detection limit and is suitable for in situ monitoring, high-precision sensing of DNA molecules, and other related fields, such as gene diagnosis, kinship judgment, environmental monitoring, and so on.

Gas-sensing and label-free detection of biomaterials employing multiple rings structured plasmonic nanosensor

In this paper, a refractive index sensor based on three circular rings coupled with a straight metal-insulator-metal (MIM) waveguide is presented. At near-infrared (NIR) spectrum, the spectral characteristics of the sensor are extensively analyzed using the finite element method (FEM). Moreover, the refractive index sensing property is comprehensively investigated by altering the design parameters. The results show a maximum sensitivity of 3573.3 nm/RIU with a figure of merit of 21.9, which is suitable for gas-sensing applications. The proposed sensor has also displayed prominent tolerance against manufacturing defects. Furthermore, the sensor proves to be highly sensitive for the label-free detection of blood components and DNA hybridization.

Label-free rapid electrochemical detection of DNA hybridization using ultrasensitive standalone CNT aerogel biosensor

We report the development of an ultrasensitive label-free DNA biosensor device with fully integrated standalone carbon nanotube (CNT) aerogel electrode. The multi-directional tenuous network of clustered CNT embedding into the CNT aerogel electrode demonstrates linear ohmic and near isotropic electrical properties, thereby providing high sensitivity for nucleic acid detection. Using this device, the target DNA hybridization is detected by a quantifiable change in the electrochemical impedance, with a distinct response to the single-stranded probe alone or double-stranded target-probe complex. The target DNA is specifically detected with limit of detection (LoD) of 1 pM with a turnaround time of less than 20 min, which is unprecedented for a miniaturized CNT aerogel sensor and impedance spectroscopy without an intermediate DNA amplification step. Moreover, this system is able to differentiate between the closely related target sequences by the distinct impedance response rendering it highly specific. To the best of our knowledge, this is the first report showing the use of standalone bare CNT aerogel electrode without any substrate support, coupled with electrochemical impedance spectroscopy, for the detection of DNA hybridization. Altogether, the results show that our system is fast, sensitive and specific for label-free rapid direct DNA detection, promising a novel avenue for bio-sensing.

Design and mechanism of photocurrent-modulated graphene field-effect transistor for ultra-sensitive detection of DNA hybridization

Field-effect transistors (FET) using low-dimensional materials has attracted attention for detection of DNA hybridization. Here, we proposed a photocurrent-modulated FET sensor, where the Iphotocurrent(gate)+Iphotocurrent(DNA) dramatically enhance the response signal, Icurrent, compared to a traditional FET sensor. The proposed sensor successfully detects DNA signals with a limit of detection (LOD) down to attomolar concentrations that is nearly 100x lower than a traditional FET sensor. The sensing mechanism is postulated and discussed. The results suggest that photo-coupled modulation opens new avenues for further development of the FET in biosensing applications.

Confocal Raman Microscopy Enables Label-Free, Quantitative, and Structurally Informative Detection of DNA Hybridization at Porous Silica Surfaces.

Characterization of DNA at solid/liquid interfaces remains a challenge because most surface-sensitive techniques are unable to provide quantitative insight into the base content, length, or structure. Surface-enhanced Raman scattering measurements of DNA hybridization on plasmonic-metal substrates have been used to overcome small Raman-scattering cross-sections; however, surface-enhanced Raman spectroscopy measurements are not generally quantitative due to the fall-off in the scattering signal with the decay of the electric field enhancement from the surface, which also limits the length of oligonucleotides that can be investigated. In this work, we introduce an experimental methodology in which confocal Raman microscopy is used to characterize hybridization reactions of ssDNA immobilized at the solid/liquid interface of porous silica particles. By focusing the femtoliter confocal probe volume within a single porous particle, signal enhancement arises from the ∼1500-times greater surface area detected compared to a planar substrate. Because the porous support is a purely dielectric material, the scattering signal is independent of the proximity of the oligonucleotide to the silica surface. With this technique, we characterize a 19-mer capture strand and determine its hybridization efficiency with 9-mer and 16-mer target sequences from the scattering of a structurally insensitive phosphate-stretching mode. Changes in polarizability and frequency of scattering from DNA bases were observed, which are consistent with Watson-Crick base pairing. Quantification of base content from their duplex scattering intensities allows us to discriminate between hybridization of two target strands of equivalent length but with different recognition sequences. A duplex having a single-nucleotide polymorphism could be distinguished from hybridization of a fully complementary strand based on differences in base content and duplex conformation.

DNA Hybridization Detection based on Plasmonic Photonic Crystal Fiber

A novel design of surface plasmon (SP) photonic crystal fiber (PCF) for DNA hybridization detection is proposed and analyzed. The suggested biosensor relies on plasmonic D-shaped PCF configuration. Accordingly, the core guided mode in the silica core is coupled with the SP mode near the plasmonic layer. The resonance wavelength is sensitive to the DNA hybridization process. Therefore, the suggested bio-sensor is studied to maximize the DNA hybridization detection sensitivity by adjusting the structural geometrical parameters. The numerical results are obtained using full vectorial finite element method with perfectly matched layer boundary condition and non-uniform meshing capabilities. The reported D-shaped PCF offers high wavelength sensitivity of 405.4 nm/RIU with a corresponding amplitude sensitivity of 5.65 RIU−1. Consequently, the applications based on DNA classification can be potentially implemented by the reported biosensor.

Surface charge transduction enhancement on nano-silica and - Alumina integrated planar electrode for hybrid DNA determination

This study represents the surface charge transduction, an efficient and inexpensive biosensor with modifications by silica-alumina entities and determination of gene sequence hybridization. The sensing surface was made by the planar aluminium interdigitated electrode on silicon substrate. Silica and alumina nanoparticles were engineered on the planar transducer surface and the device sensitivity was investigated. The morphology of silica and alumina particles was characterized through the high-resolution election microscopic analyses and revealed the spherical shaped nanoscale sizes at the range of 45–100 nm. The elemental compositions of silica and alumina nanomaterial were affirmed through energy disperse spectroscopy as prominent peaks of Si, Al and O were observed. Selected area electron diffraction analysis of silica and alumina justified their crystalline and amorphous nature, respectively. XRD analysis revealed the expending cristobalite state of silica crystal and γ-alumina for planar electrode surface enhancement. Fourier transform infrared spectroscopy peak observed at 1094 cm−1 revealed the asymmetric stretching of silica nanoparticles whereas the projecting peak observed at 806 cm−1. Additionally, Al–O stretch and Al–O–Al bending modes were justified with the peaks at 585 and 825 cm−1, respectively. Band gap values of silica and alumina computed were 6.75 eV and 3.20 eV, respectively. The results of DNA probe immobilization and complementation have affirmed that silica modified transducer shows the lowest detection at 10 aM whereas alumina modified transducer displayed insignificant current signal and failed to detect DNA hybridization. To investigate the effect of silica entity and its nanocomposite in detecting DNA hybridization, aluminosilicate nanocomposite was deposited on transducer and attained highly sensitive gene detection. Based on the coefficient regression value, aluminosilicate nanocomposite modified planar transducer has shown good device sensitivity (R2 = 0.96) in contrast to silica and alumina entities.

Performance Analysis of Graphene-Coated GaAs SPR Sensor for Detection of DNA Hybridization

Performance Analysis of Graphene-Coated GaAs SPR Sensor for Detection of DNA Hybridization

A disposable and cost-effective electrochemical DNA sensor using nanocomposite modified screen-printed gold electrode

This research involved the preparation of an electrochemical biosensor using a disposable screen-printed gold electrode (SPGE) for the DNA hybridization detection. An electrochemical DNA biosensor was successfully fabricated based on DNA probe tagged with methylene blue (MB) as redox hybridization indicator, was immobilized on the nanocomposite modified electrode. The modified SPGE was characterized by using cyclic voltammetry (CV) and scanning electron microscopy (SEM) with energy dispersion x-ray spectroscopy (EDS). The current signal of target DNA hybridization was monitored using differential pulse voltammetry (DPV). These DNA biosensor showed a good current response with the complementary target DNA concentration range from 1.0 x 10-11 to 1.0 x 10-7 M. This fabricated genosensor could also be regenerated easily and can be reused 36 times for hybridization studied.

CMOS Biosensors for the Detection of DNA Hybridization in High Ionic-Strength Solutions

Label-free detection of biomolecules using ion-sensitive field-effect transistors (ISFETs) in physiological solutions is limited by the Debye charge-screening effect of the electrical double layer. Most ISFET measurements are therefore performed in diluted ionic-strength solutions to detect the interface potential change on specific binding of biomolecules. The novel CMOS ISFETs proposed in this study have a capacitor structure in the oscillator readout to provide modulation of the surface electric field to reduce the charge screening and nonideal signal drift. Signal modulation was applied at frequencies higher than the ion-strength-dependent cut-off frequency, with the highest applied frequency being approximately 100 MHz among the four proposed designs. The measured results revealed a pH sensitivity from 52.3 to 54.4 mV/pH in terms of the floating-gate potential change. Direct DNA hybridization in a high ionic-strength solution was successfully measured with a near picomolar-level resolution.

Gold nanoparticle-assisted plasmonic enhancement for DNA detection on a graphene-based portable surface plasmon resonance sensor

The impact of different gold nanoparticle (GNP) structures on plasmonic enhancement for DNA detection is investigated on a few-layer graphene (FLG) surface plasmon resonance (SPR) sensor. Two distinct structures of gold nano-urchins (GNu) and gold nanorods (GNr) were used to bind the uniquely designed single-stranded probe DNA (ssDNA) of Mycobacterium tuberculosis complex DNA. The two types of GNP-ssDNA mixture were adsorbed onto the FLG-coated SPR sensor through the π-π stacking force between the ssDNA and the graphene layer. In the presence of complementary single-stranded DNA, the hybridization process took place and gradually removed the probes from the graphene surface. From SPR sensor preparation, the annealing process of the Au layer of the SPR sensor effectively enhanced the FLG coverage leading to a higher load of the probe DNA onto the sensing interface. The FLG was shown to be effective in providing a larger surface area for biomolecular capture due to its roughness. Carried out in the DNA hybridization study with the SPR sensor, GNu, with its rough and spiky structures, significantly reinforced the overall DNA hybridization signal compared with GNr with smooth superficies, especially in capturing the probe DNA. The DNA hybridization detection assisted by GNu reached the femtomolar range limit of detection. An optical simulation validated the extreme plasmonic field enhancement at the tip of the GNu spicules. The overall integrated approach of the graphene-based SPR sensor and GNu-assisted DNA detection provided the proof-of-concept for the possibility of tuberculosis disease screening using a low-cost and portable system to be potentially applied in remote or third-world countries.

Plasma treated graphene FET sensor for the DNA hybridization detection

Room-temperature plasma treated graphene based FET was firstly proposed for the DNA hybridization detection. Affinity and electrical properties of the graphene based DNA-FET sensor were studied and improved benefits from the surface modification. The facile room-temperature Ar plasma easily removes residues from the graphene surface and changes the hydrophilic properties of graphene, which is important for our solution gated DNA-FET sensor. Limit of the detection of below 10 aM is obtained in our experiment. Especially, DNA concentration (CDNA)/the amount of net drain current (ΔI) and the negative shift in the VCNP value of the GFET sensor with the plasma treated 30 s are all improved compared with that without treatment. It shows that the easily plasma treatment of the graphene surface can be used for the solution gated FET sensor.

Theoretical Analysis of a Simultaneous Graphene-Based Circular Plasmonic Refractive Index and Thickness Bio-Sensor

A simultaneous plasmonic refractive index and thickness bio-sensor has been investigated theoretically and numerically to detect DNA hybridization and biomolecules attached to the inner wall of nano-ring resonators. The finite element method has been used to better appreciate the derived transmission formula based on both transfer matrix and coupled mode theories. For the first time, by applying a monolayer of graphene around the nano-ring resonators and introducing a MIM circular coupled waveguide, the power coupling coefficient, figure of merit and efficiency of the bio-sensor have been enhanced. Also, the coupling distance and optical properties including the chemical potential of graphene have been considered and studied to obtain optimal results. The maximum attained sensitivity and figure of merit of the bio-sensor are 1100 nm/RIU and 200 RIU <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> , respectively. By employing a strong coupling condition, the full-width at half-maximum and extinction ratio have been obtained as 5 nm and 40 dB, respectively. Finally, the potential of the proposed structure as simultaneous AND and NOR logic gates have been studied with the intensity contrast ratios of 57 and 102.6 dB, respectively. Due to the excellent performance of the graphene-based circular plasmonic structure, it can find significant applications in photonic integrated circuits and on-chip nano-sensors.

DNA Hybridization Measured with Graphene Transistor Arrays.

Arrays of field-effect transistors are fabricated from chemical vapor deposition grown graphene (GFETs) and label-free detection of DNA hybridization performed down to femtomolar concentrations. A process is developed for large-area graphene sheets, which includes a thin Al2 O3 layer, protecting the graphene from contamination during photolithographic patterning and a SiOx capping for biocompatibility. It enables fabrication of high-quality transistor arrays, exhibiting stable close-to-zero Dirac point voltages under ambient conditions. Passivation of the as-fabricated chip with a layer composed of two different oxides avoids direct electrochemical contact between the DNA solutions and the graphene layer during hybridization detection. DNA probe molecules are electrostatically immobilized via poly-l-lysine coating of the chip surface. Adsorption of this positively charged polymer induces a positive shift of the Dirac point and subsequent immobilization of negatively charged DNA probes induces a negative shift. Spatially resolved hybridization of DNA sequences is performed on the GFET arrays. End-point as well as real-time in situ measurements of hybridization are achieved. A detection limit of 10 fm is observed for hybridization of 20-nucleotide DNA targets. Typical voltage signals are around 100mV and spurious drifts below 1mV per hour.

On-chip selective growth of SnO2 nanowires for DNA sensor development

Tin oxides nanowires were selectively grown on the working electrode of a sensor by using modified chemical vapor deposition technique with supporting shadow mask. Time and distance evolution of Sn mass transport in correlation with carrier gas pressure and flow rates in the chemical vapor deposition system was described by Comsol Multiphysics. The simulated density of SnO2 nanowires was in good agreement with that obtained by scanning electron microscope image. X-ray diffraction, high-resolution transmission electron microscopy, scanning transmission electron microscopy measurements showed that nanowire structure was tetragonal with lattice constants a = 0.474 nm and c = 0.318 nm. The nanowires were around 25 nm in diameter and 3.5 μm in length. A simple immobilization of a DNA sensor was conducted by a surface modification of tin oxide nanowire using 3-amino-propyl-tri-ethoxysilance hydroxylation in vapor phase; creating the amino functional groups to which the phosphate groups of probe ss-DNA (Epstein-Barr virus) bound. Differential voltage measurements were conducted to detect DNA hybridization. The response time was 2.5 s and the limit of detection was 3.2 pM.

Experimental Demonstration of DNA Hybridization Using Graphene Based Plasmonic Sensor Chip

Parvovirus B19 (B19V) and human bocavirus (HBoV) are notable dangerous human pathogens based on ssDNA, which cause infectious diseases. Although label-free molecular level quantification of these pathogens is extremely challenging, it can be achieved by trending surface plasmon resonance (SPR) sensor. Here, a graphene-based plasmonic chip, essential in the SPR sensor, is developed for the specific label-free detection of ssDNA based pathogens. The absorption curves reveal that graphene has a significantly stronger interaction with ssDNA than the plasmonic metal due to π-stacking bonding with carbon rings of nucleobases present in ssDNA. Further, reflectance curves show that shift in resonance angle for graphene is more than twice without graphene even for very low concentration, i.e., 0.23 μM of the target ssDNA. Additionally, the penetration depth of the electric field in the sensing medium for graphene is 2.5 times of the plasmonic metal, i.e., silver, which makes it suitable for the detection of comparatively larger molecules. The combination of extraordinary chemical bonding and optical properties of graphene represents a highly sensitive detection of DNA hybridization. It provides a confident track for the diagnosis of ssDNA based infectious diseases.