Detection Of DNA Hybridization Research Articles

Retraction of "Highly Sensitive Detection of DNA Hybridization on Commercialized Graphene-Coated Surface Plasmon Resonance Interfaces".

Retraction of "Highly Sensitive Detection of DNA Hybridization on Commercialized Graphene-Coated Surface Plasmon Resonance Interfaces".

Cascade amplification-based triple probe biosensor for high-precision DNA hybridization detection of lung cancer gene

As an essential biomarker for diagnosing and treating various diseases, low-cost, quantitative detection methods for complementary DNA (cDNA) have received much attention. The surface plasmon resonance (SPR) sensing technique is an effective measurement scheme, but the ambient temperature and pH variations have a non-negligible impact. In this work, we developed a triple-probe SPR sensing system for detecting cDNA concentration, temperature, and pH. In order to satisfy the triple parameter measurements, we used a microstructured optical fiber as the sensing platform, silver and gold films as the excitation layer, and a MoS2 film as the modulation layer. First, we explore the modulation mechanism of SPR and the conditions for excitation of triple SPR and demonstrate that the carrier concentration is a crucial factor affecting the resonance wavelength. Then, the feasibility of the sensing system for triple-probing is theoretically analyzed. Finally, in the experiment, the optimal parameters of the sensor were determined, and the triple parameter detection was successfully realized. The experimental results show that the three probes can work independently, and the hybridized DNA probe can realize the selective detection of cDNA with a sensitivity of 0.249 nm/(nmol/l). The maximum sensitivity of the pH probe and the temperature probe are 51.5 nm/pH and 6.14 nm/°C. In addition, the experimental results show that the sensing probes have excellent reproducibility. This paper’s innovation is using the fiber optic SPR effect to achieve quantitative detection for cDNA, temperature detection, and pH detection. Therefore, the sensor has a promising future in early diagnosis and biosensing.

Ultra-sensitive DNA detection with single-base mismatch resolution using a tapered thin-diameter photonic crystal fiber interferometer.

A tapered thin-diameter photonic crystal fiber interferometer (TTD-PCFI) biosensor is proposed and demonstrated for DNA hybridization detection with an ultra-low limit of detection (LoD) and high specificity. The TTD-PCFI is fabricated by arc-discharged melting and adiabatic tapering, with a lower loss and stronger evanescent optical field. The fabricated TTD-PCFI with a diameter of 8.63 µm achieves a high refractive index sensitivity of 3842.5 nm/RIU. DNA hybridization detection of concentration ranging from 1 fM to 1 pM is achieved, with a sensitivity of 632 pm/lg(fM). The measured LoD is as low as 410 aM. Single-base mismatch detection of 25-base target single-stranded DNA is also achieved. The proposed label-free DNA biosensor has the advantages of the ultra-low LoD, high specificity, and real-time detection, which has great application prospects in the fields of disease diagnosis, microbial detection, and environmental science.

Deep eutectic solvent-assisted synthesis of gold nanoflowers supported on glassy carbon electrode for DNA sensor application

Gold nanoflowers (AuNF) were synthesized on a glassy carbon electrode via a one-step, eco-friendly protocol in deep eutectic solvent (DES) of choline choloride and urea, called reline, for label-free detection of DNA hybridization. DES is eco-friendly, low-cost, biocompatible, and nontoxic, and it can be used as an electrolyte to synthesize nanomaterials by using the electrochemical method. In this protocol, highly branched and stable AuNFs were obtained without using any surfactants for DNA sensor application. The electrochemical performance of the AuNF-modified electrode was studied by cyclic voltammetry and electrochemical impedance spectroscopy. Under optimal conditions, the AuNF-based DNA biosensor exhibited a sensitivity of 294.9 Ω nM−1cm−2 and 218 μA nM−1cm−2 and a limit of detection (LOD) of 10−9 M. The remarkable sensitivity and low LOD could be attributed to the good conductivity of AuNFs for accelerating electron transfer, resulting in obvious signal amplification. The DNA biosensor showed good reproducibility (RSD <3.65 %) and acceptable stability and selectivity. Its excellent performance in DNA detection suggested that the proposed electrochemical DNA sensor has great application potential in clinical diagnosis.

Chiral-Induced Spin Selectivity Modulated Time-Correlated Single-Photon Counting for DNA Hybridization Detection.

The chiral-induced spin selectivity (CISS) effect can distinguish between the spin of electrons as they pass through chiral molecules by backscattering one of the spin components. Herein, we explore the role of the CISS effect in time-correlated single-photon counting measurements to detect DNA hybridization. We observe that the average lifetime of optical excited states of quantum dots attached to double-stranded DNA (dsDNA) varies with directions of the applied magnetic field. Specifically, the difference in the nonradiative average decay lifetime for the two orientations of the applied magnetic field is 2.21 ns in the case of hybridized strands, which is 130 times higher than that observed with quantum dots attached to single-strand DNA. Additionally, we investigate the application of Fourier transform infrared (FTIR) spectroscopy for detecting double-stranded DNA in the presence of a magnetic field, establishing a theoretical framework to substantiate the experimental evidence of magnetic field-dependent FTIR spectroscopy for dsDNA.

Numerical investigation into impact of halide perovskite material on the optical performance of prism-loaded hybrid surface plasmon resonance biosensor: A strategy to increase sensitivity

The technology of surface plasmon resonance (SPR) is widely recognized and valued for its ability to rapidly and sensitively investigate biomolecular interactivities in real-time. Herein, we numerically investigate the collective influence of metal/ transition metal dichalcogenide (TMDC)/halide perovskite (HP)/2D carbon (C) and phosphorus (P) allotropes on the functionality of an SPR biosensor deploying Kretschmann configuration. The incident light wavelength is held constant at 633 nm, and radiative properties of the hybrid structure are determined using the attenuated total reflection and transfer matrix techniques. Crucial performance metrics such as quality factor (QF), figure of merit (FoM), sensitivity, and detection accuracy are calculated. The comparison is conducted and evaluated against the current literature using performance outcomes in terms of several prisms such as BK7, BAK1, BAF10, SF5, SF10, SF11, 2S2G, CaF2, and CsF, several TMDCs such as WS2, MoS2, WSe2, MoSe2, and PtSe2, several HPs such as CsPbI3, KSnI3, CsSnI3, and FASnI3, and 2D C/P allotropes such as Graphene, MXene, Black phosphorene (BP), and Blue phosphorene (BlueP) in order to search optimum parameters, and then we implement the best one in each layer of this biosensor design. It is noticed that the SPR heterostructure based on BAK1 prism, plasmonic metal Ag, tungsten disulfide (WS2) TMDC, formamidinium tin iodide (FASnI3) HP and 2D BP exhibits outstanding performance with regard to sensor performance characteristics. The observed FoM and sensitivity are 48.2/RIU and 402°/RIU, respectively. The investigation of the electric field distribution within this biosensor along the normal to the interface is also conducted using the finite difference time domain (FDTD) approach to demonstrate the unique contribution of FASnI3. The findings presented in this study are anticipated to play a key role in the improvement of plasmonic resonance-based biosensing domains like DNA hybridization or formalin detection by employing halide perovskite as an additional layer in SPR biosensors.

Label-Free DNA Hybridization Detection Using a Highly Sensitive Fiber Microcavity Biosensor.

A novel label-free optical fiber biosensor, based on a microcavity fiber Mach-Zehnder interferometer, was developed and practically demonstrated for DNA detection. The biosensor was fabricated using offset splicing standard communication single-mode fibers (SMFs). The light path of the sensor was influenced by the liquid sample in the offset open cavity. In the experiment, a high sensitivity of -17,905 nm/RIU was achieved in the refractive index (RI) measurement. On this basis, the probe DNA (pDNA) was immobilized onto the sensor's surface using APTES, enabling real-time monitoring of captured complementary DNA (cDNA) samples. The experimental results demonstrate that the biosensor exhibited a high sensitivity of 0.32 nm/fM and a limit of detection of 48.9 aM. Meanwhile, the sensor has highly repeatable and specific performance. This work reports an easy-to-manufacture, ultrasensitive, and label-free DNA biosensor, which has significant potential applications in medical diagnostics, bioengineering, gene identification, environmental science, and other biological fields.

Rapid and quantitative detection of DNA hybridization using a simplified Fabry-Perot interferometric biosensor.

This study introduces a miniaturized fiber-optic Fabry-Perot (FP) interferometric biosensor, distinctively engineered for cost-effective, rapid, and quantitative DNA sequence detection. By leveraging the interference patterns generated within a Fabry-Perot microcavity, our sensor precisely monitors DNA hybridization events in real-time. We have verified the sensor's biofunctionalization via fluorescent labeling and have extensively validated its performance through numerous hybridization and regeneration cycles with 1 μM single-stranded DNA (ssDNA) solutions. Demonstrating remarkable repeatability and reusability, the sensor effectively discerns ssDNA sequences exhibiting varying degrees of mismatches. Its ability to accurately distinguish between sequences with 2 and 7 mismatches underscores its potential as a valuable asset for swift DNA analysis. Characterized by its rapid response time-typically yielding results within 6 minutes-and its adeptness at mismatch identification, our biosensor stands as a potent tool for facilitating accelerated DNA diagnostics and research.

Expression of Concern for "Highly Sensitive Detection of DNA Hybridization on Commercialized Graphene-Coated Surface Plasmon Resonance Interfaces".

Expression of Concern for "Highly Sensitive Detection of DNA Hybridization on Commercialized Graphene-Coated Surface Plasmon Resonance Interfaces".

Lab on a single fiber: A three-parameter sensor based on triple-SPR for one-to-one detection of DNA, pH and temperature

In order to realize the one-to-one correspondence between outputs and inputs in the multiparameter detection field, a multiparameter DNA hybridization sensor with temperature and pH detection channels based on a fiber-based triple surface plasmon resonance (Triple-SPR) effect is demonstrated in this paper. Compared with previous works, the significant innovation of this paper is the independent temperature testing and pH testing channels implemented based on a single fiber optic structure, and the high-sensitivity DNA hybridization detection channel. Polydimethylsiloxane and the self-assembled materials formed by polyacrylic acid (PAA) and chitosan (CS) are used for the real-time detection of temperature and pH. With the help of these two materials, the instantaneous response of the Triple-SPR sensor to temperature and pH has been realized, and the response times (RT) are less than 1 s and 20 s, respectively. After the modification of probe DNA (pDNA), the selective detection of complementary DNA (cDNA) is achieved. The sensitivity and detection limit (DL) reaches 0.09 nm/(nmol/L) and 3.69 nmol/L, respectively. The experimental results demonstrate that an approximately one-to-one correspondence exists between inputs and outputs. The output signals can be used to provide feedback signals for achieving stable temperature and pH environments. The advantages of multi-parameter independent detection, high-sensitivity as well as fast response of the fiber-based Triple-SPR sensing technology are of great significance in the field of future multi-parameter sensing, compensated detection as well as real-time bio-monitoring.

Label free optofluidic DNA hybridization detection based on suspended core fiber whispering gallery mode resonator

An optofluidic DNA biosensor based on a suspended core fiber (SCF) has been proposed for the detection of specific DNA sequence fragments. The sensor is formed by coupling a micro/nano tapered optical fiber to the cladding of an SCF, producing a whispering gallery mode (WGM) effect. The WGM resonance is sensitive to samples within the channels of the SCF. The diameter of the SCF is reduced by etching to increase refractive index sensitivity, up to 274 nm/RIU. Biomarkers are captured on the inner surface of the microfluidic channel leading to a change in the local refractive index. The experimental results show that the sensor can quantitatively detect complementary DNA (cDNA) by immobilizing probe DNA (pDNA) on the surface of the microfluidic channel with a limit of detection of 1.5 nM. The proposed DNA biosensor provides a label-free method for DNA detection, which has great potential for multiplexed detection and realizing disease diagnostics.

Zinc selenide based dual-channel SPR optical biosensor for HIV genome DNA hybridization detection

Simultaneous measurement of human immunodeficiency virus (HIV) genome DNA hybridization and the DNA melting temperature in a prism-based surface plasmon resonance (SPR) biosensor is modeled theoretically using a simple dual-channel construction. The proposed sensor consists of a BK7 prism coated with silver as a plasmonic material. The metal surface is divided into two channels to detect medium refractive index (RI) and temperature. One half is covered with zinc selenide (ZnSe) semiconductor to enhance the hybridization detection sensitivity and to protect silver from oxidation. The other half is covered with polydimethylsiloxane (PDMS) polymer to detect the temperature variations. The proposed sensor is optimized numerically, and the optimum structure provides an excellent sensitivity of 208 deg/RIU, thanks to the use of the ZnSe layer, which is greater than double the reported dual-channel prism-based sensor in thickness. The polymer channel shows high sensitivity to the temperature variations of − 0.125 deg/°C, which is nearly 10 times the response of the RI channel to temperature variations. The data obtained from the polymer channel is used to compensate for the thermal perturbations of the sensing medium RI, and at the same time, to monitor the increments of the temperature in order to avoid reaching the DNA melting temperature. A mathematical expression is provided to consider the effect of the temperature variations on the RI of the sensing medium to get a better accurate detection process. The DNA hybridization detection of HIV is theoretically discussed in detail starting from the preparation of the sensing medium with the different ingredients until the hybridization between probe and complementary target DNA (ct-DNA) molecules.

In-situ label-free temperature-compensated DNA hybridization detection with a fiber-optic interferometer and a fiber Bragg grating for microfluidic chip

We demonstrated a temperature-compensated optofluidic DNA biosensor available for microfluidic chip. The optofluidic sensor was composed of an interferometer and a fiber Bragg grating (FBG) by femtosecond laser direct writing micro/nano processing technology. The sensing arm of the interferometer was suspended on the inner wall of the microchannel and could directly interact with the microfluid. With the immobilization of the single stranded probe DNA (pDNA), this optofluidic biosensor could achieve specific detection of single stranded complementary DNA (scDNA). The experimental results indicated that a linear response within 50 nM and the detection limit of 1.87 nM were achieved. In addition, the optofluidic biosensor could simultaneously monitor temperature to avoid temperature fluctuations interfering with the DNA hybridization detection process. And, the optofluidic detection channel could achieve fast sample replacement within 10 s at a flow rate of 2 μL/min and sample consumption only required nanoliters. This optofluidic DNA biosensor had the advantages of label-free, good specificity, dual parameter detection, low sample consumption, fast response, and easy repeatable preparation, which was of great significance for the field of DNA hybridization research and solving the temperature sensitivity problem of biosensors and had good prospects in biological analysis.

Detection of Interleukin-6 Protein Using Graphene Field-Effect Transistor.

Universal platforms to analyze biomolecules using sensor devices can address critical diagnostic challenges. Sensor devices like electrical-based field-effect transistors play an essential role in sensing biomolecules by charge probing. Graphene-based devices are more suitable for these applications. It has been previously reported that Graphene Field-Effect Transistor (GFET) devices detect DNA hybridization, pH sensors, and protein molecules. Graphene became a promising material for electrical-based field-effect transistor devices in sensing biomarkers, including biomolecules and proteins. In the last decade, FET devices have detected biomolecules such as DNA molecules, pH, glucose, and protein. These studies have suggested that the reference electrode is placed externally and measures the transfer characteristics. However, the external probing method damages the samples, requiring safety measurements and a substantial amount of time. To control this problem, the graphene field-effect transistor (GFET) device is fabricated with an inbuilt gate that acts as a reference electrode to measure the biomolecules. Herein, the monolayer graphene is exfoliated, and the GFET is designed with an in-built gate to detect the Interleukin-6 (IL-6) protein. IL-6 is a multifunctional cytokine which plays a significant role in immune regulation and metabolism. Additionally, IL-6 subsidizes a variability of disease states, including many types of cancer development, and metastasis, progression, and increased levels of IL-6 are associated with a higher risk of cancer and can also serve as a prognostic marker for cancer. Here, the protein is desiccated on the GFET device and measured, and Dirac point shifting in the transfer characteristics systematically evaluates the device's performance. Our work yielded a conductive and electrical response with the IL-6 protein. This graphene-based transducer with an inbuilt gate gives a promising platform to enable low-cost, compact, facile, real-time, and sensitive amperometric sensors to detect IL-6. Targeting this pathway may help develop treatments for several other symptoms, such as neuromyelitis optica, uveitis, and, more recently, COVID-19 pneumonia.

Whispering Gallery Mode Microresonator Sensor Integrated in Exposed Core Fiber for Label-Free DNA Hybridization Detection

A novel optical fiber sensor using exposed-core fiber (ECF) to excite whispering gallery modes (WGMs) within a high refractive index barium titanate glass microsphere is proposed for achieving label-free real-time specific DNA detection. The microsphere is encapsulated into the exposed channel of the ECF allowing for physical stability while excited WGMs via the evanescent field. The structure enables the sensing area to be exposed to a large amount of aqueous solution and better contact with the sample to be analyzed. Using a transmission measurement, a high Q-factor in the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> is obtained in an aqueous environment. To the best of our knowledge, this is the best Q-factor level obtained by the in fiber WGM sensor in an aqueous environment. Specific sequences of probe DNA are then bound to the surface of the microsphere so that specific detection of complementary DNA can be realized by tracking the wavelength shift the WGM resonance. Experimental results show a red shift of 5.6 pm for complementary DNA hybridization detection and less than 1 pm fluctuation for non-complementary DNA detection. The portable integrated sensor with miniature size has great potential for aqueous environmental sensing applications in the fields of diseases diagnostics, chemical analysis, and environmental protection.

The Optimization of a Label-Free Electrochemical DNA Biosensor for Detection of Sus scrofa mtDNA as Food Adulterations

Fast, sensitive, and easy-to-use methods for detecting DNA related to food adulteration, health, religious, and commercial purposes are evolving. In this research, a label-free electrochemical DNA biosensor method was developed for the detection of pork in processed meat samples. Gold electrodeposited screen-printed carbon electrodes (SPCEs) were used and characterized using SEM and cyclic voltammetry. A biotinylated probe DNA sequence of the Cyt b S. scrofa gene mtDNA used as a sensing element containing guanine substituted by inosine bases. The detection of probe-target DNA hybridization on the streptavidin-modified gold SPCE surface was carried out by the peak guanine oxidation of the target using differential pulse voltammetry (DPV). The optimum experimental conditions of data processing using the Box–Behnken design were obtained after 90 min of streptavidin incubation time, at the DNA probe concentration of 1.0 µg/mL, and after 5 min of probe-target DNA hybridization. The detection limit was 0.135 µg/mL, with a linearity range of 0.5–1.5 µg/mL. The resulting current response indicated that this detection method was selective against 5% pork DNA in a mixture of meat samples. This electrochemical biosensor method can be developed into a portable point-of-care detection method for the presence of pork or food adulterations.

Genosensing on a 3D-printed nanocarbon electrode

In this paper we present the characterization of 3D-printed nanocarbon electrodes (3DnCes) and their application in electrochemical enzyme-linked detection of DNA hybridization. The approach takes advantage of a facile procedure based on adsorption of target DNA on the electrode surface followed by hybridization with a biotinylated probe and binding of streptavidin–alkaline phosphatase conjugate. The alkaline phosphatase converts 1-naphthyl phosphate in the background electrolyte into electrochemically oxidizable 1-naphthol, which is subsequently detected using linear sweep voltammetry. The preparation, characterization, and analytical performance of the 3DnCes are reported. The results show the applicability of such 3DnCes in detection of target DNA hybridization specifically with the complementary biotinylated probe, and indicate the potential of 3D printed electrodes for use in various bioanalytical approaches.

In-situ detection scheme for EGFR gene with temperature and pH compensation using a triple-channel optical fiber biosensor

An advanced multi-parameter optical fiber sensing technology for EGFR gene detection based on DNA hybridization technology is demonstrated in this paper. For traditional DNA hybridization detection methods, temperature and pH compensation can not be realized or need multiple sensor probes. However, the multi-parameter detection technology we proposed can simultaneously detect complementary DNA, temperature and pH based on a single optical fiber probe. In this scheme, three optical signals including dual surface plasmon resonance signal (SPR) and Mach-Zehnder interference signal (MZI) are excited by binding the probe DNA sequence and pH-sensitive material with the optical fiber sensor. The paper proposes the first research to achieve simultaneous excitation of dual SPR signal and Mach-Zehnder interference signal in a single fiber and used for three-parameter detection. Three optical signals have different sensitivities to the three variables. From a mathematical point of view, the unique solutions of exon-20 concentration, temperature and pH can be obtained by analyzing the three optical signals. The experimental results show that the exon-20 sensitivity of the sensor can reach 0.07 nm nM−1, and the limit of detection is 3.27 nM. The designed sensor gives a fast response, high sensitivity, and low detection limit, which is important for the field of DNA hybridization research and for solving the problems of biosensor susceptibility to temperature and pH.

Sensing Beyond the Debye Length: Development of a 32 × 32 CMOS DNA Sensor Array

This letter reports a large complementary metal-oxide semiconductor DNA array with more than 1000 sensors to demonstrate sensitive and wide-range detection under strong Debye charge screening. To this end, we electrically modulated the extended-gate field effect transistors (FETs) under study to extend the Debye length and compare results at different frequencies. Operation at higher frequencies showed better DNA sensitivity than at low frequencies. The array exhibited a pH sensitivity of 38 mV/pH in floating-gate potential changes. Detection of DNA hybridization showed a sensitivity of 19 mV/log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sub> [DNA] in 1× phosphate buffered saline from 0.1 fM to 10 nM at 15 MHz.

Light-Amplified CISS-Based Hybrid QD-DNA Impedimetric Device for DNA Hybridization Detection.

We design and build a novel light-amplified electrochemical impedimetric device based on the CISS effect to detect DNA hybridization using a hybrid quantum dot (QD)-DNA monolayer on a ferromagnetic (FM) Ni/Au thin film for the first time. Using spin as a detection tool, the current research considers the chiral-induced spin selectivity (CISS) phenomenon. After injecting a spin current into the QD-DNA system with opposite polarities (up and down), the impedimetric device revealed a large differential change in the charge-transfer resistance (ΔRct) of ∼100 ohms for both spins. Nearly, a threefold increase in the ΔRct value to ∼270 ohms is observed when light with a wavelength of 532 nm is illuminated on the sample, owing to the amplified CISS effect. The yield of spin polarization as extracted from the Nyquist plot increases by a factor of more than 2 when exposed to light, going from 6% in the dark to 13% in the light. The impact of light on the CISS effect was further corroborated by the observation of the spin-dependent asymmetric quenching of photoluminescence (PL) in the same hybrid system. These observations are absent in the case of a noncomplementary QD-DNA system due to the absence of a helical structure in DNA. Based on this, we develop a spin-based DNA hybridization sensor and achieve a limit of detection of 10 fM. These findings open a practical path for the development of spin-based next-generation impedimetric DNA sensors and point-of-care devices.