Detection Of DNA Bases Research Articles

Detection of DNA Bases via Field Effect Transistor of Graphene Nanoribbon With a Nanopore: Semi-Empirical Modeling.

DNA sequencing techniques are critical in order to investigate genes' functions. Obtaining fast, accurate, and affordable DNA bases detection makes it possible to acquire personalized medicine. In this article, a semi-empirical technique is used to calculate the electron transport characteristics of the developed z-shaped graphene device to detect the DNA bases. The z-shaped transistor consists of a pair of zigzag graphene nanoribbon (ZGNR) connected through an armchair graphene nanoribbon (AGNR) channel with a nanopore where the DNA nucleobases are positioned. Non-equilibrium Green's function (NEGF) integrated with semi-empirical methodologies are employed to analyze the different electronic transport characteristics. The semi-empirical approach applied is an extension of the extended Hückel (EH) method integrated with self-consistent (SC) Hartree potential. By employing the NEGF+SC-EH, it is proved that each one of the four DNA nucleobases positioned within the nanopore, with the hydrogen passivated edge carbon atoms, results in a unique electrical signature. Both electrical current signal and transmission spectrum measurements of DNA nucleobases inside the device's pore are studied for the different bases with modification of their orientation and lateral translation. Moreover, the electronic noise effect of various factors is studied. The sensor sensitivity is improved by using nitrogen instead of hydrogen to passivate the nanopore and by adding a dual gate to surround the central semiconducting channel of the z-shaped graphene nanoribbon.

Detection of DNA bases and environmentally relevant biomolecules and monitoring ssDNA hybridization by noble metal nanoparticles decorated graphene nanosheets as ultrasensitive G‐SERS platforms

AbstractSurface‐enhanced Raman scattering (SERS) and graphene‐mediated surface‐enhanced Raman scattering (G‐SERS) are attractive analytical techniques for the detection of chemical and biological molecules at a single‐molecule level registering their chemical fingerprints. Graphene‐based surface enhancement (or G‐SERS) boosted traditional SERS phenomenon producing signal enhancement from both electromagnetic (EM) and chemical enhancement (CE) mechanisms. Thus, graphene oxide (GO) nanosheets coated with silver (Ag [30 nm]) and gold (Au [40 nm]) nanoparticles smart array platforms, for direct detection and differentiation of DNA bases, namely, adenine (A), cytosine (C), guanine (G), thymine (T), and environmental relevant β‐carotene (β‐C) and malachite green (MG) biomolecules, are developed. The size and interparticle gap were controlled via dispersion and loading on GO surface to achieve optimal enhancement factors. The morphology of these substrates was characterized by scanning electron microscopy and atomic force microscopy. The Raman spectra consisted of discrete bands occurring at (A: 732.8 cm−1; C: 792 cm−1; G: 658 cm−1; T: 796 cm−1; β‐C: 1416 cm−1; MG: 1174 cm−1) that are characteristic of molecular modes of vibration and serve as chemical fingerprint of three‐dimensional structure, intramolecular interaction and steady‐state dynamics, of biomolecule ensemble. The GO‐decorated nanoparticles are capable of sensitive biomolecular detection over a broad concentration range 100 nM to 100 μM with limit of detection (LOD) noted at <1 ppm for A, C, G, T, β‐C, and MG. Moreover, the experimental results illustrated five to six orders of magnitude signal enhancement in the following order: GO/Ag30 > GO/Au40 > Ag30 > Au40 > GO. Moreover, ssDNA probe and complementary target C‐ssDNA were monitored simultaneously during hybridization on the same substrates assigned confidently to base, local chemical structure, and global conformation of resulting dsDNA. The experimental findings suggest a strong GO‐nanoparticle coupling leading to interfacial orbital hybridization (charge transfer) and polarization affected by biomolecule orientation, and it will help in designing ultrasensitive platforms covering range of inorganic nanoparticles and nanostructured surfaces for a wealth of biomedicine and environmental applications.

Detection of DNA Bases Using Fe Atoms and Graphene**Supported by the National Natural Science Foundation of China under Grant Nos 51301119 and 11204201, and the Natural Science Foundation for Young Scientists of Shanxi Province under Grant No 2013021010-1.

The adsorption of DNA bases on a magnetic probe composed of Fe atoms and graphene is studied by using first-principles calculations. The stability of geometry, the electronic structure and magnetic property are investigated. The results indicate that four DNA bases, i.e., adenine, thymine, cytosine and guanine, can all be adsorbed on the probe solidly. However, the magnetic moments of the composite structure can be observed only when adenine adsorbs on the probe. In the cases of the adsorption of the other three bases, the magnetic moments of the composite structure are zero. Based on the significant change of magnetic moment of the composite structure, adenine can be distinguished conveniently from thymine, cytosine and guanine. This work may provide a new way to detect DNA bases.

Electrochemical Treatment of Glassy Carbon for Label‐Free Detection of DNA Bases and Neurotransmitters

AbstractElectrochemically reduced glassy carbon (r‐GC) showed a superior electrochemical sensing performance, compared to oxidized GC (ox‐GC) and untreated GC for the oxidation of 4 DNA bases and neurotransmitters (epinephrine, norepinephrine and serotonin). r‐GC exhibited not only the largest current intensities of all redox biomolecules, but also displayed an excellent selectivity in detecting coexisting redox biomolecules. The enhanced performance of r‐GC was attributed to the improved surface cleanliness of electrode and its catalytic surface functional groups. The results presented herein imply that simple electrochemical treatments are a viable method to produce sensitive and selective electrodes for label‐free biosensing.

Single-Layer Molebdenum Disulphide Nanopore for DNA Detection

Nanopore-based DNA sequencing has paved the way toward fast, label-free and high-resolution recognition and detection of DNA bases. Solid-state and biological nanopores have low signal-to-noise ratio (SNR) ( 5 nm) to be able to distinguish between bases distinctly. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ∼3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies (i.e., nanopore and nanochannel). DNA sticks to the surface of graphene nanopore which is the origin of noise generation. MoS2 surface shows non-sticky behavior and bases translocate through the pore without sticking. MoS2 nanopore also shows four distinguishable ionic current signals for single-nucleobase detection with low noise. In addition, a single-layer MoS2 shows a characteristic change/response in the total density of states for each base. The band gap of MoS2 is significantly changed compared to other nanomaterials (e.g., graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.

Automation Highlights from the Literature

Automation Highlights from the Literature

DNA base detection using a single-layer MoS2.

Nanopore-based DNA sequencing has led to fast and high-resolution recognition and detection of DNA bases. Solid-state and biological nanopores have low signal-to-noise ratio (SNR) (< 10) and are generally too thick (> 5 nm) to be able to read at single-base resolution. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ∼3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies (i.e., nanopore and nanochannel). A MoS2 nanopore shows four distinct ionic current signals for single-nucleobase detection with low noise. In addition, a single-layer MoS2 shows a characteristic change/response in the total density of states for each base. The band gap of MoS2 is significantly changed compared to other nanomaterials (e.g., graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.

Detection of DNA Bases and Oligonucleotides in Plasmonic Nanoslits Using Fluidic SERS

Raman spectroscopy is a widely used vibrational spectroscopic technique to identify and study chemical compounds. The signal can be strongly enhanced in the presence of metal nanostructures resulting in so-called surface-enhanced Raman scattering (SERS). Here, we describe the use of SERS for the molecular characterization of DNA molecules inside a nanoslit across a thin, metal-coated membrane. Nanoslits with two different dimensions were examined. More specifically, relatively long nanoslits (over 700 nm) with a strong, broad plasmonic coupling mode as well as short nanoslits (100 nm) with a strong Fabry-Pérot resonance for a specific wavelength. Both geometries were fabricated using standard lithographic processes and were coated with gold to enable the excitation of surface plasmons, needed for SERS. Using electrophoresis to actuate the analytes across the nanoslits, we were able to record SERS spectra of a typical DNA base, namely adenine. Similarly, short DNA oligonucleotides were also successfully detected. It is expected that the nanoslit-based fluidic SERS will become a promising real-time detection tool, especially for DNA.