Tunable graphene quantum point contact transistor for DNA detection and characterization.

A graphene membrane conductor containing a nanopore in a quantum point contact geometry is a promising candidate to sense, and potentially sequence, DNA molecules translocating through the nanopore. Within this geometry, the shape, size, and position of the nanopore as well as the edge configuration influences the membrane conductance caused by the electrostatic interaction between the DNA nucleotides and the nanopore edge. It is shown that the graphene conductance variations resulting from DNA translocation can be enhanced by choosing a particular geometry as well as by modulating the graphene Fermi energy, which demonstrates the ability to detect conformational transformations of a double-stranded DNA, as well as the passage of individual base pairs of a single-stranded DNA molecule through the nanopore.

Gate-Modulated Graphene Quantum Point Contact Device for DNA Sensing.

In this paper, we present a computational model to describe the electrical response of a constricted graphene nanoribbon (GNR) to biomolecules translocating through a nanopore. For this purpose, we use a self-consistent 3D Poisson equation solver coupled with an accurate three-orbital tight-binding model to assess the ability for a gate electrode to modulate both the carrier concentration as well as the conductance in the GNR. We also investigate the role of electrolytic screening on the sensitivity of the conductance to external charges and find that the gate electrode can either suppress or enhance the screening of biomolecular charges in the nanopore depending on the value of its potential. Translocating a double-stranded DNA molecule along the pore axis imparted a large change in the conductance at particular gate voltages, suggesting that such a device can be used to sense translocating biomolecules and can be actively tuned to maximize its sensitivity.

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green's function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA via transverse electronic conductance can widen the potential use of graphene-based nanosensors for DNA detection.

Graphene quantum point contact transistor for DNA sensing.

By using the nonequilibrium Green's function technique, we show that the shape of the edge, the carrier concentration, and the position and size of a nanopore in graphene nanoribbons can strongly affect its electronic conductance as well as its sensitivity to external charges. This technique, combined with a self-consistent Poisson-Boltzmann formalism to account for ion charge screening in solution, is able to detect the rotational and positional conformation of a DNA strand inside the nanopore. In particular, we show that a graphene membrane with quantum point contact geometry exhibits greater electrical sensitivity than a uniform armchair geometry provided that the carrier concentration is tuned to enhance charge detection. We propose a membrane design that contains an electrical gate in a configuration similar to a field-effect transistor for a graphene-based DNA sensing device.

Detection and quantification of methylation in DNA using solid-state nanopores.

Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated in the presence of only a single bound protein, thereby giving a resolution of a single methylated CpG dinucleotide. The extent of methylation of a target molecule could also be coarsely quantified using this novel approach. This nanopore-based methylation sensitive assay circumvents the need for bisulfite conversion, fluorescent labeling, and PCR and could therefore prove very useful in studying the role of epigenetics in human disease.

Computational investigation of DNA detection using graphene nanopores.

Nanopore-based single-molecule detection and analysis have been pursued intensively over the past decade. One of the most promising applications in this regard is DNA sequencing achieved through DNA translocation-induced blockades in ionic current. Recently, nanopores fabricated in graphene sheets were used to detect double-stranded DNA. Due to its subnanometer thickness, graphene nanopores show great potential to realize DNA sequencing at single-base resolution. Resolving at the atomic level electric field-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics simulations, in principle, can achieve such resolution and are employed here to investigate the effects of applied voltage, DNA conformation, and sequence as well as pore charge on the translocation characteristics of DNA. We demonstrate that such simulations yield current characteristics consistent with recent measurements and suggest that under suitable bias conditions A-T and G-C base pairs can be discriminated using graphene nanopores.

Catheter-tip sensor to monitor production of hydrogen peroxide in small biosamples.

Recently, it was shown that antibodies in the presence of ultraviolet (UV) light give rise to singlet oxygen which ultimately leads to the production of hydrogen peroxide (H2O2). In this research, we are interested in understanding the role of H2O2 in T-cell activity during inflammation. Since the T-cell receptor has been shown to have the same oxidative catalytic potential as antibodies, we started experiments measuring H2O2 production in antibodies and T cells. After showing that a positively polarized Clark oxygen electrode can be used in measuring H2O2 production in antibodies and T-cells, it is the goal of the current study to characterize the use of a catheter-tip sensor under similar conditions. Our catheter has a platinum ring which acts as the anode and a silver/silver chloride tip which acts as the cathode. Although this newly designed amperometric biosensor works on the same principles of electrochemistry, its compact size equips us with the potential for in vivo use and small sample testing. Operating at a polarizing voltage of 0.7 Volts v/s Ag/AgCl, the bare sensor produced a current of 8 +/- 2 nA per microM H2O2 with a 10 seconds response time, over a range of 0-50 microM H2O2. For use with biosamples, we added a hydrophilic H2O2 permeable membrane, which reduced the electrode current to 0.48 +/- 0.1 nA/microM H2O2 and increased the response time to 2 minutes. On the other hand, the addition of the membrane improved the signal to noise ratio and the selectivity of the sensor. Using this sensor, we reproduced the light mediated H2O2 production which was recorded at the rate of 20 nM per minute for 1 milliliter of 6.7 microM rat IgG solution. We further discuss the usefulness, limitation and the future scope of this real time monitoring system for H2O2 research using small biosamples.