Functionalized carbon nanotube electrodes for controlled DNA sequencing

A Step toward Amino Acid-Labeled DNA Sequencing: Boosting Transmission Sensitivity of Graphene Nanogap

Existing obstacles in next-generation DNA sequencing techniques, for instance, high noise, high translocation speed, and configurational fluctuations, call for approaches capable of reaching the goal and accelerating the process of personalized medicine development. The labeling nucleotide approach has the potential to overcome these barriers and boost the recognition sensitivity of a solid-state nanodevice. In this theoretical report, the first-principles density functional theory calculations have been employed to study the role of three different labels, tyrosine (Tyr), aspartic acid (Asp), and arginine (Arg), for labeling DNA nucleotides and study their effect in rapid and controlled DNA sequencing at atomic resolution. Remarkable differences in interaction energy values are noticed in all three cases of differently labeled nucleotides. The zero-bias transmission spectra confirm that proposed labels have the ability to detect the individual nucleotide, amplifying the tunneling current sensitivity by several orders of magnitude. The current-voltage characteristics of Arg-labeled nucleotides are found to be promising for single nucleotide recognition even at a very low bias voltage of 0.1 V.

Towards a graphene semi/hybrid-nanogap: a new architecture for ultrafast DNA sequencing

The tremendous upsurge in the research of next-generation sequencing (NGS) methods has broadly been driven by the rise of the wonder material graphene and continues to dominate the futuristic approaches for fast and accurate DNA sequencing. The success of graphene has also triggered the search for many new potential NGS methods capable of ultrafast, reliable, and controlled DNA sequencing. The present study delves into the potential of a new NGS architecture utilizing graphene, namely, a 'semi/hybrid-nanogap' for the identification of DNA nucleobases with single-base resolution. In the framework of first-principles density functional theory methods, we have calculated the transmission function and current-voltage (I-V) characteristics which are of particular significance for DNA sequencing applications. It is noted that the interaction energy values are significantly reduced compared to the previously reported graphene nanodevices, which can lead to a controlled translocation during experimental measurements. Based on the transmission function, each nucleobase can be identified with pertinent sensitivity. It is noticed that the use of highly conductive nucleobase analogs can facilitate improved single nucleobase sensing by increasing the transmission sensitivity. Therefore, we believe that the present study opens up promising frontiers for sequencing applications.

Identification of DNA nucleotides by conductance and tunnelling current variation through borophene nanogaps

Rapid and inexpensive DNA sequencing is critical to biomedical research and healthcare for the accomplishment of personalized medicine. Solid-state nanopores and nanogaps have marshalled themselves in the fascinating paradigm of nano-research since the advent of its application in DNA sequencing by analyzing the quantum conductance and electric current signals. In this study, the feasibility of the considered borophene nanogaps for DNA sequencing purposes via the electronic tunnelling current approach was investigated by utilizing combined density functional theory with non-equilibrium Green's function (DFT-NEGF) techniques. The interaction energy (E_i) and the charge density difference (CDD) plots exploit the charge modulation around the nanogap edges due to the presence of each nucleotide. Our results revealed a distinct variation in the tunnelling conductance, as a characteristic fingerprint of each nucleotide at the Fermi level. The calculated tunnelling current variation across the nanogap under an applied bias voltage was also significant due to the effective coupling of nucleotides with the electrode edges. The current was in the picoampere (pA) range, which was fairly higher than the electrical background noise and also experimentally detectable by the canning tunnelling microscopy (STM) technique. Our findings demonstrated that in the borophene nanopore vs. nanogap scenario, the nanogap has several advantages and is a more promising nanobiosensor. Moreover, we also compared our results with various previous experimental and theoretical reports on nanogaps as well as nanopores for gaining better insights.

Conductance and tunnelling current characteristics for individual identification of synthetic nucleic acids with a graphene device

Based on combined density functional theory and non-equilibrium Green's function quantum transport studies, in the present work we have demonstrated the quantum interference (QI) effect on the transverse conductance of Hachimoji (synthetic) nucleic acids when placed between the oxygen-terminated zigzag graphene nanoribbon (O-ZGNR) nanoelectrodes. We theorize that the QI effect could be well preserved in π-π coupling between a target nucleobase molecule and the carbon-based nanoelectrodes. Our study indicates that the QI effect, such as anti-resonance or Fano-resonance, affects the variation of transverse conductance depending on the nucleobase conformation. Furthermore, a variation of up to 2-5 orders of magnitude is observed in the conductance upon rotation for all the nucleobases. The current-voltage (I-V) characteristics results suggest a distinct variation in the electronic tunnelling current across the proposed nanogap device for all five nucleobases with the applied bias voltage ranges from 0.1-1.0 V. The different rotation angles keep the distinct feature of the nucleobases in both transverse conductance and tunnelling current features. Both features could be utilized in an accurate synthetic DNA sequencing device.

Identifying Single-Stranded DNA by Tuning the Graphene Nanogap Size: An Ionic Current Approach

Solid nanopore-based deoxyribonucleic acid (DNA) sequencing has led to low-cost, fast, reliable, controlled, and amplified or label-free and high-resolution recognition and identification of DNA nucleotides. Solid-state materials and biological nanopores have a low signal-to-noise ratio (SNR) and generally are too thick to read at single-nucleotide resolution. The issue with solid-state nanopores is that the DNA strands stick to the nanopore sides and on the surface during the translocation process. The coexistence of DNA nucleotides on the surface and the nanopore sides will complicate the ionic current signals, making nucleotide detection difficult. Therefore, different sized nanogaps can be promising to overcome some of these issues. Using all-atom molecular dynamics (MD) simulations, we have studied the translocation of single-stranded (ss) DNA through solid-state nanogaps embedded in a graphene membrane device. A nucleotide-specific DNA sequencing technique is proposed based on unique differences in the ionic current responses for all the four ssDNA nucleotides (dAMP₁₆, dGMP₁₆, dTMP₁₆, and dCMP₁₆). As the individual homogeneous ssDNA translocate through the nanogaps, characteristic changes are observed in the ionic current. Our results show that ssDNA nucleotides can translocate through the proposed graphene nanogap devices by applying an external electric field. In addition, the sticking issue can be resolved using graphene nanogaps during the ssDNA translocation processes. Therefore, the significant difference in ionic current sensitivity and the translocation event/time yielded by the graphene nanogap-based devices reveal possibilities for utilizing it for ultrafast nanogap-based DNA sequencing.

Identifying DNA Nucleotides via Transverse Electronic Transport in Atomically Thin Topologically Defected Graphene Electrodes

Extended line defects in graphene (ELDG) sheets have been found to be promising for biomolecule sensing applications. By means of the consistent-exchange van der Waals density-functional (vdW-DF-cx) method, the electronic, structural, and quantum transport properties of the ELDG nanogap setup has been studied when a DNA nucleotide molecule is positioned inside the nanogap electrodes. The interaction energy (E_i) values indicate charge transfer interaction between the nucleotide molecule and electrode edges. The charge density difference plots reveal that charge fluctuates around the ELDG nanogap edges adjacent to the nucleotides. This charge redistribution grounds the modulation of electronic charge transport in the ELDG nanogap device. Further, we study the electronic transverse-conductance and tunnelling current-voltage (I-V) characteristics across two closely spaced ELDG nanogap electrodes using the density functional theory and the nonequilibrium Green's function methods when a DNA nucleotide is translocated through the nanogap. Our outcomes indicate that the ELDG nano gap device could allow sequencing of DNA nucleotides with a robust and consistent yield, giving the tunneling electric current signals that vary by more than 1 order of magnitude electric current (I) for the different DNA nucleotides. So, we predict that the ELDG nanogap-based tunneling device can be suitable for sequencing DNA nucleobases.

A high performance N-doped graphene nanoribbon based spintronic device applicable with a wide range of adatoms

Designing and fabricating nanosize spintronic devices is a crucial task to develop information technology of the future. However, most of the introduced spin filters suffer from several limitations including difficulty in manipulating the spin current, incapability in utilizing a wide range of dopants to provide magnetism, or obstacles in their experimental realization. Here, by employing first principles calculations, we introduce a structurally simple and functionally efficient spin filter device composed of a zigzag graphene nanoribbon (ZGNR) with an embedded nitrogenated divacancy. We show that the proposed system, possessing a robust ferromagnetic (FM) ordering, exhibits perfect half metallic behavior in the absence of frequently used transition metals (TMs). Our calculations also show that the suggested system is compatible with a wide range of adatoms including basic metals, metalloids, and TMs. It means that besides d electron magnetism originating from TMs, p electrons of incorporated elements of the main group can also cause half metallicity in the electronic structure of the introduced system. Our system exploiting the robustness of doping-induced FM ordering would be beneficial for promising multifunctional spin filter devices.