Zigzag phosphorene antidot nanoribbons (ZPANRs) for the detection of nucleobases: A DFT based study (original) (raw)
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arXiv (Cornell University), 2021
The ability to detect and discriminate DNA bases by reading it directly using simple and costeffective methods is an important problem whose solution can produce significant value for areas such as cancer and human genetic disorders. Two-dimensional (2D) materials have emerged as revolutionary materials for electronic DNA sequencing with strong potentials for fast, single-nucleotide direct-read DNA sequencing with a minimum amount of consumables. Among 2D materials, graphene is the most explored for DNA sequencing. This is due to its commercial availability. The major hindrance of graphene is its hydrophobicity, which causes DNA bases to stick to its surface, slowing down translocation speed, and making single-base discrimination difficult as multiple bases interact with graphene at any given time. It is therefore essential that other elemental 2D materials beyond graphene be investigated. Using density functional theory (DFT), we studied the electronic interaction of DNA bases physisorped onto the surface of nanoribbons from graphene, phosphorene, and silicene. By comparing the change in energy band gap, binding energy and density of states (DOS), we observe that phosphorene performs better than graphene and silicene for DNA sequencing using the physisorption modality.
Master Thesis, 2017
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Integrated nanoparticle–biomolecule systems for biosensing and bioelectronics
Biosensors and Bioelectronics, 2007
The similar dimensions of biomolecules such as enzymes, antibodies or DNA, and metallic or semiconductor nanoparticles (NPs) enable the synthesis of biomolecule-NP hybrid systems where the unique electronic, photonic and catalytic properties of NPs are combined with the specific recognition and biocatalytic properties of biomolecules. The unique functions of biomolecule-NP hybrid systems are discussed with several examples: (i) the electrical contacting of redox enzymes with electrodes is the basis for the development of enzymatic electrodes for amperometric biosensors or biofuel cell elements. The reconstitution of the apo-glucose oxidase or apo-glucose dehydrogenase on flavin adenine dinucleotide (FAD)-functionalized Au NPs (1.4 nm) associated with electrodes, or on pyrroloquinoline quinone (PQQ)-functionalized Au NPs (1.4 nm) associated with electrodes, respectively, yields electrically contacted enzyme electrodes. The aligned, reconstituted enzymes on the electrode surfaces reveal effective electrical contacting, and the glucose oxidase and glucose dehydrogenase reveal turnover rates of 5000 and 11,800 s −1 , respectively. (ii) The photoexcitation of semiconductor nanoparticles yields fluorescence with a wavelength controlled by the size of the NPs. The fluorescence functions of semiconductor NPs are used to develop a fluorescence resonance energy transfer (FRET) assay for nucleic acids, and specifically, for analyzing telomerase activity in cancer cells. CdSe-ZnS NPs are functionalized by a primer recognized by telomerase, and this is elongated by telomerase extracted from HeLa cancer cells in the presence of dNTPs and Texas-red-functionalized dUTP. The dye integrated into the telomers allows the FRET process that is intensified as telomerization proceeds. Also, the photoexcited electron-hole pair generated in semiconductor NPs is used to generate photocurrents in a CdS-DNA hybrid system associated with an electrode. A redox-active intercalator, methylene blue, was incorporated into a CdS-duplex DNA monolayer associated with a Au electrode, and this facilitated the electron transfer between the electrode and the CdS NPs. The direction of the photocurrent was controlled by the oxidation state of the intercalator. (iii) Biocatalysts grow metallic NPs, and the absorbance of the NPs provides a means to assay the biocatalytic transformations. This is exemplified with the glucose oxidase-induced growth of Au NPs and with the tyrosinase-stimulated growth of Au NPs, in the presence of glucose or tyrosine, respectively. The biocatalytic growth of the metallic NPs is used to grow nanowires on surfaces. Glucose oxidase or alkaline phosphatase functionalized with Au NPs (1.4 nm) acted as 'biocatalytic inks' for the synthesis of metallic nanowires. The deposition of the Au NP-modified glucose oxidase, or the Au NP-modified alkaline phosphatase on Si surfaces by dip-pen nanolithography led to biocatalytic templates, that after interaction with glucose/AuCl 4 − or p-aminophenolphosphate/Ag + , allowed the synthesis of Au nanowires or Ag nanowires, respectively.
2021
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, w...
Physical Review B, 2016
Structural, electronic, mechanical, and transport properties of two different types of phosphorene nanoribbons are calculated within the density functional theory and nonequilibrium Green's function formalisms. Armchair nanoribbons turn out to be semiconductors at all widths considered. Zigzag nanoribbons are metallic in their layerterminated structure, but undergo Peierls-like transition at the edges. Armchair nanoribbons have smaller Young's modulus compared to a monolayer, while zigzag nanoribbons have larger Young's modulus. Edge reconstruction further increases the Young's modulus of zigzag nanoribbons. A two-terminal device made of zigzag nanoribbons show negative differential resistance behavior that is robust with respect to edge reconstruction. We have also calculated the I-V characteristics for two nonzero gate voltages. The results show that the zigzag nanoribbons display strong p-type character.
Narrower Nanoribbon Biosensors Fabricated by Chemical Lift-off Lithography Show Higher Sensitivity
Wafer-scale nanoribbon field-effect transistor (FET) biosensors fabricated by straightforward top-down processes are demonstrated as sensing platforms with high sensitivity to a broad range of biological targets. Nanoribbons with 350 nm widths (700 nm pitch) were patterned by chemical lift-off lithography using high-throughput, low-cost commercial digital versatile disks (DVDs) as masters. Lift-off lithography was also used to pattern ribbons with 2 μm or 20 μm widths (4 or 40 μm pitches, respectively) using masters fabricated by photolithography. For all widths, highly aligned, quasi-one-dimensional (1D) ribbon arrays were produced over centimeter length scales by sputtering to deposit 20 nm thin-film In 2 O 3 as the semiconductor. Compared to 20 μm wide microribbons, FET sensors with 350 nm wide nanoribbons showed higher sensitivity to pH over a broad range (pH 5 to 10). Nanoribbon FETs functionalized with a serotonin-specific aptamer demonstrated larger responses to equimolar serotonin in high ionic strength buffer than those of microribbon FETs. Field-effect transistors with 350 nm wide nanoribbons functionalized with single-stranded DNA showed greater sensitivity to detecting complementary DNA hybridization vs 20 μm microribbon FETs. In all, we illustrate facile fabrication and use of large-area, uniform In 2 O 3 nanoribbon FETs for ion, small-molecule, and oligonucleotide detection where higher surface-to-volume ratios translate to better detection sensitivities.