We propose novel nano-plasmonic-based structures for rapid sequencing of DNA molecules. The optical properties of DNA nucleotides have notable differences in the ultraviolet (UV) region of light. Using nanopore, bowtie, and bowtie-nanopore compound structures, probable application of the surface plasmon resonance (SPR) in DNA sequencing is investigated by employing the discrete dipole approximation method. The effects of different materials like chromium (Cr), aluminum (Al), rhodium (Rh), and graphene (Gr) are studied. We show that for Cr/Al/Gr/Rh, the nucleotide presented shifts the SPR spectra for the nanopore 1/29/5/34 to 14/39/15/67 nm, bowtie 8/2/49/38 to 31/20/79/55 nm, and bowtie-nanopore compound 25/77/5/16 to 80/80/22/39 nm. The Cr-based compound structure shows excellent sensitivity and selectivity which can make it a promising methodology for DNA sequencing.
We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (
MoS
2
) nanopores. In this method, GO and
MoS
2
is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and
MoS
2
we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and
MoS
2
nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or
MoS
2
nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.
We propose a potential sensing mechanism for DNA nucleotides by using interband π surface plasmon resonance (SPR) of graphene nanopore. The SPR and field enhancement properties are investigated by employing discrete dipole approximation (DDA) and finitedifference-time-domain (FDTD) methods, respectively. For graphene nanopores smaller than 10 nm in length, increasing the pore diameter redshifts the SPR peak wavelength and for larger sheets, it is rather unchanged by variation of the pore diameter. Presentation of a single nucleotide to the pore significantly changes SPR properties of the graphene nanopore and each nucleotide has a unique SPR properties. Each nucleotide induces 2 nm to 12 nm shift in the peak wavelengths of each SPR modes and if we consider simultaneously all the modes, type of the presented DNA nucleotide can be clearly determined. Our results show that the small-sizesensitive interband π plasmon in graphene nanopore is probably applicable as a new sensing mechanism for DNA nucleotides.
Taking advantage
of a nanopore-based DNA sequencing concept, a
variety of recognition approaches have been intensively explored.
We have recently presented a potential mechanism for DNA sequencing
based on interband π plasmons of graphene nanopores. In this
paper, a realistic ab initio analysis of the proposed method based
on π and also π+σ plasmons is investigated making
use of graphene quantum dots (GQDs) with a nanopore. The plasmonic
properties are studied by post processing the density functional theory
(DFT) calculations. The first principle study provides an unprecedented
fully theoretical description of the proposed structure. The critical
features such as passivating atoms, structure relaxation, DNA-graphene
interactions, and nucleobase rotations are considered, which result
in a more accurate and realistic description of the presented method.
Our calculations show a 0.04 to 0.28 eV shift to the energy of the
plasmonic modes related to each inserted nucleobase in the nanopore
of GQD, which demonstrates the promising potential of the method.
Studying DNA rotations proves that the type of inserted nucleobase
can be clearly determined under this condition. The proposed method
can truly classify any unknown DNA bases into one of the possible
classes adenine, cytosine, guanine, and thymine if the signal-to-noise
ratio is greater than 12 dB. Our first principle study reveals that
interband plasmons in GQD nanopores are applicable as a new sequencing
mechanism for DNA nucleobases.
where he designed standard single power supply building 1957, and has done graduate work at the Uni-block circuits for automotive and industrial applications. He is now inversity of California, Los Angeles. volved with data acquisition systems which will interface with micro-From 1957 to 1963, he was employed as a processors and currently is working on the design of a standard line of Development Engineer with Motorola Systems A/D converters. He has over 35 patents on linear integrated circuits
We propose a novel, to the best of our knowledge, plasmonic-based methodology for the purpose of fast DNA sequencing. The interband surface plasmon resonance and field-enhancement properties of graphene nanopore in the presence of the DNA nucleobases are investigated using a hybrid quantum/classical method (HQCM), which employs time-dependent density functional theory and a quasistatic finite difference time domain approach. In the strong plasmonic–molecular coupling regime where the plasmon and DNA absorption frequencies are degenerated, the optical response of DNA molecule in the vicinity of the nanopore is enhanced. In contrast, when the plasmon and nucleobases resonances are detuned the distinct peaks and broadening of the molecular resonances represent the inherent properties of the nucleobase. Due to the different optical properties of DNA nucleobases in the ultraviolet (UV) region of light, the signal corresponding to the replacement of nucleobases in a DNA block can be determined by considering the differential absorbance. Results show the promising capability of the present mechanism for practical DNA sequencing.
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