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.

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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.