Nano-plasmonic-based structures for DNA sequencing

Abstract

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.

Petahertz-frequency plasmons in graphene nanopore and their application to nanoparticle sensing

“…The real-space grid for FDTD is about 0.005 nm in all directions. The FDTD results are in good agreement with the results of electric-eld distribution and eld enhancements previously reported in [11,23]. The timestep is 0.1 fs and simulations are done for 1000 fs.…”

“…We obtain longitudinal and transverse modes by setting the direction of the x axis and the polarization direction (direction of the electric eld) to zero or 90 , respectively ( Figure 2). Our simulation results are provided for the transverse mode, because in monolayer graphene, the transverse mode dominates and the longitudinal mode can be neglected [11,12,24]. As shown in Figure 4, the SPR spectra have one dominant mode (M 1 ) and corresponding energy decreases from 15.7 to 14.1 eV when the nanosheet length increases from 1 to 14 nm.…”

“…Recently, graphene has been utilized as pressure sensor [8], dipolar-antenna in the terahertz frequency range [9], and membrane for DNA translocation detection [10]. Surface Plasmon Resonances (SPR) and plasmon propagation in graphene have attracted attention due to their great application in nano-photonics, biology, sensing, gap detection, and DNA sensing [8,[11][12][13]. Di erent types of the plasmon in graphene are: (1) collective-intraband excitation of the conductance electrons with 0-3 eV energy, (2) collective-interband excitations of the valance electrons with 4-12 eV energy, and (3) collective-interband excitations of all valence electrons ( + plasmon) with 14-33 eV energy [14][15][16][17][18][19][20][21].…”

“…The SPR properties of interband plasmon of monolayer and multilayer graphene nanodiscs show strong small-size and eld-enhancement e ects [24]. Also, the interband plasmon resonance behaviour for the graphene nanosheets and graphene nanopores, and their application to DNA nucleotide sensing have been investigated [11,12]. The SPR properties of the interband plasmons in graphene nanopore can be used in near future as a new methodology for DNA sequencing or other single-molecule detection mechanisms [11,12].…”

“…Also, the interband plasmon resonance behaviour for the graphene nanosheets and graphene nanopores, and their application to DNA nucleotide sensing have been investigated [11,12]. The SPR properties of the interband plasmons in graphene nanopore can be used in near future as a new methodology for DNA sequencing or other single-molecule detection mechanisms [11,12]. This is because of the fact that interband and + plasmons in graphene are strongly localized and plasmon wavelength is about 0 =200, where 0 is the free-space wavelength equal to 250 and 80 nm for the interband and + plasmons in graphene, respectively.…”