DNA Nucleobases Sensing by Localized Plasmon Resonances in Graphene Quantum Dots with Nanopore: A First Principle Approach

Abstract

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.

Plasmonic Biosensors for Single-Molecule Biomedical Analysis

“…Recent technological advancements have permitted the emergence of DNA sequencing as a viable approach to obtain specific information about the disease onset and progress. Specifically, the recognition of single nucleotides, adenine (A), thymine (T), cytosine (C), and guanine (G), is the primary aim of the synthesis-sequencing strategies [ 26 , 34 , 35 , 45 , 46 ]. In this vein, nanopore biosensors have proved to be compatible with the determination of DNA nucleotides at the single-molecule level with sufficient sensitivity and accuracy.…”

“…For example, single molecule analysis of nucleic acids using nanopores present various limitations due to the low control of certain parameters such as high salt conditions, high temperature and pH [ 34 , 35 , 36 ]. Likewise, the limited residence time of DNA nucleotides inside the nanopore and the elevated ionic current noise are also potential drawbacks of nanopore sensors [ 45 ].…”

“…Another singular strategy made use of experimental calculations to study the effects of the optical absorption spectrum of DNA bases on the interband plasmons of graphene quantum dots [ 35 ]. The work also investigated the sensitivity and selectivity factors as well as the association between the insertion of DNA bases and the optical excitation of graphene quantum dots within nanopores ( Figure 4 ).…”

“…The classification rate is the percentage of the noisy samples, which are classified correctly to a type of DNA nucleobase. Adapted with permission from Abasifard et al [ 35 ] Copyright © 2019 American Chemical Society.…”

An electro-optical system for improving graphene nanopore DNA Sequencing

“…There are still many other challenges such as low sensitivity, low selectivity, fast translocation speed, and slow sensing mechanisms to achieve errorless sequencing and single-nucleotide resolution [6][7][8]. Localized and intense plasmons in two-dimensional materials such as graphene and MoS 2 are currently considered a candidate for rapid nanopore DNA sequencing [9,10]. Consequently, plasmonic fields make an enhanced local force that can control DNA translocation speed through the nanopore [11][12][13].…”