A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS2 Nanopores

Vahid Faramarzi,Bashir Fotouhi,Mostafa Abasifard,Vahid Ahmadi

doi:10.1038/s41598-019-41165-6

Abstract

We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 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 MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 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 MoS2 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.

Highlights

Rapid DNA sequencing methods are excellent tools for the growing field of personalized medicine and have been developed theoretically and experimentally[1,2,3,4,5,6,7]
It is assumed that the nanopore, with a diameter of 1.5 nm, to be symmetrically made in the center of graphene oxide (GO) or MoS2 nanopore and DNA molecule passes through the nanopore
Absorbance peaks of the quantum dot (QD) and DNA nucleobases complex are similar to the peaks of the bare A, C, G and T nucleobases reported by Tsolakidis et al.[23]

Summary

Introduction

Rapid DNA sequencing methods are excellent tools for the growing field of personalized medicine and have been developed theoretically and experimentally[1,2,3,4,5,6,7]. We propose and analyze a novel concept for sequencing DNA molecules by absorption and emission properties of fluorescent materials. The impact of presented DNA nucleobases at the nanopores on the photoabsorption spectra, band-gap energies, electric field enhancements and emission wavelengths of GO and MoS2 nanopores is investigated. Regarding the excitation wavelength dependent emission properties of GO and MoS2 nanosheets, emitted light wavelengths from the GO and MoS2 nanopores are calculated and analyzed in the presence of all types of the DNA nucleobases, individually. The influence of presented DNA nucleobase at the nanopore on the optical properties of the nanopore membrane material is investigated. The selectivity factor which is the capability of distinguishing between two different nucleobases is defined For this purpose, we search the maximum difference between absorbance peaks in absorption spectra of the membrane nanopore + DNA nucleobases complexes. The thickness of GO and MoS2 nanopores are assumed to be 1 and 0.65 nm, respectively

Objectives

Methods

Results

Conclusion