Identifying Single-Stranded DNA by Tuning the Graphene Nanogap Size: An Ionic Current Approach

Abstract

Solid nanopore-based deoxyribonucleic acid (DNA) sequencing has led to low-cost, fast, reliable, controlled, and amplified or label-free and high-resolution recognition and identification of DNA nucleotides. Solid-state materials and biological nanopores have a low signal-to-noise ratio (SNR) and generally are too thick to read at single-nucleotide resolution. The issue with solid-state nanopores is that the DNA strands stick to the nanopore sides and on the surface during the translocation process. The coexistence of DNA nucleotides on the surface and the nanopore sides will complicate the ionic current signals, making nucleotide detection difficult. Therefore, different sized nanogaps can be promising to overcome some of these issues. Using all-atom molecular dynamics (MD) simulations, we have studied the translocation of single-stranded (ss) DNA through solid-state nanogaps embedded in a graphene membrane device. A nucleotide-specific DNA sequencing technique is proposed based on unique differences in the ionic current responses for all the four ssDNA nucleotides (dAMP16, dGMP16, dTMP16, and dCMP16). As the individual homogeneous ssDNA translocate through the nanogaps, characteristic changes are observed in the ionic current. Our results show that ssDNA nucleotides can translocate through the proposed graphene nanogap devices by applying an external electric field. In addition, the sticking issue can be resolved using graphene nanogaps during the ssDNA translocation processes. Therefore, the significant difference in ionic current sensitivity and the translocation event/time yielded by the graphene nanogap-based devices reveal possibilities for utilizing it for ultrafast nanogap-based DNA sequencing.

The Merits of a Folded Graphene Nanodevice for Reliable DNA Sequencing

“…Furthermore, toward the development of next-generation DNA sequencing devices which are capable of reading DNA or an entire human genome inexpensively and conclusively leading toward personalized medicine, the role of low-dimensional (2D) materials has emerged into the picture with promising potential, and important research efforts have been dedicated into their development in the past few years. − , Interestingly, special attention has been devoted to discovering graphene-based nanodevices, which include graphene nanopores/nanogaps, graphene nanoribbons, ,,,− ,,,− and carbon nanotubes (CNTs) ,, as potential nanoelectrode materials. Graphene nanopores/nanogaps are outstanding solid-state materials to achieve single-nucleobase resolution due to their one-atom thickness. ,− Traversi and co-workers have found that the solid-state materials based nanopore combined with the graphene nanoribbon could be used as a nanodevice for the individual identification of DNA nucleobases .…”

Conductance and tunnelling current characteristics for individual identification of synthetic nucleic acids with a graphene device

“…6 The experimental proof of artificial genetic characters presents a challenge to a low-cost, label-and amplification-free, rapid, and controlled next-generation sequencing (NGS) technique such as nanogap, nanopore, and nanochannel-based smart sensors for healthcare applications. 3,4,[7][8][9][10][11][12][13][14][15][16] In NGS, DNA nucleobases can electrophoretically be passed through nanogaps or nanopores, which changes the ionic or tunneling/ transverse currents, which can be used in real-time sequencing. On the other hand, nanochannel-based devices are also quite promising for NGS applications.…”