DNA Sequencing by Hexagonal Boron Nitride Nanopore: A Computational Study

Abstract

The single molecule detection associated with DNA sequencing has motivated intensive efforts to identify single DNA bases. However, little research has been reported utilizing single-layer hexagonal boron nitride (hBN) for DNA sequencing. Here we employ molecular dynamics simulations to explore pathways for single-strand DNA (ssDNA) sequencing by nanopore on the hBN sheet. We first investigate the adhesive strength between nucleobases and the hBN sheet, which provides the foundation for the hBN-base interaction and nanopore sequencing mechanism. Simulation results show that the purine base has a more remarkable energy profile and affinity than the pyrimidine base on the hBN sheet. The threading of ssDNA through the hBN nanopore can be clearly identified due to their different energy profiles and conformations with circular nanopores on the hBN sheet. The sequencing process is orientation dependent when the shape of the hBN nanopore deviates from the circle. Our results open up a promising avenue to explore the capability of DNA sequencing by hBN nanopore.

Keywords: hexagonal boron nitride; molecular dynamics simulation; ssDNA sequencing.

Figure 1

Scheme of single-strand DNA (ssDNA) sequencing with hexagonal boron nitride (hBN) nanopore. The ssDNA is placed right above the hBN nanopore and perpendicular to the hBN sheet. The red, orange, pink and grey areas represent the adenine (A), thymine (T), cytosine (C) and guanine (G) nucleotides separately.

Figure 2

Evolution of binding energy between hBN and four basic nucleotides.

Figure 3

Evolution of binding energy between graphene and four basic nucleotides.

Figure 4

Contribution of van der Waals (vdW) and electrostatic interaction in the binding energy between hBN and four basic nucleotides.

Figure 5

Conformation of stretching process of ssDNA before passing through the hBN nanopore (a–d); Evolution of real-time process of passing-through the hBN nanopore (e–h); Evolution of real-time radius of gyration (i).

Figure 6

Hexagonal boron nitride (hBN) nanopores of different geometries and illustration of nucleotides passing through the nanopore: (a) circular nanopore; (b) elliptical nanopore.

Figure 7

Energy profile when ssDNA passed through the circular hBN nanopores. The energy peak values for different nucleotides are extracted from the energy profile.

Figure 8

Energy profile when ssDNA passes through the elliptical hBN nanopores. The energy peak values for different nucleotides are extracted from the energy profile.