Spontaneous DNA translocation through a van der Waals heterostructure nanopore for single-molecule detection

Abstract

Solid-state nanopore detection and sequencing of a single molecule offers a new paradigm because of its several well-recognized features such as long reads, high throughput, high precision and direct analyses. However, several key technical challenges are yet to be addressed, especially the abilities to control the speed and direct the translocation of the target molecules. In this work, using molecular dynamics (MD) simulations, we found a spontaneous translocation of single-stranded DNA (ssDNA) through a van der Waals (vdW) heterostructure nanopore formed by stacking two graphenic materials, namely those of BC₃ and C₃N. Our results showed that, without using an external stimulus, ssDNA can be spontaneously transported through such a vdW nanopore from its BC₃ side to its C₃N side, with the C₃N surface demonstrating a stronger capability than the BC₃ surface to attract DNA bases. Thus, the distinct binding strengths of BC₃ and C₃N were concluded to drive the ssDNA translocation. The results indicated the vdW forces playing a leading role during the translocation process. Our simulations also showed, at the edges of the nanopore, a clear energy barrier for nucleotides, resulting in a translocation speed slowed to a value of 0.2 μs per base, i.e., twice as slow as that indicated for the latest published methods. The present findings provide a new architecture for biomolecule detection and sequencing, which may be considered some of the most important functions of nanomaterials in biological and chemical analyses.