Computational Biological Center , IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States.
ACS Nano. 2018 Apr 24;12(4):3886-3891. doi: 10.1021/acsnano.8b01297. Epub 2018 Apr 12.
The effective transport of a single-stranded DNA (ssDNA) molecule through a solid-state nanopore is essential to the future success of high-throughput and low-cost DNA sequencing. Compatible with current electric sensing technologies, here, we propose and demonstrate by molecular dynamics simulations the ssDNA transport through a quasi-two-dimensional nanopore in a heterostructure stacked together with different 2D materials, such as graphene and molybdenum disulfide (MoS). Due to different chemical potentials, U, of DNA bases on different 2D materials, it is energetically favorable for a ssDNA molecule to move from the low- U MoS surface to the high- U graphene surface through a nanopore. With the proper attraction between the negatively charged phosphate group in each nucleotide and the positively charged Mo atoms exposed on the pore surface, the ssDNA molecule can be temporarily seized and released thereafter through a thermal activation, that is, a slow and possible nucleotide-by-nucleotide transport. A theoretical formulation is then developed for the free energy of the ssDNA transiting a heterostructure nanopore to properly characterize the non-equilibrium stick-slip-like motion of a ssDNA molecule.
单链 DNA（ssDNA）分子通过固态纳米孔的有效传输对高通量和低成本 DNA 测序的未来成功至关重要。与当前的电传感技术兼容，在这里，我们通过分子动力学模拟提出并证明了 ssDNA 通过堆叠在一起的不同二维（2D）材料的准二维纳米孔的传输，例如石墨烯和二硫化钼（MoS）。由于不同二维材料上 DNA 碱基的化学势 U 不同，ssDNA 分子从低 U MoS 表面通过纳米孔移动到高 U 石墨烯表面在能量上是有利的。由于每个核苷酸中的带负电荷的磷酸基团与暴露在孔表面上的带正电荷的 Mo 原子之间存在适当的吸引力，ssDNA 分子可以通过热激活（即缓慢且可能是逐个核苷酸的传输）暂时被捕获和释放。然后，我们为 ssDNA 穿过异质结构纳米孔的自由能开发了一个理论公式，以正确描述 ssDNA 分子的非平衡粘滑样运动。
