Huang Changxiong, Li Zhen, Zhu Xiaohong, Ma Xinyao, Li Na, Fan Jun
Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China.
School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao266580, China.
ACS Nano. 2023 Feb 28;17(4):3301-3312. doi: 10.1021/acsnano.2c05002. Epub 2023 Jan 13.
Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the and directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.
尽管固态纳米孔测序技术具有长读长和高效率的革命性优势，但目前它面临着随机孔堵塞以及DNA通过纳米孔时速度过快的问题。这两个问题都与测序过程中分子运输的控制有关。为了控制DNA的运动并识别四种碱基，我们提出了基于二维石墨烯和六方氮化硼平面异质结构的纳米狭缝传感技术。通过分子动力学模拟研究了带有纳米狭缝传感器的异质结构上DNA分子的运动。结果表明，DNA分子被限制在异质结构的六方氮化硼（HBN）区域内。并且可以通过调整条纹长度来优化异质结构的限制效应。此外，DNA通过纳米狭缝有两种方式：在施加电压的情况下，DNA可以沿着 和 方向穿过或横向穿过纳米狭缝。这两种检测模式分别被命名为跨狭缝和横向狭缝。在这两种模式下，当纳米狭缝被DNA占据时，都可以观察到离子电流下降。并且可以同时检测离子电流和停留时间来识别四种不同的DNA碱基。这项研究可以阐明基于平面异质结构纳米狭缝传感器的传感机制，并为设计在纳米孔测序过程中控制分子运输的设备提供理论指导。
