Molecular Dynamics Simulation Studies of Nanopore Sequencing Based on Two-Dimensional Materials Nanoslits


Student thesis: Doctoral Thesis

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Awarding Institution
Award date21 Dec 2021


The single-molecule detection technique by nanopore is revolutionary because it is theoretically able to sense any analytes by detecting their ionic current signals through the nanopore. The thinness of two-dimensional materials enables the single-base-level resolution of sequencing. Compared with classical DNA and protein sequencing methods, the nanopore sequencing technique has advantages of rapidness, long readability, high resolution, and being label-free. Despite these advantages, 2D materials solid-state nanopore sequencing is still confronted with challenges when it comes to actual applications such as protein and DNA sequencing.

Two main challenges are in the way of protein nanopore sequencing: the urgent demand for a suitable driving force and distinguishable signals. To tackle the distinguishability problem, Molecular Dynamics (MD) simulations are performed on sequencing peptides under pulling force and applied electric field, while a graphene nanoslit sensor is adopted to collect the corresponding two signals to distinguish 20 residues. Results show that distinguishable force and current signals can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between Tyrosine and Alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents.

The foremost importance for DNA sequencing is to control the translocation speed because suitable speeds guarantee sequencing efficiency and signal differentiability. Reducing the geometry of high-symmetric nanopores, like circular, triangular, quadratic, and hexagonal pores, can de-speed the translocation, but also results in a reduction of signal amplitude. To balance between translocation speed and signal distinguishability, we choose nanoslit geometry with two adjustable dimensions, the width, and the length. It reveals that reducing the width leads to slowing down of DNA translocation while the detection range remains because of ions flow allowed by the nanoslit length. The underlying cause of the slowing down is the increasing energy barrier with the decreasing nanoslit width. Besides, adjusting applied electric voltages can further control the DNA translocation speed in a non-linear way. The translocation can be speeded up within a voltage range, beyond which increasing the voltage will be much less effective because of repulsive effects of solutions induced by the high external electric field near confined volume.

Rectifying the conformational variation of the DNA chain can reduce the structural changes during sequencing, thus stabilizing the detected ionic current signals. We apply the nanoslits into the graphene/HBN heterostructure and propose two new detection modes, cross-slit transversal ionic current detection, and trans-slit longitudinal ionic current detection. The DNA molecules can be patterned on the HBN domain while tailoring the width of the HBN stripe can linearize the DNA chains. The four DNA bases can be identified by the nanoslit sensor on heterostructures, which have conformational rectification of DNA molecules and stabilized ionic current signals.

Taken together, the less symmetric nanoslit is applied as a nanopore sensor to sequence protein and DNA, and different problems can be solved by the unique nanoslit geometry. First, tailoring nanoslit geometries enables simultaneous sensing of force and current signal, which enhances distinguishability. More proteinogenic amino acids can be identified by detecting the multi-dimensional signals, which is significant for protein nanopore sequencing. Second, the geometric and electrophoretic insights into controlling DNA translocation speed through nanoslits can provide theoretical support for designing sequencing devices and optimizing the influencing parameters. Last, two new detection modes are proposed based on the nanoslits of planar heterostructures, which can confine molecule motion, thus rectifying conformation and stabilizing signals when sequencing. The simulation works based on nanoslit sensors in this thesis can provide alternative geometric choices for nanopore sensing and are expected to pave the way for single-molecule sequencing of DNA and protein.