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RESEARCH PRODUCT

Design and computer simulations of 2D MeX2 solid-state nanopores for DNA and protein detection analysis

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Solid-state nanopores (SSN) have emerged as versatile devices for biomolecule analysis. One of the most promising applications of SSN is DNA and protein sequencing, at a low cost and faster than the current standard methods. SSN sequencing is based on the measurement of ionic current variations when a biomolecule embedded in electrolyte is driven through a nanopore under an applied electric potential. As a biomolecule translocates through the nanopore, it occupies the pore volume and blocks the passage of ions. Hence, ultrafast monitoring of ionic flow during the passage of a biomolecule yields information about its structure and chemical properties. The size of the sensing region in SSN is determined by the size and thickness of the pore membrane. Therefore, two-dimensional (2D) transition metal dichalcogenides such as molybdenum disulfide (MoS2) arise as great candidates for SSN applications as an alternative to graphene. In the present work, we investigated the feasibility of using MoS2 nanopores for protein sequencing from all-atom molecular dynamics (MD) simulations. First, we studied the ionic conductance of MoS2 nanoporous membranes by characterizing the KCl electrolyte conductivity through MoS2 nanopores with diameters ranging from 1.0 to 5.0 nm and membranes from single to five-layers. Using MD simulations, we showed the failure of the usual macroscopic model of conductance for the nanoporous membranes with the smallest diameters and developed a modified model which proves usefulness to interpret experimental data. Second, we investigated the threading and translocation of individual lysine residues and a model protein with poly-lysine tags through MoS2 nanopores under the application of an electric potential. A proof-of principle technique based on the use of positively or negatively charged amino acids for protein translocation was proposed to promote the entrance of proteins through SSN in experiments. By analyzing the current-voltage curves simulated, we established the relationship between the translocation sequence events through the nanopores observed at the atomic scale in MD simulations, and the computed current fluctuations. Finally, experimental evidence of ionic conductance measurements in sub-nanometer (sub-nm) pores made of atomic defects has been recently reported. To give a better insight of the ionic transport through atomic scale pores, we performed MD simulations of sub-nm defect MoS2 pores using the reactive potential ReaxFF. Here, we characterized the variations of the atomic structure of the pores in vacuum and then we investigated the ionic conductance performance of one of the MoS2 defect pore membranes. ReaxFF potential was also useful to investigate the possible reactivity of MoS2 defect pore membranes with ethanol molecules. In addition, these simulations might provide a better understanding of the experimental setup of DNA sequencing, in which ethanol plays an unknown role in the sample preparation of the SSN.