Water-compression gating of nanopore transport

James Wilson, and Aleksei Aksimentiev
Physical Review Letters 120(26) 268101 (2018)  BibTex

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Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.

Abstract

Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.

PDF icon Supporting Information

Animation illustrating a 10 ns MD trajectory of a dsDNA molecule translocating through a nanopore in a graphene membrane under a 100 mV bias. Harmonic restraints were applied to the DNA molecule to maintain its coaxial arrangement with the nanopore. Graphene atoms are shown as gray spheres. Some graphene atoms are not shown to depict the location of the pore more clearly.

Animation illustrating a 20 ns MD trajectory of a dsDNA molecule failing to translocate through a graphene membrane under a 1 V bias. Harmonic restraints were applied to the DNA molecule to maintain its coaxial arrangement with the nanopore. Graphene atoms are shown as gray spheres. Some graphene atoms are not shown to depict the location of the pore more clearly.

Animation illustrating a 20 ns MD trajectory of a dsDNA molecule held above a graphene membrane under a 1 V bias. Harmonic restraints were applied to the DNA molecule to maintain its coaxial arrangement with the nanopore. Graphene atoms are shown as gray spheres. DNA is able to rotate about its helical axis.

Animation illustrating a 20 ns MD trajectory of a dsDNA molecule held above a graphene membrane parallel to the membrane under a 1 V bias. Harmonic restraints were applied to the DNA molecule to maintain its parallel arrangement with the nanopore. The DNA is able to rotate about its helical axis and about the pore axis. Graphene atoms are shown as gray spheres.