TCB Publications - Abstract

Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten. Microscopic kinetics of DNA translocation through synthetic nanopores. Biophysical Journal, 87:2086-2097, 2004. (PMC: 1304610)

AKSI2004B We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick MOS (Metal-Oxide-Semiconductor)-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of mechanism for sequencing DNA are avidly being pursued. The key attribute of the sensor is the electric field-induced (voltage-driven) translocation of the DNA molecule in an electrolytic solution across the membrane through the nanopore. To complement ongoing experimental studies developing such pores and measuring signals in response to the presence of DNA, we conducted molecular dynamics simulations of DNA translocation through the nanopore. A typical simulated system included a patch of a silicon nitride membrane dividing water solution of potassium chloride into two compartments connected by the nanopore. External electrical fields induced capturing of the DNA molecules by the pore from the solution and subsequent translocation. Molecular dynamics simulations suggest that 20 base pairs double stranded DNA can transit a nanopore of a 2.4$\pm$0.2 nm cross-section in a few microseconds at experimental fields. Hydrophobic interactions between DNA bases and the pore surface can slow down translocation of single stranded DNA and might favor unzipping of double stranded DNA inside the pore. DNA occluding the pore mouth blocks the electrolytic current through the pore; these curent blockades were found to have the same magnitude as the blockade observed when DNA transits the pore.

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