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$\pm0ドル.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.