2006 APS March Meeting
Monday–Friday, March 13–17, 2006;
Baltimore, MD
Session H7: Nanopore Biophysics
11:15 AM–2:15 PM,
Tuesday, March 14, 2006
Baltimore Convention Center
Room: 307
Sponsoring
Unit:
DBP
Chair: Xinsheng Sean Ling, Brown University
Abstract ID: BAPS.2006.MAR.H7.5
Abstract: H7.00005 : Microscopic Kinetics of DNA Translocation through Synthetic and Biological Nanopores
1:39 PM–2:15 PM
Preview Abstract
Abstract
Author:
Aleksei Aksimentiev
(University of Illinois at Urbana-Champaign)
Using highly focused electron beams, artificial pores of nanometer diameters
can be manufactured in ultra-thin silicon membranes with a sub-nanometer
precision. A trans-membrane voltage bias can drive DNA strands through such
pores; the resulting electrical signals can be recorded. As the diameter of
the pore as well as the thickness of the silicon membrane can be made to
match precisely the dimensions of a DNA nucleotide, the electrical signals
produced by the interaction of DNA with the pore were proposed to contain
information about the DNA sequence. In order to relate the DNA sequence to
the measured electrical signals we characterized DNA conformations inside
the pore through molecular dynamics simulations. A typical simulated system
included a patch of a silicon membrane dividing electrolyte solution 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. To calibrate our methodology, we carried out MD
simulations of DNA translocation through an $\alpha $-hemolysin channel
suspended in a lipid bilayer. Our results suggest that the rate-limiting
step for DNA translocation through narrow synthetic pores is not the actual
transit of DNA, but rather the search for such initial conformation that
facilitates subsequent translocation. At the same time, hydrophobic adhesion
of DNA bases to the pore walls may considerably slow down or halt DNA
translocation. We observed a threshold electric field for translocation of
double stranded DNA through pores smaller in diameter than a DNA double
helix occurring due to the overstretching transition at load forces of $\sim
$60 pN. In narrow pores, DNA bases were observed to tilt collectively
towards the 5'-end of the strand, which explains experimentally observed
directionality of single stranded DNA in the transmembrane pore of $\alpha
$-hemolysin.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2006.MAR.H7.5