New DNA Sequencing Method proposed
Researchers in Aleksei Aksimentiev's group are developing a method for high-throughput sequencing of DNA using a nanopore in a semiconductor chip, as reported December 11 in Nano Letters.
"In our method," said Aksimentiev, "a DNA molecule is driven back and forth through the pore to produce an electrostatic fingerprint that is used to recognize its nucleotide sequence. By performing atomic-scale simulations of DNA translocation, we demonstrate that DNA permeates the pore in a stepper-motor-like manner—long pauses separate rapid advances."
The type of single DNA nucleotide that is about to enter the pore was found to determine the rate with which the DNA advances through the pore. From these observations, the researchers were able to suggest a device for detecting DNA sequences that operates like a programmable biological restriction enzyme; under a sequence-specific, periodic electric field pulse, DNA slides through the nanopore until the target sequence is encountered, which arrests DNA motion to undulations in concert with the applied electric field.
A goal of this work is to enable a technology that would dramatically reduce the costs of whole genome sequencing, making individualized medicine a reality.
Watch a movie of the simulation (requires QuickTime player).
The work was funded by the National Institutes of Health and the University of Illinois. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funders.