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April 10, 2006

Nanoscale tech: Nanopore DNA sequencing status

DNA sequencing by passing a DNA strand through a “nanopore” to detect electrical changes as the strand of DNA is passed through it could speed up DNA sequencing more than 200 times. US physicists at the University of California, San Diego have made a detailed computer simulation of over 100,000 interacting atoms and shown theoretically how to get the necessary resolution on the sensing. The challenge lies in refining the method to improve its resolution to be able to detect single bases. Using the current methods, a nucleotide needs to be repeated in a sequence about 100 times successively in order to produce a measurable characteristic change. The concept of nanopore sequencing has been around since at least 2000.

Previous attempts to sequence DNA using nanopores were not successful because the twisting and turning of the DNA strand introduced too much noise into the signal being recorded. The new idea takes advantage of the electric field that drives the current perpendicular to the DNA strand to reduce the structural fluctuations of DNA while it moves through the pore, thus minimizing the noise. The University of California, San Diego researchers caution that there are still hurdles to overcome because no one has yet made a nanopore with the required configuration of electrodes, but they think it is only a matter of time before someone successfully assembles the device. The nanopore and the electrodes have been made separately, and although it is technically challenging to bring them together, the field is advancing so rapidly that they think it should be possible in the near future.

The work is part of a project to sequence a mammal-sized genome for $1,000.

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