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Nanoscale DNA sequencing technique to advance personalized medicine

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August 22, 2010

Illustration depicting a single strand of DNA moving through a nanopore that is being used...

Illustration depicting a single strand of DNA moving through a nanopore that is being used to sequence the DNA (Image: Ian Derrington)

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One of the long held hopes for DNA sequencing is that it will usher in an era of personalized, predictive medicine by providing individualized blueprints of genetic predispositions for specific conditions and diseases, such as cancer, diabetes and addiction. Researchers have now devised a method that works at a very small scale to sequence DNA quickly and relatively inexpensively that could open the door to more effective individualized medicine.

The technique creates a DNA reader that combines biology and nanotechnology using a nanopore taken from Mycobacterium smegmatis porin A. The nanopore has an opening 1 billionth of a meter in size, just large enough to measure a single strand of DNA as it passes through. The nanopore has an opening 1 billionth of a meter in size, just large enough to measure a single strand of DNA as it passes through.

The scientists placed the pore in a membrane surrounded by potassium-chloride solution. A small voltage was applied to create an ion current flowing through the nanopore, and the current's electrical signature changed depending on the nucleotides traveling through the nanopore. Each of the nucleotides that are the essence of DNA – cytosine, guanine, adenine and thymine – produced a distinctive signature.

The electrical signatures of the DNA nucleotides -- guanine, thymine, cytosine and adenine...

One at a time please

The team had to solve two major problems. One was to create a short and narrow opening just large enough to allow a single strand of DNA to pass through the nanopore and for only a single DNA molecule to be in the opening at any time. Michael Niederweis at the University of Alabama at Birmingham modified the M. smegmatis bacterium to produce a suitable pore.

The second problem was that the nucleotides flowed through the nanopore at a rate of one every millionth of a second, far too fast to sort out the signal from each DNA molecule. To compensate, the researchers attached a section of double-stranded DNA between each nucleotide they wanted to measure. The second strand would briefly catch on the edge of the nanopore, halting the flow of DNA long enough for the single nucleotide to be held within the nanopore DNA reader. After a few milliseconds, the double-stranded section would separate and the DNA flow continued until another double strand was encountered, allowing the next nucleotide to be read.

The delay, though measured in thousandths of a second, is long enough to read the electrical signals from the target nucleotides.

"We can practically read the DNA sequence from an oscilloscope trace," said Jens Gundlach, a University of Washington physics professor and lead author of a paper describing the new technique published the week of Aug. 16 in the Proceedings of the National Academy of Sciences.

About the Author
Darren Quick Darren's love of technology started in primary school with a Nintendo Game & Watch Donkey Kong (still functioning) and a Commodore VIC 20 computer (not still functioning). In high school he upgraded to a 286 PC, and he's been following Moore's law ever since. This love of technology continued through a number of university courses and crappy jobs until 2008, when his interests found a home at Gizmag.   All articles by Darren Quick
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