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Reading DNA sequences from single molecules of polymerase using nanotechnology

A new nanotech method of DNA sequencing is 30,000 times faster than current DNA sequencing methods. The method, developed by a team at Pacific BioSciences in Menlo Park, California, uses a nanostructured array of thousands of waveguides—tiny hollow metal cylinders, each holding about a zeptoliter (10-21 liter)—to isolate a single molecule of DNA and a single molecule of DNA polymerase. Each of the four nucleotide bases is labeled with a different colored fluorescent label, with the fluorescent dye attached to the portion of the nucleotide that is cleaved and removed after the nucleotide is added to the growing DNA chain. As each nucleotide base is incorporated into the growing DNA chain within one waveguide, a spot of light of the corresponding color first appears, and then disappears. The sequence of flashes in each well reveals the DNA sequence copied in that well in real time. The array allows the simultaneous observation of thousands of single molecule DNA sequencing reactions. Preliminary experiments published in Science (abstract) report 100% accuracy with test DNA templates 150 bases in length. For more, see the article in NewScientist Tech written by Jessica Griggs: “Molecular fireworks could produce ’30-minute genomes’” (thanks to KurzweilAI.net for the link):

So far, the team has built a chip housing 3000 ZMWs [waveguides], which the company hopes will hit the market in 2010. By 2013, it aims to squeeze a million ZMWs [waveguides] onto a single chip and observe DNA being assembled in each simultaneously. Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.

Griggs quotes an independent authority as being skeptical of the 2013 extrapolation. Even for such an elegant technique, it is a long jump from 150 to 3 billion bases.
—Jim

7 Responses to “Reading DNA sequences from single molecules of polymerase using nanotechnology”

  1. Says:

    Er, you don’t want to jump from 150 to 3 billion bases. Read up on shotgun sequencing. The mere fact that a given chunk is 150 bases is immaterial, though of course if you could lengthen that by a factor of five or ten it would improve accuracy and reduce computation on assembling the whole thing.

  2. Says:

    This independent authority doesn’t sound too smart. There are 3000 waveguides on the current chip at 150bases per waveguide for 450,000 bases. Granted it is still a long jump from 450,000 to 3 billion, but the jump is much smaller. Also, the only thing they have to do is increase the number of waveguides. The hard part appears to be done (i.e. getting the tehcnology to work at all).

  3. Nuve metodiche di sequenza del DNA « Daemons & Dependancies Says:

    [...] Nuve metodiche di sequenza del DNA “A new method of DNA sequencing published this week in science identifies incorporation of single bases by fluorescence. This has been shown to increase read lengths from 20 bases (454 sequencing) to >4000 bases, with a 99.3% accuracy. Single molecule reading can reduce costs and increase the rate at which reads can be performed. ‘So far, the team has built a chip housing 3000 ZMWs [waveguides], which the company hopes will hit the market in 2010. By 2013, it aims to squeeze a million ZMWs [waveguides] onto a single chip and observe DNA being assembled in each simultaneously. Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.’” [...]

  4. Says:

    I took a shower today

  5. Says:

    All by myself

  6. Says:

    Now we need to add a Quantum Computer and Grovers algorithm.
    http://www.dwavesys.com/
    http://en.wikipedia.org/wiki/Grover‘s_algorithm
    This would allow exhaustive DNA searches of many genomes simultaneously.
    The real advance will not be cheap human genomes it will rather be all the other species genomes we could compare to the human genome to gain context of the expressions of the human genomes 18K genes. By comparative genomics we will finally understand the functions of genes.
    This epigenetics revolution may eventually lead to human life extension.

    A recent advance in creating a cell phone microscope may lead to massive sequencing of all 7 billion people.
    http://science.slashdot.org/article.pl?sid=08%2F12%2F20%2F2012230&from=rss
    http://www.wired.com/science/discoveries/multimedia/2008/12/gallery_microscope_phone
    If a cell phone microarray can be developed genomic information can be read in the field any where. CSI to WHO.
    http://www.mailman.hs.columbia.edu/news/Lipkin_GreeneChip.html

  7. Says:

    As the sequences get longer, aren’t you going to have more trouble ensuring that only one piece of DNA arrives in each well?

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