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Old 02-28-2012, 01:32 PM   #47
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 824

Originally Posted by Markiyan View Post
I remember reading somewhere (2-3 month ago), that there were two main types of the nanopores in their's R&D -
1. Protein nanopore fused with Exonuclease, and the nucleotides are first cleaved away by the exonuclease, than they flow through the pore, and the change in the current flowing through it is detected. Difference in the ion charge is then analysed and is used for basecalling.
2. Purely solid state nanopores - not much details on those - whether they are chopping the DNA up (as in 1, or threading it through)?

From our current error profile report it confirms 1, that the deletions are caused by the bases, that had "run away" from the pore.
If you read their website, you might notice it's actually (2) that they're marketing (I might as well link to it once again). The exonuclease is being done in something approximating a partnership with Illumina:

  • "Strand sequencing" is a technique that passes intact DNA polymers through a protein nanopore, sequencing in real time as the DNA translocates the pore. Oxford Nanopore intends to commercialise this technology independently within 2012.
  • "Exonuclease sequencing" is a technique that passes individual nucleotides through a protein nanopore, aided by a processive exonuclease enzyme. Oxford Nanopore signed a commercialisation agreement with Illumina for this technology however commercialisation timelines have not been disclosed.
Of course, it's not quite "pure" solid state. They manufacture the membranes, and a solution of nanopores (created from bioreactors) is added in just before the run is started. The pure solid-state stuff may come in the future when things like graphene nanopores are worked out.

Last edited by gringer; 02-28-2012 at 01:34 PM.
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