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Old 02-28-2012, 01:11 PM   #46
Markiyan
Senior Member
 
Location: Cambridge

Join Date: Sep 2010
Posts: 115
Lightbulb Possible curent Oxford Nanopore DNA sequencing implementation.

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.
I think going for the low temperatures enzymes may reduce the noise caused by the molecular motion, but then the secondary structures may became even bigger issue. (any reaction conditions reports)?

PS: near the end of the run you should see the increase in the insertions (caused by the saturation of the run-away bases, being finally dragged in by the electric current).

PPS:
Fortunately it doesn't have the fundamental flaw of the current pacbio implementation, there the presence of the base in the active centre doesn't 99% warranty it's incorporation (it does in ~87% cases :-).
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