Quantapore have been around since 2009, and according to Crunchbase have raised $52M in total. Most recent investment seems to have come from Chinese funds (Foothill wrote a post about their investment for those interested). About 4 years ago they were talking about “starting the early-adopter program” using funds from their then recent round. But I’ve not heard much since then…
It’s been a long time since I looked into the approach, and I decided to go hunting for patents again and see if there was any experimental data, and indeed a patent published in May last year shows a few interesting plots!
Approach
The essential idea behind Quantapore is the development of an optical Nanopore DNA sequencing platform. In this approach, strands are driven through a Nanopore (much like in Oxford Nanopore devices) but they are detected optically using fluorophores labels.
A template (input DNA) is used to synthesize a complementary strand where all the nucleotides have a fluorescent label (one for each base type). This strand is translocated through a pore. Why do you need a pore at all if you’re labeling the strand anyway? Well, the pore serves a few different purposes.
Firstly the nanopore has a FRET donor attached to it. FRET is an approach where two fluorophores are used. The first “donor” is excited, which then excites a second fluorophore (the acceptor). You therefore only get emission from the acceptor when the two fluorophores are in close proximity.
In this case, FRET is used to confine emissions to only those nucleotides near the nanopore. The donor, attached to the pore, excites the labeled nucleotides as they exit the pore. While the labeled nucleotides are in the pore, they are also squeezed into an orientation where they will not be excited by the FRET field.
An issue not yet addressed is motion control, that is to say, strands of DNA generally pass through nanopores too quickly to sense (millions of bases/s). So, you need some method of slowing the strand down. Oxford Nanopore do this enzymatically, but what about Quantapore?
Well, here they suggest that fluorescent modified nucleotides just translocate slower:
“The resulting [fluorescently] labeled nucleic acid has an increased nominal diameter which results in a decreased translocation velocity when pulled through a nanopore… a most preferred translocation rate of 200-600 nucleotides per second.”
Disadvantages
The approach has a few clear disadvantages over Ionic current nanopore sequencing (Oxford Nanopore). The first is that you’re not sequencing native material, this means no direct RNA sequencing or detection of base modifications. You also need to have a complete single molecule optical imaging system (they use Hamamatsu sCMOS cameras, these cost…