Back to NPN nanofilter experiments
Just a quick update on my status:
I got the NPN pre-filters from Greg in Montreal and finished testing 15 of them last week, so this week I will start doing additional experiments. I plan to explore the size separation capabilities in KCl, which should give even tighter distributions than LiCl. I don’t plan on having it make it into this paper, but we’ll see how the timelines work out.
The new analysis I put into the paper on folding distributions this round strongly supports the idea that folding suppression is due to double-threading rather than small NPN pore size. The current wafer we’ve ordered from Simpoer has small pores, so it will at least confirm this if nothing else. Going forward, however, we’ll probably want to set up NPN to promote double threading. This means minimizing the distance between adjacent pores without actually increasing the pore size, i.e. high number density of pores. I’ll post something about it on the Simpore Basecamp as well.
Are there other experiments you would like me to do with the new nanofilters in the meantime?
Is there a chance we can test out cleaning ‘dirty’ samples with the nanofilter? Is it possible to devise a mixture of DNA and beads (or protein) to make it realistic? Your original experiments showed that the lifetimes of the devices weren’t affected by the presence of the prefilter; both tented and untented had many thousands of events.
Probably possible. The issue is finding a particle which translocates a pore slow enough to be detected in the unfiltered case while also being large enough for the filter to stop it. Translocation speeds of typical nanobeads are usually too fast to detect reliably. I’ll look into bulky protein options.
Does your system have the capacity to introduce DNA in a controlled continuous flow while you do detection?
Currently no. There are systems in the lab and in some neighboring labs that could, which would have to be adjusted for this form factor of chip. What did you have in mind?
Planning to examine the impact of continuous flow on capture rate. We are working on some relevant simulations. We will test locally using nanoparticle capture by NPN, but the real test will eventually involve DNA detection by single nanopores.
With the tiny forces pulling DNA through NPN I would suspect that flow will pretty much halt capture of DNA unless it was small enough to fit through the NPN pores in its native state. However, there could be some interesting devices which incorporate an electrode between the two layers to improve capture through the NPN.
Simulations will be interesting, for sure.
Well you just made my simulations more complicated. We’ll do the basics to get transport times to approach NPN, but then I think we’ll need to recruit Hendrick’s team.