Anyone ever see electrophoresis where the gel was rolled?

[Nathan McCorkle]

I am thinking something like a pinwheel, or a rolled capacitor:
http://www.electronics-tutorials.ws/capacitor/cap3.gif

but instead of using metal, this would be insulator, and instead of
electrolyte, this would be agarose/gel.

There could be a few ways to assemble something like this that I can
imagine, starting with something as simple as a sheet of plastic or
rubber, then dispensing a line of molten agarose down the center.
After hardening, the sheet would get rolled. You'd then need some
fixtures to hold the roll so it didn't unravel, and also you'd need to
ensure the spiral-path didn't short out around the edges. Maybe the
unraveling-preventer could seal one end, while the other was upright
and exposed to air, allowing you to then pour in running buffer.

Anyway, I'm just thinking of unconventional ways to emulate capillary
electrophoresis, mainly so I don't have to purchase a traditional gel
box... but also thinking to reduce setup/cleanup time involved, and
reducing reagent consumption.

--
-Nathan

[Lee Nelson]

Nice thinking. Would the DNA sample be introduced on one side and migrate lengthwise to the other end? How would you image it? Where would the ladder go? What are the  advantages of this approach?  I think you are on to something but I can't put my finger on it. Go for it. You probably have everything you need for a prototype around the lab and house. 

[Kermit Henson]

What happens if the roll is not perfect parallel to the support? when you run a polyacrylamide gel, is easy to get distorted lanes

But,hey, nice concept. It can works :)

[John Griessen]

On 03/16/2017 05:54 AM, Nathan McCorkle wrote:
> Maybe the
> unraveling-preventer could seal one end, while the other was upright
> and exposed to air, allowing you to then pour in running buffer.
>
> Anyway, I'm just thinking of unconventional ways to emulate capillary
> electrophoresis, mainly so I don't have to purchase a traditional gel
> box... but also thinking to reduce setup/cleanup time involved, and
> reducing reagent consumption.

I like the idea. Here are my thoughts:

Don't do a tight roll, but use a filler cylinder in the center so
rolling/unrolling is not too different radius/ curvature from inside to outside.

Is unrolling needed at all? If thinking of "the usual way" it seems to be needed so you can see
the gel -- and use the center of the moving blobs of molecules and reject fuzzy edges.
So, unrolling is probably needed until some near perfect shaped rolled channel can be made filled with gel
inexpensively -- perhaps 3D printing the insulating channel in a spiral would be good...

If rolling sheet material then running electrophoresis, the best sharpest part of bands in the middle could be cut out
by chopping through the whole thing with a guillotine like cigar cutter machine. Would that distort bands some?
Yes, if they were soft

Use two layers of insulator so unrolling goes without tearing chunks of gel out.

3D printing the insulating channel in a spiral:

After making a spiral channel, fill with gel and any buffer wanted, then wipe or squeegee to get top edges
dry. This could be done like litho printing and scale up. Next apply a film and bond it with pressure to seal in
gel and insulate. Next connect terminals for volts and current. Terminals might be part of the 3D channels, or maybe bits of
wire stabbed through top film in early tests. For terminals that are part of the 3D channels the film would cover them,
and next they would be uncovered by laser-cutting such that the terminal conductors don't cut through, but the film does get
blasted away to reveal a contact surface. The whole thing could be engineered to be translucent and image through it
to quantify electrophoresis -- either post-processed or as it moves.

John Griessen

[John Griessen]

On 03/17/2017 01:08 PM, John Griessen wrote:
> After making a spiral channel, fill with gel and any buffer wanted, then wipe or squeegee to get top edges
> dry. This could be done like litho printing and scale up. Next apply a film and bond it with pressure to seal in
> gel and insulate. Next connect terminals for volts and current. Terminals might be part of the 3D channels, or maybe bits of
> wire stabbed through top film in early tests. For terminals that are part of the 3D channels the film would cover them,
> and next they would be uncovered by laser-cutting such that the terminal conductors don't cut through, but the film does get
> blasted away to reveal a contact surface.

To get back to your desire to add buffer later, this might work: perforations in the top film could be made with the same laser
cutting used for electrophoresis contacts. The steps to infuse an array of gel rolls with a buffer solution could be:
1. lay a paper towel on it
2. apply buffer solution
3. wait x minutes for it to absorb
4. store in a zip lock bag.

This approach could make a mass produced gel roll array useful for many different buffers/conductivities. After 3D
printing the prototypes, a mold could make smoother spiral channels by injection molding. The small surface
lumps inherent in FDM 3D printing might not matter much
in macro sized 3D printed spiral channels, but 3DP gives pinholes that could be a leakage path for electrophoresis HV driven
current, and smoothness is essential as you go more micro in size.

John Griessen

[Nathan McCorkle]

On Mar 16, 2017 6:58 AM, "Kermit Henson" <kerm...@gmail.com> wrote:
>
> What happens if the roll is not perfect parallel to the support? when you run a polyacrylamide gel, is easy to get distorted lanes
>

Hmm, good point. I guess you would need to ensure the gel was straight, at least the center where you'd want to load the DNA.