UV Transilluminator and mini gel electrophoresis

[Dakota Hamill]

Just got the UV Transilluminator project in my instructables weekly newsletter and thought it looked pretty nice and that others might want to check it out.  Turns out her other project (gel box) is pretty slick and finished looking too.

http://www.instructables.com/id/UV-Transilluminator/

http://www.instructables.com/id/Gel-electrophoresis-system-mini/

[Alex Hoekstra]

Don't get me wrong, I love that directions for these are made
available so that anyone so inclined can make their own, but I feel as
though it's still out of the reach for many. Laser-cut acrylic
components? Hmm. Maybe I'll just hit up ebay...

[Jeswin]

Are they using black acrylic for the box? Never seen that before.

I think the blue LED Pearl box is better for a DIYbio lab. Less
dangerous equipment = safer lab. I mean, who you gonna call when you
do something stupid?

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[Mackenzie Cowell]

I think that is a terrific instructable.  The sub-$100 UV transilluminator is a milestone.  Especially cool are the instructions on sourcing the pro-grade UV light source for $28 and the appropriate socket and ballast for it.  (Cat# 11-2122 at http://www.fotodyne.com/content/trans_access).

I have experimented with making my own transilluminator for GelGreen and SybrSafe stains, similar to the Pearl Biotech transilluminator instructable you linked to. I have found that 2424 Blue Acrylic works as prefilter and 2422 Orange Acrylic works as a postfilter for those stains. I got sample sheets from ridout plastics.  Attached is a photo of a gelgreen-stained dye sandwiched between these two acrylics illuminated underneath via a blue LED array.

Any interest in working on a design for open-source reusable gel cassettes for making precast gels?  It would be possible to create these cassettes directly out of the filtering acrylics.

I left similar comments for the author of the instructable.

Mac

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[John Griessen]

On 12/12/2011 07:44 PM, Mackenzie Cowell wrote:
> Any interest in working on a design for open-source reusable gel cassettes for making precast gels? It would be possible to
> create these cassettes directly out of the filtering acrylics.

Sounds like a good product for your cofactorbio site. But how do you make
them reusable and precast at the same time? What I could find for sale was throw away.

I was searching along those lines
and saw a funny ad video with a smiling gal using a sonic welded solid disposable
mini cassette and her alter ego on the right pouring melted gel after fumbling with
assembling a reusable casting frame and it runs out a leak in the bottom...boss frowns...
version of gal on left wins award...version on right..watches award presentation.

Trade names like snap a gel, and mentions of freedom from gel, running
gels in a cassette "anywhere, any time" abound.

Still, making a reusable casting frame doesn't have to be impossible -- O-rings
seal anything. I've been wanting to try CO2 laser ablating acrylic to make
a trough instead of cut all the way through, but not done yet. A laser ablated trough
might be a good place to put some sealing rubber strip to seal against
sheet material with UV clear and filtering abilities.

Electrodes on ends seem even harder to seal -- maybe one of the sheets filter
or UV clear, whichever costs less, could be solvent welded to so the
electrode could be embedded in solvent cemented acrylic to get out of the box
without making a leak. One of the sheets will need to be changed from a
simple sheet anyway -- there's gotta be some distance between electrode
and starting wells, and that is going to be holes in one of the sheets that make
the sides of the cassette. Those holes are a place that can leak, but not much head
pressure since only 1 cm away from top of poured gel.

John

[Mackenzie Cowell]

I predict one of the larger design challenges will be an efficient way of discarding a used gel from the cassette - this may be at odds with a design which makes it easy to cast the gels.  I guess the simplest design would be to make the ceiling of the cassette (the orange post-filter) removable so gels could be poured in and cast or dumped out when done.

John

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[Antonio García Guerra]

Did you guys consider the possibility of self assembly materials?

I'm curious about it.

Antonio.

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[Mackenzie Cowell]

No.  What are you talking about?

2011/12/13 Antonio García Guerra <antgar...@gmail.com>

[John Griessen]

On 12/13/2011 02:15 PM, Antonio García Guerra wrote:
> possibility of self assembly materials?

If you mean self assembled as in DIY, sure. Nano-crystalline gel box assembles self? No.

[Antonio García Guerra]

I just got the email and i think about the possibility of reusable gels.

Maybe i got it wrong,

My bad.

Antonio

[Nathan McCorkle]

silicone? easy to buy at home depot, or other hardware stores... can
be flexed for easy cleaning and sterilization if you would want that
(or boil rather, to dissolve old gel)

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[Jeswin]

are we talking about a way to cast the gels or make a self-contained
system where you pour the gel in the tray, add buffer and run the gel?
Sort of like a polyacrylamide gel?

[John Griessen]

On 12/13/2011 02:09 PM, Mackenzie Cowell wrote:
> I guess the simplest design would be to make the ceiling of the cassette (the orange post-filter) removable so gels could be
> poured in and cast or dumped out when done.

That's what I was imagining.

I like vertical for smaller desktop footprint, and vertical is how you pour
melted gel in, so why not view in that angle also with an illuminator behind.

If you wanted to keep it slim, having some of the edges welded together would
help. an end plug with silicone ridges might be good for where the "bottom",
or destination electrode is, and it could come out to let dishwasher spray
flow through and clean well.

On 12/13/2011 02:24 PM, Nathan McCorkle wrote:
> silicone? easy to buy
Right.

Sketches anyone?

[John Griessen]

On 12/13/2011 02:25 PM, Jeswin wrote:
> are we talking about a way to cast the gels or make a self-contained
> system where you pour the gel in the tray, add buffer and run the gel?

We probably need sketches soon, but I think we're talking about
mini sized cassette systems for running one or 2D gels like:

http://www.precastgels.com/mini%20gels%20page.htm

http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/Products?OpenDocument&moduleid=40213
http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/Products?OpenDocument&moduleid=40213
http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/Products?OpenDocument&moduleid=40213

http://www.precastgels.com/novex.htm

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/DNA-RNA-Purification-Analysis/Nucleic-Acid-Gel-

Electrophoresis/E-Gel-Electrophoresis-System/E-Gel-Go.html

The last one is most like the concept Mac started with.

John

[Cathal Garvey]

Ooo, silicone is a nice idea! Clear silicone running tray that sits
inside a casting silicone mould. You fit the running tray into the
casting mould, then flex the latter off when cast. The silicone can be
made transparent to permit blue light.

However, mightn't be UV permissive or might break down on exposure to
UV; would require use of blue-illuminating dyes.

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[Mackenzie Cowell]

Has anyone actually tried electrophoresing dna through silicone?  Can't find any literature on it.

[Cathal Garvey]

I don't think nathan was suggesting electrophoresing *through* silicone,
just using silicone as a casting and running rig instead of perspex.

That said, I'm planning to test someday whether microbial cellulose
would work as an alternative to agarose; crystal structure of pure
microbial cellulose isn't that different to agarose. Uncharged, linear
sugar polymers. You could grow gels with wells cast in them using a
derivative of the common "kombucha" culture, treat them with peroxide
and/or HCl to remove remnant biological bits and native DNA, and then
try them out as gels.

Reuse by UV irradiation to fragment "used" DNA, electrophoresis to
remove, diffusion in fresh buffer.

/speculative

On 13/12/11 22:12, Mackenzie Cowell wrote:
> Has anyone actually tried electrophoresing dna through silicone? Can't
> find any literature on it.

[Simon Quellen Field]

It would seem a lot easier to simply vacuum form the trays than to either

glue together Plexiglas or cast silicone.

Make a positive mold of the tray. This can be as simple as cutting a block

of wood, or placing wood strips on a cookie sheet.

Cut out the sides of a 2 liter soda bottle, and uncurl it so that it lies somewhat

flat on top of the wood. You can place a wood block on top so that it doesn't

uncurl.

Bake in an oven at low heat. The plastic will soften and conform to the mold.

You can make a negative mold to fit on top if there are tight places where the

plastic film doesn't fall into place. Or you can actually make a simple vacuum

forming rig, and connect your dust-buster or household vacuum to it.

This is how many of the blister-packages for consumer goods are made, and

it should serve quite well for the trays, and it is dirt cheap and simple to DIY.

 

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[John Griessen]

On 12/13/2011 07:30 PM, Simon Quellen Field wrote:
> It would seem a lot easier to simply vacuum form the trays than to either
> glue together Plexiglas or cast silicone.

Yes, the illuminated side UV clear acrylic probably can be vacuum formed
without much distortion you would care about and make a good shape for a
flat sheet to seal to -- with a gasket groove formed in. Stainless steel
spring clips on the edges to hold together.

[Meredith L. Patterson]

There are eighty freaking squillion types of industrial silanes, and
the other day I ran across a site that indexes them by property (such
as cure time, optical characteristics, &c) and points you at where to
get them. I expect a suitable one could be found pretty easily. Apart
from UV permissiveness and resistance to UV breakdown, what other
properties are needed? I assume reasonably flexible but with decent
shear strength.

--mlp

[Nathan McCorkle]

On Wed, Dec 14, 2011 at 6:06 AM, Meredith L. Patterson
<clon...@gmail.com> wrote:
> There are eighty freaking squillion types of industrial silanes, and
> the other day I ran across a site that indexes them by property (such
> as cure time, optical characteristics, &c) and points you at where to
> get them. I expect a suitable one could be found pretty easily. Apart
> from UV permissiveness and resistance to UV breakdown, what other
> properties are needed? I assume reasonably flexible but with decent
> shear strength.

link? sounds like a good web page!

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