Fast gel electrophoresis - any affordable/open systems?

[Ra Ramana]

Objective:  Easy & quick ways to id DNA after endpoint PCR in places where one can't expect to find agarose etc. available easily. 

Pre-cast gels will be good.  (No gels & alternative systems such as imaging a la PCR + optics integrated will be ideal any time)

Currently doing: Building some open source/ low-cost regular gel boxes & trans-illuminators. Towards this, revisting threads from 2012 such as https://groups.google.com/forum/?hl=en#!msg/diybio/UO6JnUTjE_Y/xXrt_vO5yXoJ;context-place=forum/diybio & making these open design systems [@Cameron from Biocurious, couldn't find your designs/ files. Please share them again including any updates. ] 

I've the blue gel system from MiniPCR guys and it's appreciated much around here (in India). But something cheaper & without need for gel casting etc., will be better. 

The only fast gels systems available that I find are : E-gel (Thermo) and Flashgel (Lonza) both of which are expensive. 

Seeking: 

Better/ low-cost designs/suggestions for gel + transilluminator system. 

Are there open source or low-cost versions available for the quick electrophoresis systems? Pre-cast ones.

(i think e-gel patents are almost expiring or are already). Have alternative approaches such as paper-based ones been developed 

by folks & not yet mainstreamed. (there is a thread here from 2013  on paper electrophoresis with many good references)

What's the take of the community on this? 

Any recommendations or alternative systems (designs for PCR integrated with imaging at low costs) 

Thanks,

ravi

[Abizar Lakdawalla]

Check this out 

http://www.instructables.com/id/DIY-Simple-Cheap-Electrophoresis-Setup-for-DNA-Sep/

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[Patrik D'haeseleer]

For the gel box, you can get away with a plastic sandwich box from the dollar store, two pieces of stainless steel wire, and a couple of 9V batteries stacked end-to-end. Works just fine...

As for the gel, desert grade agar-agar does work, but it's more opaque, and you won't get very sharp bands because it's more heterogeneous. If you just want to know whether or not you got a single band of approximately the right size, that may be enough though.

I'm a little puzzled about the fact that you said you want a solution for places where you can't expect to find agarose, and yet precast gels are OK? It would seem to me that agarose should be much easier to find than precast gels.

Patrik

On Thursday, October 12, 2017 at 1:09:04 PM UTC-7, Abizar Lakdawalla wrote:

Check this out 

http://www.instructables.com/id/DIY-Simple-Cheap-Electrophoresis-Setup-for-DNA-Sep/

On Thu, Oct 12, 2017 at 10:19 AM, Ra Ramana <emailrav...@gmail.com> wrote:

Objective:  Easy & quick ways to id DNA after endpoint PCR in places where one can't expect to find agarose etc. available easily. 

Pre-cast gels will be good.  (No gels & alternative systems such as imaging a la PCR + optics integrated will be ideal any time)

Currently doing: Building some open source/ low-cost regular gel boxes & trans-illuminators. Towards this, revisting threads from 2012 such as https://groups.google.com/forum/?hl=en#!msg/diybio/UO6JnUTjE_Y/xXrt_vO5yXoJ;context-place=forum/diybio & making these open design systems [@Cameron from Biocurious, couldn't find your designs/ files. Please share them again including any updates. ] 

I've the blue gel system from MiniPCR guys and it's appreciated much around here (in India). But something cheaper & without need for gel casting etc., will be better. 

The only fast gels systems available that I find are : E-gel (Thermo) and Flashgel (Lonza) both of which are expensive. 

Seeking: 

Better/ low-cost designs/suggestions for gel + transilluminator system. 

Are there open source or low-cost versions available for the quick electrophoresis systems? Pre-cast ones.

(i think e-gel patents are almost expiring or are already). Have alternative approaches such as paper-based ones been developed 

by folks & not yet mainstreamed. (there is a thread here from 2013  on paper electrophoresis with many good references)

What's the take of the community on this? 

Any recommendations or alternative systems (designs for PCR integrated with imaging at low costs) 

Thanks,

ravi

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[Abizar Lakdawalla]

You also need a buffer - making one out of Boric Acid - cockroach killer powders in US stores are ~100% Boric Acid. Plus NaOH (lye). Will send out recipe for making later on.

Agree with Patrik on why you would use precast gels. They are very expensive (about $10/gel) and they only work on commercial gel boxes specifically designed for the precast gel.

What are you planning on using agarose gel electrophoresis for? Agar-agar can be cleaned up for sharper bands but again what is your end use.

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[Ra Ramana]

Thanks Abizar & Patrick.  Yes, have seen the instructables gelbox (also Iorodeo) and building a few. 

@Abizar - will look out for the boric acid based recipe - interesting. 

Agar-agar surely is a cheaper alternative, but it has established drawbacks. Here is a comparison : 

http://citizensciencequarterly.com/2012/01/cheapass-science-comparison-of-agarose-agar-agar-and-cleaned-agar-agar-for-gel-electrophoresis-of-dna/ 

Of course, I will also do some tests too later for my applications - mainly demo'ing DNA extraction, amplification (PCR) & verification - so sharp single bands should do. 

In this vein, came across two easy approaches to recover agarose from agar-agar that may be of use: (purifying own agarose) 

1) Agarose using glycol : http://www.freepatentsonline.com/4990611.html

2) Using DMSO: https://www.e-algae.org/upload/pdf/08You-Jin%20Jeon-%EC%98%A4.pdf 

Agree that pre-cast gels are more expensive. My point with them is that they are much quicker & ready-to-use.  And mainly wondering if we have any open alternatives/approaches for achieving something similar! You touched this exactly, when you said these approaches are restricted to proprietary everything including their own instrumentation. So, if any of us want fast electrophoresis, are we stuck? No alternatives or are there any?   

[Scott]

Look at IO Rodeo (https://iorodeo.com/). They make an open source gel electrophoresis system and power supply. You can get everything pre-assembled or as kits that you assemble yourself. If you have access to a makerspace you can download the plans and cut the acrylic yourself. I go to a local Plastics company and can get free scraps of 1/4" acrylic sheet that can be cut to size. You can buy the PCB fro $5 from IO Rodeo and built the power supply yourself if you have the components.

Cheers,

Scott

Open Science Network

Vancouver, BC, Canada

http://opensciencenet.org/

[Ra Ramana]

Thanks Scott. Making the IORodeo one already.. they are easy & good.

[Scott]

Of course you don't have to use platinum wire but if you want to IORodeo told me a few years ago that they buy their's from a company called Myron-Toback in New York. You can ask them for whatever length of wire you need and they ship it that day or the next. You can ask them for as much or as little as you want. They do have a website (http://www.myrontoback.com/calculator) but for ordering IORodeo said it is best to call them at 212-398-8300 and ask to order platinum wire, part # PT010RSW. This is the 0.010" round soft wire.