[DIYbio] electrophoresis... path length design strategies (was: Paper electrophoresis... . . .)

On 01/30/2013 09:44 PM, Nathan McCorkle wrote:
> On Wed, Jan 30, 2013 at 6:55 PM, John Griessen <john@industromatic.com> wrote:
>> On 01/30/2013 05:49 PM, Nathan McCorkle wrote:
>>>
>>> But DNA migration depends on the e-field not on the power through it
>>
>>
>> Sure, that's true. And I was talking about the e-field also.
>> Ohms per square are the Ohms that resist the e-field. Look it up.
>
> I'm not sure why you're mentioning current or the resistance of the
> media, or what you want me to look up.

I am offering to show you how to simplify thinking about design choices
for electrophoresis. What you can neglect when thinking about path length.

> You only want to keep current low enough such that the media doesn't
> become too hot, and that depends on ion (salt and buffer)
> concentrations.

The above are side issues of path length that you will "get" when you get that
the "length" does not affect resistance of a path of gel or whatever independently,
you need to consider the Ohms per square shape based resistance of a path to get
an independent variable you can use to get what you want, whether that be a
particular current, or power level, etc.



>> The aspect ratio of an electrophoresis path determines how conductive it is
>> if all other variables are the same, (salts, buffers, conductive stuff in
>> solution,
>> gooeyness, amount of duct tape used, viscosity, Coriolis effect, what have
>> you)
>
> Sure that's going to reduce the overall current, that's a good thing.
> Automated Sanger sequencing systems use 50 micron capillaries to do
> electrophoresis.
>
> 310 Capillary, 61cm x 50µm (50 cm well-to-read) - for sequencing
> applications. Internally uncoated. 2 capillaries/package (100
> runs/capillary).
> https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catProductDetail&productID=402840&catID=602042&backButton=true

All that above was on a side issue again, so back to defining the relative path shape
based effect on "a normal electrophoresis system":



>> simplify and give you design insights.
>>
>
> You'd probably get close just. . .just worry
> about Volts per distance?
>
> Are we on the same page?

Not yet. Sounds like you aren't patient enough, but here's another try:

With all other variables held constant, (which means stop talking about particular
designs of machines in specific and extract what is their path shape for purposes of
this discussion), the depth and length and width of a straight path for electrophoresis
analytes to travel on is going to make a big change on how fast they move at the same voltage applied.
In the case of paper The thinness of paper is a linear factor of change you can figure out quickly
if you consider a square area to get a measurement of ohms or current from when same volts per square
is applied. Volts per square goes back to the concept of conductivity of a square piece of a sheet
of known sheet resistance, (sheet resistance is specified in ohms per square).

Converting a particular Ohms measurement to "per square" is the first step when changing
things around a lot as in comparing a gel box to paper strip electrophoresis. Otherwise
you would get lost in details and find they are all interdependent.

A quick example is a gel box twice as long as wide. It has 2 squares of uniform
sheet area. On is the same as the other. Analytes moving along in one square move the same
as in the other. So the Ohms measurement
of volts end to end divided by current end to end is the end to end Ohms. The end to end Ohms
divided by 2, ( 2 squares), gives its sheet resistivity.

Sheet resistivity is useful to use in designing a new shape electrophoresis path for whatever
current, and therefore voltages you desire.

That's the page I've been on. Only a general concept page, no specifics.

Back to work.

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