Re: [DIYbio] How does Gelgreen stain DNA? Thoughts on placement in well instead of gel or buffer?

From the Biotium (the compkany that makes gelgreen and gelred) the
stain works on both ssDNA and dsDNA, so its not just doing
intercalation.

From the same document it seems like the company doesn't even really
know... or they are being a bit obscure
"What is the binding mechanism
of GelRed/GelGreen?"
"GelRed and GelGreen most likely bind by a combination
of intercalation and electrostatic interaction."

Also:

"In which direction does
GelRed/GelGreen migrate?"

"GelRed and GelGreen do not migrate through the gel as
easily as EB. It is not necessary to add additional dye to
the running buffer, and the gel will be stained more
homogenously than that of EtB"

(where EB and EtB are assumed to be Ethidium Bromide, which has a +
charge and migrates in the opposite direction of DNA)

http://www.biotium.com/product/product_info/other/GelRed%20and%20GelGreen%20FAQ.pdf

I personally think post-staining is the best method, as you KNOW it
won't affect the migration of the DNA bands at all. Post-staining
solution keeps working well for at least 1.5 - 2 months before you
need to add a little more stock solution.

On Mon, Feb 6, 2012 at 2:19 PM, cameron <seluronking@gmail.com> wrote:
> There's a small group of us that are working with GelGreen at
> Biocurious in an effort to find the most efficient and cost-effective
> way to use it.  We've tried pre-staining (in gel) and post-staining
> (in buffer) and both work well.  We were wondering if there is any way
> to combine the stain with the DNA prior to or at the time of -
> insertion into the well of the gel.  We haven't been able to find any
> information about how it actually stains. We ran a quick test last
> night and found that it does migrate with the DNA but not cleanly.
> Does this make any sense or are we wasting our time? Has anyone
> experimented with this or know how Gelgreen stains the DNA?
> Thanks,
> Cameron
>
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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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