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

I have no specific information on GelGreen, but some insights on general
stains might help.

For starters, it's not unusual for DNA stains to have a positive charge,
which helps/enables them to bind to the negatively charged DNA. As a
result, the dyes tend to be "pulled" to the opposite terminal to the DNA
itself.

When there's already a hefty background of dye in your gel, the results
of this are probably invisible, but your "unclean" migration of dye
might be the result; dye getting stripped from the DNA as it migrates
and travelling up to the negative terminal.

In-gel staining is usually the least wasteful method of staining, both
because the DNA collects dye as it travels, requiring less dye-per-cm3
of gel to get the same dye-to-DNA ratio, and because less dye gets left
in the buffer as buffer-gel dye equilibrium sets in.
So I'd strongly suggest leaving post-run staining for dyes that you
can't use in-gel. If you're using stains with a cancer hazard of course,
in-gel makes even more sense; you can't easily spill a gel onto
yourself, but buffer's another story!

On 06/02/12 19:19, cameron 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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