Methylene Blue for DNA gels

Dr. Peter Gegenheimer PGegen at UKans.nolospamare.edu
Fri Sep 11 19:57:05 EST 1998


On Mon, 7 Sep 1998 12:29:58, "Joseph C. Bagshaw" <jbagshaw at wpi.edu> wrote:

> Methylene blue is not specific for RNA; it stains DNA pretty well.  Ive
> been using it for years to staine DNA that I want to recover from the gel
> and use for, e.g., sub-cloning.  The efficiency of sub-cloning is several
> fold higher than if I stain with EB.  There are however drawbacks.  MB is
> less sensitive than EB, so you have to use at least twice as much DNA.
> Also, you usually have to destain the gel.  I soak my gels in 0.02% MB,
> then destain in distilled water just enough to see the bands.  Don't worry
> if your recovered DNA solution is blue, it won't matter.  Another
> advantage of MB is that it is non-toxic, so it can be used where EB can
> not, e.g. in a high school.
>
> Someone responding to this question mentioned crystal violet, which also
> works.  If you look at the chemical structures, you will see that both
> dyes, as well as several others, have very similar structures.  A few
> years ago I tried all the dyes of this type that I could find in our
> stockroom, and methylene blue was clearly the most sensitive.  However, if
> anyone out there knows of a better non-intercallating dye I'd love to hear
> about it.

If methylene blue stains DNA better than crystal violet, I'm all for it! (Even
if I did tell the world that it can't possible work... that's what you get for
asking questions on the Internet.) A student in my lab tried crystal violet,
and it worked, but the low sensitivity made it almost useless.

I should point out, however, that I have _seen_ a paper which claimed to use
methylene blue as an agent in UV-crosslinking of protein to RNA. If this is
true, one should remember to keep the UV light off when using these stains.

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