PCR-What is in my reaction?

[Perry J. Bushong]

I'm just trying to figure out what is in my PCR
reaction. After amplification, I always find a
stringy, snotty-looking mess in the bottom of all of
my tubes. I put some under the light microscope and
at 400X it appeared as a thin clear ribon. It
doesn't seem to interfere with my reaction, but it
tends to clog up my pipette tips when I'm loading my
gels. My PCR protocol includes: BSA, template,
primers, MgCl, water, buffer, dNTPs, Taq, and I add
some Cresol Red dye to for visibility. I do not use
any mineral oil because my tubes have caps. I guess
the ribbon might be a product of the BSA or the
Cresol Red.
Does anyone have any ideas on what this stuff is, or
how to easily get rid of it?
Thanks.
Perry

[Nick Jacobsen]

Hi there,
Concerning your PCR reactions- In the past I have used BSA for
pulsed field digests. Prior to using the BSA I put it in a boil bath for
10 minutes (to rid it of nuclease activity), this turned the BSA into a
stringy mess similar to what you described. I consequently had to disgard
it. Im not sure that you put enough BSA in your PCR reaction to cause a
visible precipitate but it might be possible. I never use BSA in PCR
reactions myself.

I hope this helps

Nick Jacobsen.