Thank you everyone for your help in response to my querie:

Hi Everyone

I have been using a 10% Acrylamide gel to run PCR products of
approximately 96-100bp in size.  In trying to avoid using acrylamide, I
have converted to use a product call "QA agarose, high resolution" at 6%
and encountered some problems.
Has anyone  have any experience, with runnning fragments of approx. the
above size, using the QA agarose? I'd appreciate any input at all on the
matter.

Thank you.

Nga Dang.
Teaching technician
Dept. of Biological sciences
Monash University
Clayton 3800 VIC
Australia.

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I've used NuSieve agarose at 6% for fragments a little bit bigger (150bp) -
and this worked fine for distinguishing between fragments about 6 bp apart.
I found that the most important 'tricks' are to make sure you heat the
agarose really well (and add it slowly to the buffer so it does not clump)
since it melts much more slowly than traditional agarose. Second is that you
have to run the gel much more slowly (not over 90v) to avoid warping the
fragments.

I hope this helps.
Alexis

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Every time I've tried using one of the supposed high-resolution agaroses, I
end up cursing them and going back to acrylamide, though I've never used it
at 10%; we've gone as high as an 8% (0.35mm thickness)- to resolve
microsatellite polymorphisms in fragments ranging in size from 100-200bp.
More recently, we tried using NuSieve at 4%, but again, could not resolve
the size differences.  And making gels that thick is a pain.  

We have been silver-staining the acrylamide gels, but will try a DNA stain
called FMC Gel-Star.  

I'm curious to know what sort of apparatus you are running your acrylamide
gels in.  We typically use the Bio-Rad Sequi-Gen 38x30cm setup, because we
can load 48 samples across.  We tried using their protein-oriented Protean
II system, but the gels are thicker, and not set up to run at high enough
temperatures, or at least I think that's what our problem was.  Bio-Rad tech
support could offer no help b/c they said the unit is meant for proteins.  

I'd very much like to know what your experience is, and what you learn from
others.  

Best wishes,
Bob Marra

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   We don't use QA agarose but we do use NuSieve GTG Agarose to resolve
fragments that size. We usually use 2.8% gels to resolve fragments 80-120 bp
in size. It is low melting too so you can cut out the bands and use them for
reamplification, cloning etc.

Cheers,
Anne

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Nga.Dang-Lien@sci.monash.edu.au