DNA oligomers on acrylamide vs. agarose gel

Nina Rosario L. Rojas nrlrojas at phoenix.princeton.edu
Thu Mar 2 20:29:38 EST 1995

This has nothing to do with the referenced post, but everything to
do with the sunject header.
I'm working on a series of PCR reactions based on the overlap extension
method of Paese et al.  After the first round of PCR, I ran the products
on a Phastgel (Pharmacia) 8-25% acrylamide gel, native buffer, and saw
my expected product (120 bp) and a larger piece ~750 bp.  I then ran
a preparative 3% NuSieve (FMC) agarose gel in TAE of the PCR products
to separate the the desired piece from the other product and the plasmid
template.  I did not see the 750-mer on this gel, and when I ran the
sample extracted from the 120-mer agarose gel band on a Phastgel again,
I got back both 120-mer and 750-mer bands.  It seems then that the
750-mer is probably some oligomeric state of the 120-mer that is stable
under Phastgel conditions but not under agarose gel/TAE conditions.
Can anyone shed light on this?

Nina Rojas
Dept. of Chemistry
Princeton U.
nina at berthaw.princeton.edu

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