DNA size standards, odd bands, & polyA gels

Russell S. Pfau pfau at tarleton.edu
Thu Aug 9 11:06:01 EST 2001


I've recently begun using a 20cm x 20cm x 1.5mm polyacrylamide gel format
for SSCP and microsatellite analyses. Two things have happened regarding
the appearance of the DNA size standards that I can't explain, and I'm
wondering if anyone else can.

One size standard, a 100 bp ladder from New England Biolabs, exhibits bands
that are not separating as they normally should. For example, with this
size standard there are bands of the following lengths: 400 bp, 300 bp, 200
bp, 100 bp, but the 300 and 200 bp bands may be *closer* together than the
400 and 300 bp bands, the opposite of what should be true. Also, some of
the bands are missing! From what I can tell, bands 1517 & 1200 are not
there at all! 

The other size standard I'm using, a 25 bp ladder, exhibits quadruplets!
Four bands for each size category.

Images of my gels can be viewed here:

http://www.tarleton.edu/~biology/pfau/images/odd_bands.htm

Can anyone explain this?

Thanks in advance for any insight,

Russell 

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