DNA size standards, odd bands, & polyA gels

Bruno Cenni bruno.removethis.cenni at removethis.insel.ch
Fri Aug 10 01:39:48 EST 2001


hi russell,

if you're talking about SSCP gels, then the likely reason would be that they
are not denaturing and therefore DNA-fragments are not separated by size
only, but also by conformation...

bruno

""Russell S. Pfau"" <pfau at tarleton.edu> wrote in message
news:B7981A7D.9AA%pfau at tarleton.edu...
> 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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