DNA Ladders for Short Fragments

Guy Hoelzer hoelzer at unr.edu
Thu Oct 20 18:43:48 EST 1994

I am using non-denaturing polyacrylamide gels to deparate PCR amplified
fragments containing simple-sequence-repeats (SSR's).  Heterozygotes may
have fragments in the 150-300 bp range differing by only a couple of bases.
 I would like to be able to size the fragments using a DNA ladder, but the
ladder would have to contain many closely spaced fragments.  One
possibility is to use the products of a sequencing reaction, but it would
be preferable to have a ladder with regularly spaced bands using only a
single lane.  I know that there is a commercially available 10 bp ladder,
but we have not had much luck with it.  I also know that FMC has a protocol
that produces a four bp ladder, but we find that it just becomes a smear at
around 200 bp.  Is there another option?  Are there any other commercially
available ladders that might fill our needs?

Thanks in advance for any advice.

Guy Hoelzer                                                  
hoelzer at unr.edu
Dept. of Biology
University of Nevada Reno
Reno, NV  89557

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