Liz size standards

dpboyer at wisc.edu dpboyer at wisc.edu
Tue May 21 22:37:47 EST 2002

>We are doing Gene Scan on our ABI 3100, specifically SNaP Shot for SNP
>typing and have noticed that when we combine our Liz size standard with our
>reaction in HiDi formamide, the liz signal is much diminished compared to
>liz and formamide alone. What is quenching the liz signal? Anyone know the
>emission/excitation characteristics of Liz? Our product signals are fine.
>Thanks for the help. Please respond directly to mkeller at mail.tju.edu

I actually just finished struggling against this phenomenon  while
trying to create my own matrix standard (many of our customers use
filter set C which ABI doesn't support for the 3700 and 3100...but I
was successful and now I have enough for several lifetimes)... What I
finally concluded is that the reduced signal is due to competion
during the EP injection.  Basicly only so many molecules can enter the
caps during the injection and the sample molecules enter in place of
some of the size standard..  I have been using 1ul of Sizestandard
plus 3ul of Sample plus 9ul of formamide and this seems to work for
all of the customer samples that I have tried in the past month (these
include: SNaP shot, AFLP, T-RFLP, and Microsats)....  Now the only
caviat is that I run all of my Genescan stuff on 50cm caps using POP-6
which of course ABI does not support so if I have problems, too bad.

Hope this Helps,
Daniel Boyer
DNA Sequencing/Synthesis Facility
Biotech Center
Univ. of Wisc. Madison


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