DNAseq: POP5 on 3700

Stephanie Johnson sjohnson at gene.com
Wed Mar 29 19:28:33 EST 2000

>Dear DNAseq'ers,
>one additional question for the 3700 specialists:
>When switching to v1.1 and POP5, were does base calling start (in
>bases away from the primer)? On the runs I have seen, the first about
>70 or so bases are lost due to mobility shifts. Our single 3700 is
>now running with v1.1, but we still use POP6. Has the problem been
>solved or is it anyhow only roumors?
>Thanks, Bernd


Have there been any further conclusions about what this mobility shift
is?  I have been trying to optimize our new (and only) 3700, and
regularly see these mobility shifts in the first 70 bases.  When I
called tech support, they stated that they had never heard of this
problem and were not sure of what could cause it.  So far, I have set up
experiments to test concentration of DNA in my reactions, and this
mobility problem seems to be independent of template concentration.  I
have also experimented with different injection buffers and amounts, and
have seen no effect on the mobility shift in any of my trials.  And, I
do use an increased injection time of 60 seconds (a carryover from the
signal intensity problems we encountered after setup and before laser
alignment).  I have not tested whether these shifts are related to
injection time.

Any ideas?

Thanks so much!


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