Fading out gels

Leslie Johnston-Dow leslie at thelen.org
Sun Dec 7 06:29:45 EST 1997

Hello All,
We saw this phenomenon a couple of years ago.  It was primarily seen on the
373, but I have seen also on the 377. The symptoms were that the data was
fine for about 150-200 bases and then faded out over a period of 10-15
bases. It then reappreared about 20-50 bases later. There was no loss of
resolution at all in the reappearing bases and no loss of length of read.
The fade always occurred across the entire gel, although it may be more
'intense' in some regions.  We saw it in our development lab, several
customers labs in Europe and the US. We attributed it to some type of
'quencher'  in the gel or running buffer, however, we could not reproduce
it consistently.

There is a simple fix for it. It appears that this 'quencher' can be made
to migrate ahead of the data if you pre-run the gel for 15 minutes. This
completely fixed the problem for our customers and for us.

Hope this helps,
Leslie Johnston-Dow

Leslie Johnston-Dow, Ph.D.                        email:
ldow at apldbio.com
Senior Staff Scientist, HIV Group Leader   email:    leslie at thelen.org
Applied Biosystems Div. of Perkin Elmer    Voice:   650-638-5104
850 Lincoln Centre Drive                            Fax:       650-638-6177
Foster City, CA     94404

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