Pharmacia ALF problem

Andrzej Migdalski andy at
Tue Jan 31 07:42:11 EST 1995

In article <lwashing-2601951447340001 at>, lwashing at (Lawrence Washington) writes:

>In article <t.keen-1901951651410001 at>, t.keen at
>(Jeffrey Keen) wrote:
>> Has anybody had the same problem as me with their Pharmacia ALF sequencer?
>> What has developed is that I am getting a very high peak of fluorescense
>> (way off scale) passing through the gel just before the primer peak.
>> Pre-running the gel appears to allow the contamination to pass through the
>> gel before loading, but still leaves a residual background of around 45%.
>> The fluorescense isn't noisy so doesn't affect the sequence (as far as I
>> can tell anyway).
>> I've stopped using our own RO water and just use Merck Analar stuff
>> without getting rid of the problem. Swapping detergents doesn't seem to
>> help either.
>> Any suggestions 

We had identical problem. I don't know the reason, it dissappeared
after we had washed the notched plates with 5% KOH in methanol but it
could be just coincidence (background never reappeared even after
stadard plate washing). My friend believes its the problem of ethanol
impurities and careful washing with water after the ethanol will help.

>Sorry, I have no suggestions.  But I am curious about something.  How did
>Pharmacia tech support respond when you asked them about this?  I am just
>wondering how they are to deal with in matters of trouble shooting.

Oh yes, Pharmacia support! Our local Pharmacia support could solve only
hardware problems, they knew nothing about molecular biology or
sequencing at least. They even did not know how to make acrylamide gels
(for several years we were the only ALF users in Poland so they had to
learn with us).

------------  GCT TAA ATG ATT GGT GAT GCT TTG TCT AAG ATT  -------------
Andrzej Migdalski                         Tel (48-2) 658 12 24
DNA Sequencing Lab.			  Fax (48) 39 12 16 23
Institute of Biochemistry & Biophysics    Email: andy at
Polish Academy of Sciences                       andy at
Pawinskiego 5a, 02-106 Warsaw, Poland            andy at

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