Expedite chemistry oligo synthesis

James Gibbs gibbs at husc4.harvard.edu
Sun Mar 20 00:58:01 EST 1994

I'm writing to ask what others' experience has been with expedite 
chemistry used to synthesize oligonucleotides. We have had a Biosearch 
Cyclone oligo synthesizer for over four years. We use it very heavily. 
It has never given us any problems until we switched over from 
beta-cyanoethyl chemistry to Expedite chemistry. 

A few months later, around Halloween, the quality of oligos produced on
the machine went down hill. Some oligos didn't work for PCR or sequencing.
Others were mostly mutated when used in PCR and cloned. When we looked at
them on an analytical gel, we found ladders of oligos in most of them 
with no single major band. Nothing changed about the way we worked except 
the chemistry.

It turns out that some gunk had narrowed up the walls of the tubing, 
slowing down the flow rate. The people from the company say they 
heard of this only from one other user (Merck, I think) that used 
their machine heavily with Expedite chemistry. They replaced *all* the 
tubing in our machine and the flow rate was back to normal for less than 
a week. Then they replaced all the tubing and all the valves. The machine 
worked again for less than a month. Now we're with the same problem of 
low flow rate, poor quality oligos. This is the third or fourth time!

After much nasty words, we now have a loaner machine running 
beta-cyanoethyl chemistry at our insistence. My boss blew his top when 
they tried to sell us Expedite chemistry again. We're assuming it was the 
Expedite chemistry that caused us all these headaches.

Anyone have similar or opposing experiences?

Jim Gibbs                                      gibbs at husc.harvard.edu
"Don't become part of someone else's bad karma."
"If George Washington were alive, he'd be rolling in his grave."

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