oligo synthesis problem

Gail Otulakowski gotulak at sickkids.on.ca
Fri Dec 12 13:39:18 EST 1997

I'm looking for suggestions to resolve a problem in oligo design and 
synthesis.  I regularly use the software OLIGO 4.1 with good success to 
design primers for sequencing and PCR.  Recently, I have been having 
trouble getting a functional oligo within a 150 bp sequence of my gene of 
interest.  I have now tried four different 22-24mers.  Some of them have 
been synthesized twice.  Each time, the A260/280 ratio comes back low 
(1.4).  Oligos seem to take up label OK in a 32P kinase reaction but fail 
to work in sequencing, primer extension, or PCR reactions.  Other oligos 
made at the same time to other regions of the gene are OK.  Is this some 
sort of bizarre secondary structure problem?  Or just bad luck?

Gail Otulakowski
Hospital for Sick Children

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