Oligo quality

Muhammad Farooq Sabar farooqsabar at hotmail.com
Wed Aug 30 05:13:22 EST 2006

Dear all,
We have an ABI 3900 DNA synthesizer machine. We are synthesizing our DNA 
primers on this machine but we are facing a problem in the quality of these 
primers. When we analyse on the 8% PAGE with 8M urea, every oligo longer 
than 20 bp shows two band. One orignal and one at 20bp. Can some one suggest 
to avoid this problem. Our synthesis scale is 200nMole. All chemicals for 
synthesis are from ABI. It is trytyl off synthesis and deprotection and 
cleavage procedure includes adding of 1.2ml of 33% ammonia, placing at 65 
degrees for 2 hours, spining for 30 minutes, placing at -20 degrees for 10 
minutes and then drying in a speed vac at 65 degees. After that it is 
reconstituted in 100ul of water, desalted by ethanol precipitation.
Consumers also complain even for primers less than 20 bp that they work in 
the beginning but after some time they give non-specificity and smears in 
their PCRs. Suggestions in this regard will be highly appreciated.

Muhammad Farooq Sabar

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