PCR with only one known primer

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einatgranot
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PCR with only one known primer

Post by einatgranot » Fri Sep 19, 2008 10:05 am

I would like to sequence a breakpoint of an inversion. I have a known specific primer on one side of the inversion (approximately 300 bp from the breakpoint) , but on the other side I have no intelligent guess for a primer close to the breakpoint.
What are my options? Can I do a PCR with one specific primer? How should I design the other primer?
Thank you!!!!!
Einat

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canalon
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Post by canalon » Fri Sep 19, 2008 1:45 pm

No, a PCR with only one specific primer would not work.

In this case I would simply clone and use the known primer as a test for the presence of the right fragment by PCR using the vector as the target for the second primer. The other quicker solution is to purify enough DNA and sequence directly.
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)

biolearner
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Re: PCR with only one known primer

Post by biolearner » Fri Oct 10, 2008 5:46 am

Your problem is not difficult to solve. Do you know the name of gene? I suggest you visit the PCR Core at:
http://www.pcrworld.blogspot.com/

The anser should be over a paper there.

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