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How to check primers are of correct sequence or not?


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#1 de ifz

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Posted 09 May 2011 - 08:24 AM

I am encountering a problem in my nested PCR reaction that I get a very small size of PCR product 250bp instead of 1500bp. I am doubted about my Primers, that may be these are not of correct sequence. How can I check their authenticity. Please help me out.
PS: what else can be causing this problem???

#2 bob1

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Posted 09 May 2011 - 04:08 PM

Use primer BLAST on the NCBI website.

#3 pcrman

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Posted 09 May 2011 - 07:09 PM

You can also do in silico PCR to check your primer location.

If your primers are right, then the smaller band may come from mispriming and the PCR conditions need optimization.




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