I have the complete FRT p element insertion sequence from fly base and have located the 34bp FRT site sequence. I designed a primer set to give me a 2kb PCR product flanking the 34bps.
I don't get the 2kb product.
Please complete your query by adding-
1. If not 2Kb amplicon, did you observe any non-specific band(s), if yes,
2. Please share your agarose gel picture to understand the issue
2Kb is a long amplicon. Have you given your polymerase enough time during elongation to complete synthesis?
Please review this info from IDT
https://www.idtdna.com/pages/support/faqs/what-are-the-criteria-for-choosing-pcr-amplicon-length-
and make sure your extension cycle time is appropriate for that size amplicon.
Also, what polymerase are you using? Have you checked what the maximum size of amplicon it can amplify is?
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