I found a 9bp repeat (3-7x) in a promoterregion. The repeat itself is GC-rich as is the surrounding sequence. Because of the GC-content I had to design primers which yield a product of 420bp, a bit too long for a 9 bp repeat. Nested PCR's yielded additional interfering PCR products (I tried different annealing temp). I have tried several primersets to amplify the repeat but I can't get rid of the heteroduplexes also. I have tried different urea gels with urea and/or formamide loading buffers. Does anybody have an idea how to solve it, or should I use labeled primers and Gene Scan to screen for this repeat (of course the products need to be separated anyway)
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DNA repeat screening in GC-rich promoterregion
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