For my prospective Chip experiment, I am designing the primers for the promoter region of target gene to include the binding site of putative TFs in the amplicon.
What should be amplicon size for such primers and is there any specific tool for this?
Beatriz Lacerda Sousa
Hello Anup
Usually I design primers so the amplicon will be between 150 to 250 bps.
Once you know the sequence for the promoter I would use UCSC genome browser (https://genome-euro.ucsc.edu/index.html) to extract the sequence that flanks the promoter.
Once you have the sequence you can use primer 3 to design the primers (http://biotools.umassmed.edu/bioapps/primer3_www.cgi).
After you have the primers designed blat them to make sure they do not target multiple regions. And you are done.
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