designing flanking primers around msp primers - (Aug/02/2005 )
I need to design primers that flank my msp primers, for a nested-pcr type reaction. The gene in question is human MGMT. I found the promoter sequence, but the msp primers that I am using don't seem to be on the sequence. Are the msp primers modified somehow so that they are different from the original promoter sequence?
Thanks for any help you can offer.
the msp primers would be to the MGMT sequence after bisulfite conversion (this is why you can't find them on your seqeunce). Thus you must take your MGMT seqeunce and "mock" bisulfte convert it using MS word or and equivalent.
Basically I find and replace all CG to NG......then find and replace all C to T and finally find and replace all NG back to CG.
Alturnatively you can use methprimer for MSP and it does it all for you in a jiffy. Just google methprimer, it's a primer3 based web interface for MSP primer design, it does pick BSP primers, but I don't think they work very well.