Questions about MSP - (Sep/20/2005 )
I just did MSP and I got bands from both "M" and "U" primer sets. How do I know if this is real or maybe my DNA partially bisulfited.
The positive control I have which treated with SssI methylase seems worked OK, only a big band in the "M" primer set. But I still don't know if bisulfite works or not. Is that right?
The other question I have is that for nested PCR why I can't use the same "M" and "U" set? Looks like you guys always suggest to use universal PCR primer for the first round.
The melting Temp for the "M" set are 59C, 59C and the "U" set are 59C, 53C. Do I have to optimise the "M"PCR and "U" PCR seperately since they have different melting temps.
Thanks! Hopefully I didn't make you guys confused.