cpgware primer design, does it work - (Jan/10/2005 )

Hi,
I´m trying to design a primer set for two genes which go true methylation analysis. I chose upstream UTR plus upstream region (1000bp upstream) from the gene. Is it ok?
Has anybody used cpgware primer design software? Does it work or should I use some other software? I´m in a bit hurry, so I would appreciate if somebody could help me!

-Karoliina

Hi Karoliina,

I would suggest that you first identify CpG islands within the promoter of your genes and then design primers on those regions.

I have not tried CpGware yet because it is not freely accessible.

Check out this post to find the necessary tools for your purpose.
http://www.protocol-online.org/forums/inde...?showtopic=4589

Hi,
I'm a new one in epigenetic. Now, I 'm trying to design a primer for MSP, I want to know whether the PCR product should contain all CpG island region? or I should design all CpG island primer of the gene's promoter for analysis the status of mythlation?
thanks

Hi Folkman,

Yes, methylation analysis should foucs on CpG island region that surrounding the promoter. If you'r gonna do MSP, design your primer on some important CpG sites. What is in the product doesn't matter because MSP can only detect methylation status of CpG sites within the primer. The product size should be around 100-200 bp but doesn't necessarily need to contain the whole CpG island.

Good luck!

pcrman, I just wanted to say thanks to you.

all the best