How to design prime detecting plant methylation? - (Feb/21/2009 )

Hi
I have a problem for help.If I want to detect the methylated state of a gene in Arabidopsis,should I design degenerate primer set or specific primer set ? And how to design the prime ?

luck on Feb 21 2009, 06:17 AM said:

You can design specific primers using methylexpress @ABI

microlight on Feb 24 2009, 05:42 AM said:

Thank you for you answer.But arabidopsis methylation include CG,CNG and CNN pattern. methylexpress @ABI designs primer sets accoding to CG pattern ,if i design specific primer by methylexpress @ABI ,how to design CNG and CNN methylation ? Could you give me more suggestion?
Thanks

luck on Feb 21 2009, 06:17 AM said:

Hi Luck,

I had the same question. I came across this online tool called Kismeth. It is supposed to help in sequence analysis after bisulfite treatment and generate primers for the input plant DNA sequence considering non-CpG as well.
Hope this helps.