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How to design primers for CpG, CpNpG, CpHpH methylation - Bisulfite Sequencing PCR (Mar/08/2005 )

hi all,
I am gonna do some methylation analyis of my gene in arabidopsis, I designed primer using MthPrimer program, but this program can only dedign primer for cpG island, if I want to check the mehylation status of C in the whole sequence, such as CpNpG, CpHpH island , which program should I use?
Thanks a lot.
Marshal Wu


Hi Marshall,

You can give Perlprimer a go, as it can design bisulfite seqeuncing primers irrespective of whether there is a island or not.

The link is herePerlprimer Link.

You can also design them by eye, the old fashioned way :-)

Good luck!



Nick, Thanks a lot for your reply.