I use Methyl Primer Express 1.0 to make an approximation and then manually change it for my convenience. I am not sure if you need to downloaded it or they e-mail you the software, but is free for sure. (http://marketing.appliedbiosystems.com/mk/get/METHYL_PRIMER_login)

This tutorial was really useful: docs.appliedbiosystems.com/pebiodocs/04370961.pdf

You can validate it with Primer3 using methylated sequence (also from MethylPrimer).

I use Methyl Primer Express 1.0 to make an approximation and then manually change it for my convenience. I am not sure if you need to downloaded it or they e-mail you the software, but is free for sure. (http://marketing.appliedbiosystems.com/mk/get/METHYL_PRIMER_login)

This tutorial was really useful: docs.appliedbiosystems.com/pebiodocs/04370961.pdf

You can validate it with Primer3 using methylated sequence (also from MethylPrimer).

My favorite is "MethPrimer".

http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi

It will present you with primers for bisulfite sequencing/enzyme digestion or methylation-specific primers. It's nice to visualize your bisulfite-treated DNA by sequence prior to designing MSPs. If you want TaqMan reagents you can finish by using Methyl Primer Express.

Have fun!

i am going to third what GV said. This is exactly what I have done in the past.

I am using Methyl Primer Express 1.0, it`s free. You can download from the link that Gardenia Vargas gave you

For in silico checking of methyl-specific primer specificity, this site is quite useful. For help in deciding inputs, just hover your pointer over each position and look at the explanation at the right under the "Help" heading.

http://bisearch.enzim.hu/?m=genompsearch

There is also a utility for MSP primer design, but I have not used it.