Hi Jana,

In fact methyl primer express only design primers on the strand you use as your input.

When you do your bisulfite conversion, your 2 strands of DNA are not complementary anymore.

e.g.  

5' --CG--3'                      --UG--

3' --GC-- 5'     ------->     --GU--

Therefore when you analyze DNA methylation you usually only assess one strand of DNA.

If you want primers which anneal on the second strand of DNA, just take the reverse-complement (http://www.bioinformatics.org/sms/rev_comp.html) of your sequence and apply methyl primer express again.

I hope it helps,

Best,

Ludovic

Thank you very much for quick answer. Now I see my error!

Thank you Ludovic Barault, I learnt a new point.