Hi! I am new in the field and I am trying to design primers for bilsulfite pyrosequencing. I tried the Meth Primer but the problem is that the primers designed by the programme are not of my interest. I understand that when there are many CpGs, the programme avoids that region because the primer should not contain many CpGs. But If this is the region of my interest, is there any possible way to overcome this problem?
And another question:
How can I design the primer for pyrosequencing?

Thanks

Hi,
Thanks for your informations about bisulfite PCR.

I am a student majoy in methylation of DNA. now I 'm quite confused by my experiment. i'm doing bisulfite sequencing and now the PCR products is not what i want.

the sequence in the agrose gel (2%)is not the target seqence, my target sequence is 243bp, but in the gel, it's may be 270bp.(fig1)

but more confused me is that i use 8% PAGE gel run my product, it indicated about 330bp(fig2). i don't know why?

can you help me?