I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that region with PCR.
For some reason I am not able to amplify the region. I designed my primer by Primer 3 plus and manually, but it is not working. The main reason is that I don't have GC pair in the primer.
Is there any other way to fix the problem?
My primer concentration is 200nm.