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PCR-amplicon too short - (May/07/2010 )

Hello everybody,

I hope, you can help me with my problem concering PCR-product length: I am trying to amplify a 400bp amplicon of bisulfite converted DNA, but when I ran a gel, the amplicon is always too short. It was 150 bp long in the beginning. We sequenced the product and the result showed that the PCR started at the correct site but the reaction stopped too early. So we tried out other polymerases and the length increased to 250bp but is still too short.
Has anybody an idea what else I can try?

Thank you for your help,


You can try to modificate the PCR program allowing the polymerase to extent more time. Which PCR program do you use?

And as a curiosity, which bisulfite treatment do you use? I mean, do you use special kit or basic protocol? I am trying to perform this procedure but I obtain bad results.