Pfu DNA Polymerase has an approximately 6-fold higher accuracy than Taq DNA Polymerase - it will make a difference, how many mutations might be introduced into your PCR product. That will be important later: you won't want to clone a PCR product with a lot of mutations.

But I'm not sure if this is the reason, why you don't get a PCR product in the first place. have you already checked and/or optimized the usual suspects (quality of primers, annealing temperarure, Mg2+ concentration)? Since you are using a different DNA polymerase, you might need to optimize the protocol again.

Alexander Trampe

Thanks for your suggestion..

Of course, Pfu polymerase-generated PCR fragments will have fewer errors than Taq-generated PCR inserts. Use the Pfu DNA polymerase especially if you are going to use the PCR product for cloning and expression.

Mahsa Mir Mohseni

Me too planning for it. Thank you so much for your suggestion..