Originally Posted by cloningproblem
i hav a Pcr product for site EcoRI and Sma I but it has got by using taq polymerase (EcoRI-cohisive site) and Pfu polymerase (Sma I-blunt site) then digest Pcr product with EcoRI and gel purified the product was ligated with vector sequencially digested with Sma I and EcoRI gel purified with good DNA concentration, however after ligation could not get any transformed colonies,
i hav this doubt that, while using Pfu tag would it removes EcoRI site of PCR product so that the ligation fails are any other incompactibility may there,
how can i do clone the EcoRI / Sma I pcr product in vector digested with Sma I and EcoRI ?
Are you using both Taq and Pfu together?
I would just use Pfu (or Pfx, anything that will create a blunt end) and then cut with EcoRI. Taq will add 3' overhangs to your PCR product.
Also with your strategy if you de-phosphorylate your cloning vector the cloning will not work.
PCR primers don't usually have 5' phosphates (unless you pay extra for them) so your SmaI-blunt end won't ligate if you have de-phosphorylated your plasmid.
If you have EcoRI and SmaI sites in your PCR primers, you could cut your product with EcoRI-SmaI and clone it. Better still you could use XmaI instead of SmaI (they cut the same site except XmaI gives you a cohesive end).