If you intend to clone a PCR fragment you MUST purify before cutting the DNA. Otherwise, the (still active) PCR enzymes and dNTPs will extend the 3' end of the cut DNA and destroy the cohesive site, preventing ligation.
Speaking of purification, can anyone confirm for sure that doing gel extraction (for the desired product) after digestion prevents ligation (of the digested PCR product) to the vector? What really happened? Did the whole process of extraction remove the sticky ends?
Would it be recommended to deactivate the RE followed by ligation?