I want to clone a 3kb DNA fragment into pGEMT EASY. On gel I can see 3kb band but I can't clone it into pGEMT EASY. Can anyone suggest how I can troubleshoot?
It all depends upon which polymerase you are using for amplification. Taq will leave an A overhang, many other enzymes will not. You can just look up the enzyme you used to see whether it adds a terminal A or not.