in deed there is no universal protocol for primer purification , because this depend on the type of the column that you have , and to be more clear each column type has its conditions for the best performance .
and you have to be sure that you have the right column that is design specifically for macromolecules which always have a pore size more than 200 angstrom ,
so tell me what column you have and i will try to help you .
note : you should have preparative or semi-preparative HPLC for this purpose .