Instead of purchasing the empty pGIPZ vector for subcloning, can I use one of the controls or just a random hairpin in pGIPZ?
Please note that we do NOT recommend this! This is because the restriction digests may not work completely and with an insert so small (~345bp), you may not be able to tell the difference between which vector band still has a hairpin (if the digest didn't work to completion) and which band is actually an empty vector. MANY colonies would have to be sequenced to confirm the presence of the new hairpin. Even if the empty pGIPZ vector is used to subclone into, we recommend sequencing one or two colonies.
Also, there is a unique BamHI site in the stuffer of the empty vector that can be used as a diagnostic cut to determine if the clone still has the original stuffer, or if a hairpin has been cloned in. If the hairpin has been cloned in, no cut will be made.