I would leave it for an hour. It should be plenty of time.
You could try site directed mutagenesis instead of error prone PCR.
Thanks for your reply. Would it be better to do a double digestion at the same time, or is it usually better to do a sequential digestion with PCR cleanup in between?
If you are using compatible buffers, then I would do a double digest. Saves time.
I am using BamH1 and Nde1 on my PCR products while BamH1, Nde1 and Nco1 on my vector. They do not use the same buffers, but the buffer recommended for the combination would be NE Buffer 3 or BamH1 Buffer. Would you still do a double digestion?