If the plasmid is really a low copy number vector, we always take a single colony, mix it into ~50 ul of media and then use 8-10 ul of that to inoculate 4 overnight cultures (5 ml each). The next morning, spin each one down, resuspend, lyse, and neutralize each one separately. After you spin them down, load all for preps onto a single collection column and follow the rest of the protocol as is.
I used the standard protocol but ensured that the zymolase I used was fresh and stored at -20. I also did the digestion step for the maximum suggested time.
Hi there, we also had trouble with low yield (especially in low copy- plasmids but not exclusifly). We changed to a no column plasmid prep that has much much higher yields! Just try with a 5ml ON- culture...