Low DNA yields
It is not uncommon to have low yields when prepping this vector -- if that occurs, use carbenicillin rather than amp as the antibiotic. Carbenicillin is an amp analog that weakens bacterial cell walls, facilitating the release of plasmid.
Sequencing problems and notes
It is not unusual to experience problems with this vector due to it's inverted nature. Additional notes from the Bellen lab include: This is the inverted nature issue.
There is nothing you can do about it.
Uncut it shows a weird pattern.
Cut it should give the correct patterns.
I [Koen] have used this vector over and over again, and there is no problem with it besides the one mentioned above.
You can sequence with T7/T3/M13-F and M13-R.
But due to the inverted nature, the sequence can be problematic as well.
I [Koen]did two overlapping PCRs over the individual attB sites and sequenced that.
The sequence for the plasmid was submitted to GenBank: https://www.ncbi.nlm.nih.gov/nuccore/347979167