Off answer

             
The best way to turn off Hin will probably using CRE or possibly regulating transcription by the Hin promoter itself.  CRE is an excellent option because it is able to 
flip the gene just once if you use lox66 or lox71.  This way we could give the system a blast of Hin to allow for some inversions and then stop.  We could also LVA tag CRE and use a reversible CRE.  The hope with that idea is that CRE would be around long enough to invert HIN and then degrade before it reversed.  At the same time we would have the ability to turn Hin back on at a later data.

 
Although the idea of inhibiting Fis and HU were tossed around at first, they regulate too many important genes and perform essential functions in the cell.  Any inhibitor 
would affect all Fis or HU; thus, harming the cell.  Using a mutant Hix site does not seem like a viable option either.  In order to get cleavage you need to working Hix sites.  It did not seem that you could have two working Hix sites and then when you do the inversion get one or two non-function Hix sites.  Finally adding ethidium bromide or binding Mg2+ so that it can't be used by the cell would not work because they affect strand exchange.  The DNA would still be cleaved even though it would not be inverted.  Literature seems to point to that cleaved DNA being lost instead of being reintegrated in its original position.

HIXC does not work efficiently under normal supercoiled conditions.  IT is 16 fold less efficient then the wild type.  No inversions were seen after 30 min.  After 1 hr 1.8% was inverted compared to 30% with wild type.  In order for HIXC to have inversion rates comparable to HIXL, the supercoiling needs to be relaxed.  Relaxed supercoiling would decrease the number of inversions that could be done.