HELP-rearranged genomic subclones

[Michael F. Gurish]

Can anyone make any suggestions on the best method to subclone unstable 
genomic fragments? I have been attempting to subclone a fragment from the 5' 
flanking region of a murine protease gene in order to do some promoter 
analysis but find that the subclones are truncated.

All of the subclonign to date has used pUC based vectors. Has anyone tried 
low copy vectors? I have one called p3CSZ but haven't tried it yet. Also what 
about different strins of E.coli? Has anyone had success by switching to 
recBC deficient strains?

Any help or suggestions would be appreciated.

Michael Gurish
 email: gurish at mbcrr.harvard.edu