I've read that the traditional cre-lox system is limited by the distance between the loxP sites, and is usually only functional up to about 2 kb. I am looking to use a site-specific recombinase with loxP sites at the start and end of an operon of about 10kB. Is there a site-specific recombinase that would be suited for this purpose?
cre-lox should work fine. While there might be a reduction in efficiency as the distance grows larger, it will still work. If you go back to the origins of Cre-Lox, they are site specific recombinases to monomerize bacteriophage P1 which genome size is about 100kb. So it has evolved to work at 100kb.
Agree with previous answer - Cre Lox should work fine. We are using it to assemble together large DNA constructs (>100kb) in vitro and it works fine. it will work for you especially if your sites are sitting on the same DNA molecule.
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