1. My strain doesn't have a recA knock out.
2. I use a 2 plasmid system for my work. One replicates through rolling circle and the other through theta replication.
2. I have toehold switch-trigger pair on the plasmids which make strong secondary structures and are probably prone to recombination.
3. I get negligible titres for my product of interest.
Is it possible to prevent this problem through simple bioprocess methods (without cloning anything extra)?
Given that rolling circle replicating plasmids are prone to recombination in general, you may have a challenge on your hands.
You could try chemical inhibition of RecA:
Article RecA Inhibitors Potentiate Antibiotic Activity and Block Evo...
Before you worry too much about recombination, you should investigate why you are not getting product. If the plasmids are recombining in a way to prevent production of your product then you can sequence them again and see how they are altered. Or it could be that the problem is something else entirely and recombination is not actually a concern for you.
Lastly, can you not just switch strains?
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