Non-specific bindings and repeats may buffer fluctuations

Some bacterial plasmids are known to have multiple binding sites in replication origins, named iterons, to which a plasmid-specific replication initiator protein binds. The potential functions of these elements have been debated for about 50 years. There are several models that try to interpret the purpose of such repeats, however, it is still not completely clarified.

Here we suggest an additional potential explanation for the nature of iterons and their role in plasmid replication – they may serve as a buffer for fluctuations in the replication initiator protein and its binding to the active site. We applied Monte Carlo computer simulation, using Gillespie algorithm, to examine the repeats` effect on noise in the system of iteron-based plasmid replication control. Our results indicate that binding repeats can serve as a buffer for fluctuations, at least under some parameters and conditions. It should be noted that while we ran the simulation with plasmid replication in mind, our results are not limited to plasmid replication only and even not limited to DNA-protein interaction - it may apply to any case of competitive binding, whether these are other systems with binding repeats or even in a case of non-specific binding.