Abstract
We consider DNA-organizing molecular machines consisting of two coupled and oppositely directed motors which act to extrude loops from the double helix that they move along, while excluding one another sterically. In the case where these machines do not dissociate from the DNA (infinite processivity), the steady-state loop distribution is exponential and is described by an effective statistical-mechanical ensemble. However, if enzyme dissociation-rebinding occurs at any finite rate (finite processivity), the steady state qualitatively changes to a highly ordered ¯¯stacked configuration with suppressed fluctuations, with tight hairpin-like condensation of the underlying DNA. This steady-state behavior can be understood via an approximate mapping to the restricted solid-on-solid model in an external field. Possible experimental realizations of these types of molecular machines are discussed, with a focus on type I restriction enzymes and condensin complexes.
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