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An acid-base switchable [c2]daisy chain rotaxane terminated with two 2,6-diacetylamino pyridine units has been self-assembled with a bis(uracil) linker. The complementary hydrogen-bond recognition patterns, together with lateral van der Waals aggregations, result in the hierarchical formation of unidimensional supramolecular polymers associated in bundles of muscle-like fibers. Microscopic and scattering techniques reveal that the mesoscopic structure of these bundles depends on the extended or contracted states that the rotaxanes show within individual polymer chains. The observed local dynamics span over several length scales because of a combination of supramolecular and mechanical bonds. This work illustrates the possibility to modify the hierarchical mesoscopic structuring of large polymeric systems by the integrated actuation of individual molecular machines.