Prolonging the lifetime of biomolecules in their functional states is critical for manyapplications where biomolecules are integrated into synthetic materials or devices.A simplified molecular shuttle system, which consists of fluorescently labelledmicrotubules propelled by kinesin motor proteins bound to the surface of a flowcell,served here as a model system to probe the lifetime of a hybrid device. In thissystem, the functional decay can easily be assayed by utilizing optical microscopy todetect motility and disintegration of microtubules. We found that the lifetimes ofthese hybrid systems were mainly limited by the stability of microtubules (MTs),rather than of kinesin. To determine the biocompatibility of polymers widelyused in microfabrication, we assembled flowcells with glass bottom surfaces andcovers fabricated from glass, poly(urethane) (PU), poly(methyl-methacrylate)(PMMA), poly(dimethylsiloxane) (PDMS) and ethylene-vinyl alcohol copolymer(EVOH). Without illumination, only PU had a substantial negative impact on MTstability, while PMMA, PDMS and EVOH showed stabilities comparable to glass.Under the influence of light, however, the MTs degraded rapidly in the presence ofPDMS or PMMA, even in the presence of oxygen scavengers. A similar effect wasobserved on glass if oxygen scavengers were not added to the medium. Strongbleaching of the fluorophores was again only found on the polymer substratesand photobleaching coincided with an accelerated depolymerization of the MTs.