Polymers play a central role in cantilever-based single molecule force spectroscopy, either as sample or as anchor of the molecular complexes under investigation. Here we investigated the role of the polymer for the coupling of thermal and mechanical fluctuations of the cantilever into the molecular complex under investigation. We first analyzed the low pass characteristics of the polymeric anchor as a function of its length and identified the optimum filter characteristics for its applications in bond rupture investigations. We then studied the propagation of mechanical fluctuations of either cantilever or anchor point via the polymer into the molecular complex under investigation. With model calculation based on measured polymer extensibilities we were able to identify the optimum combination of cantilever stiffness and anchor length for a given bond strength of the molecular complex to be investigated and to estimate the resulting resolution limit of the different combinations. (c) 2006 Elsevier Ltd. All rights reserved.