Rotaxanes are a class of interlocked compounds that have been extensively investigated for their potential utility as switches or sensors. We recently demonstrated that rotaxanes have further application as agents that transport material into cells. This novel finding prompted our investigation into the mechanism by which rotaxanes are involved in transmembrane transport. Two-dimensional NMR analysis showed that a cleft-containing rotaxane exists in two dominant conformations ("closed" and "open"). To determine the importance of conformational flexibility on the ability of the rotaxanes to bind guests and transport material into cells, the rotaxane was chemically modified to lock it in the closed conformation. Charged guests interact less favorably with the locked rotaxane, as compared to the unmodified rotaxane, both in an aqueous solution and in DMSO. In a chloroform solution, both rotaxanes bind the guests with similar affinities. The locked rotaxane exhibited a reduced capacity to transport a fluoresceinated peptide into cells, whereas the unmodified rotaxane efficiently delivers the peptide. Flow cytometry experiments demonstrated that a high percentage of the cells contained the delivered peptide (89-98%), the level of delivery is concentration dependent, and the rotaxanes and peptide have low toxicity. Cellular uptake of the peptide was largely temperature and ATP independent, suggesting that the rotaxane-peptide complex passes through the cellular membrane without requiring active cell- mediated processes. The results show that the sliding motion of the wheel is necessary for the delivery of materials into cells and can enhance the association of guests. These studies demonstrate the potential for rotaxanes as a new class of mechanical devices that deliver a variety of therapeutic agents into targeted cell populations.