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We aimed to create an autonomous on-chip system that selectively captures and transports lipid vesicles (liposomes) by using machinery that mimics biological systems. By exploiting DNA hybridization and biomolecular-motor-based motility, we demonstrate that single-stranded DNA-labeled microtubules, gliding on kinesin-coated surfaces, acted as cargo transporters, and single-stranded DNA-labeled cargo liposomes were captured onto the gliding microtubules specified by DNA base sequences. This paper is the first to demonstrate the capture and transport of specified liposomes by using the reconstituted microtubule motility. Our results will help to create biomolecular-motor-based biochemical analysis chips.