Kinesin-driven microtubules have been a focus to serve as molecular shuttles to replace multiple on-chip functions in micro total analysis systems (µTAS). Although transport, concentration, and detection of target molecules have been demonstrated, controllability of transport directions is still a major challenge. To define multiple moving directions for selective molecular transport, we integrated the bottom-up molecular design of microtubules and the top-down design of a microfluidic device. The surface charge density and stiffness of microtubules were controlled, allowing us to create three different types of microtubules with different gliding directions corresponding to their electrical and mechanical properties. The measured curvature of gliding microtubules enabled us to optimize the size and design of the device for molecular sorting in a topdown approach. The integrated bottom-up and top-down design achieved separation of stiff microtubules from negatively-charged soft microtubules with approximately 80% efficiency under an electric field. Our method is the first to sort multiple microtubules by integrating molecular control and microfluidic device design, and is applicable to multiplexed molecular sorters.not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/107458 doi: bioRxiv preprint first posted online Feb. 9, 2017; Kinesin motor proteins and microtubule (MT) cytoskeletal filaments show promise as in vitro nano-scale actuator platform for nanobiotechnology applications. MTs are rigid, polar, dynamic cytoskeletal filaments that serve as mechanically supportive cellular structures. MTs also serve as the highway system for intracellular transport by kinesin and dynein motor proteins. Such motor-driven active transport uses the hydrolysis of adenosine triphosphate (ATP) and is indispensable for maintaining cellular functions. 1,2 In the cell, kinesin motor proteins walk along MTs to deliver vesicular and small molecule cargos to destinations in an in vivo viscous environment. The MT-kinesin transport system can be reconstituted in vitro for cargo transport or inverted to have molecular motors transport MTs.The MT-kinesin system can be combined with microfluidics, to enable simultaneous control of aqueous, bulk chemical composition with direct transport of molecular-scale cargos. These systems promise unprecedented control over nanoscale delivery-not just bulk flow and chemical reactions, and has matured into a micro total analysis systems (µTAS) that could replace on-chip functions in µTAS. [3][4][5] These µTAS systems enable a wide range of applications using motor-driven MTs as molecular shuttles such as molecular transporters, sorters, concentrators, and detectors. MT-kinesin µTAS load cargos onto gliding MTs via avidin-biotin binding, 5,6 antigen-antibody interaction, 7,8 or DNA hybridization 9,10 to be sorted, transported, and detected on the chip. Although individua...