Controlling the direction of kinesin-driven microtubule movements along microlithographic tracks

Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices

Network-based biocomputation (NBC) relies on accurate guiding of biological agents through nanofabricated channels produced by lithographic patterning techniques. Here, we report on the large-scale, wafer-level fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography as the central method. To confirm the functionality of these NBC networks, we solve an instance of a classical non-deterministic-polynomial-time complete ("NP-complete") problem, the subset-sum problem. The propagation of cytoskeletal filaments, e.g., molecular motor-propelled microtubules or actin filaments, relies on a combination of physical and chemical guiding along the channels of an NBC network. Therefore, the nanofabricated channels have to fulfill specific requirements with respect to the biochemical treatment as well as the geometrical confienement, with walls surrounding the floors where functional molecular motors attach. We show how the material stack used for the NBC network can be optimized so that the motor-proteins attach themselves in functional form only to the floor of the channels. Further optimizations in the nanolithographic fabrication processes greatly improve the smoothness of the channel walls and floors, while optimizations in motor-protein expression and purification improve the activity of the motor proteins, and therefore, the motility of the filaments. Together, these optimizations provide us with the opportunity to increase the reliability of our NBC devices. In the future, we expect that these nanolithographic fabrication technologies will enable production of large-scale NBC networks intended to solve substantially larger combinatorial problems that are currently outside the capabilities of conventional software-based solvers.

Through the Eyes of Creators: Observing Artificial Molecular Motors

Inspired by molecular motors in biology, there has been significant progress in building artificial molecular motors, using a number of quite distinct approaches. As the constructs become more sophisticated, there is also an increasing need to directly observe the motion of artificial motors at the nanoscale and to characterize their performance. Here, we review the most used methods that tackle those tasks. We aim to help experimentalists with an overview of the available tools used for different types of synthetic motors and to choose the method most suited for the size of a motor and the desired measurements, such as the generated force or distances in the moving system. Furthermore, for many envisioned applications of synthetic motors, it will be a requirement to guide and control directed motions. We therefore also provide a perspective on how motors can be observed on structures that allow for directional guidance, such as nanowires and microchannels. Thus, this Review facilitates the future research on synthetic molecular motors, where observations at a single-motor level and a detailed characterization of motion will promote applications.

Motility resilience of molecular shuttles against defective motors

Myosin and kinesin are biomolecular motors found in living cells. By propelling their associated cytoskeletal filaments, these biomolecular motors facilitate force generation and material transport in the cells. When extracted, the biomolecular motors are promising candidates for in vitro applications such as biosensor devices, on account of their high operating efficiency and nanoscale size. However, during integration into these devices, some of the motors become defective due to unfavorable adhesion to the substrate surface. These defective motors inhibit the motility of the cytoskeletal filaments which make up the molecular shuttles used in the devices. Difficulties in controlling the fraction of active and defective motors in experiments discourage systematic studies concerning the resilience of the molecular shuttle motility against the impedance of defective motors. Here, we used mathematical modelling to systematically examine the resilience of the propulsion by these molecular shuttles against the impedance of the defective motors. The model showed that the fraction of active motors on the substrate is the essential factor determining the resilience of the molecular shuttle motility. Approximately 40% of active kinesin or 80% of active myosin motors are required to constitute continuous gliding of molecular shuttles in their respective substrates. The simplicity of the mathematical model in describing motility behavior offers utility in elucidating the mechanisms of the motility resilience of molecular shuttles.

Multiplication of Motor-Driven Microtubules for Nanotechnological Applications

Microtubules gliding on motor-functionalized surfaces have been explored for various nanotechnological applications. However, when moving over large distances (several millimeters) and long times (tens of minutes), microtubules are lost due to surface detachment. Here, we demonstrate the multiplication of kinesin-1-driven microtubules that comprises two concurrent processes: (i) severing of microtubules by the enzyme spastin and (ii) elongation of microtubules by self-assembly of tubulin dimers at the microtubule ends. We managed to balance the individual processes such that the average length of the microtubules stayed roughly constant over time while their number increased. Moreover, we show microtubule multiplication in physical networks with topographical channel structures. Our method is expected to broaden the toolbox for microtubule-based in vitro applications by counteracting the microtubule loss from substrate surfaces. Among others, this will enable upscaling of network-based biocomputation, where it is vital to increase the number of microtubules during operation.

Protein Based Biomaterials for Therapeutic and Diagnostic Applications

Proteins are some of the most versatile and studied macromolecules with extensive biomedical applications. The natural and biological origin of proteins offer such materials several advantages over their synthetic counterparts, such as innate bioactivity, recognition by cells and reduced immunogenic potential. Furthermore, proteins can be easily functionalized by altering their primary amino acid sequence and can often be further self-assembled into higher order structures either spontaneously or under specific environmental conditions. This review will feature the recent advances in protein-based biomaterials in the delivery of therapeutic cargo such as small molecules, genetic material, proteins, and cells. First, we will discuss the ways in which secondary structural motifs, the building blocks of more complex proteins, have unique properties that enable them to be useful for therapeutic delivery. Next, supramolecular assemblies, such as fibers, nanoparticles, and hydrogels, made from these building blocks that are engineered to behave in a cohesive manner, are discussed. Finally, we will cover additional modifications to protein materials that impart environmental responsiveness to materials. This includes the emerging field of protein molecular robots, and relatedly, protein-based theranostic materials that combine therapeutic potential with modern imaging modalities, including near-infrared fluorescence spectroscopy (NIRF), single-photo emission computed tomography/computed tomography (SPECT/CT), positron emission tomography (PET), magnetic resonance imaging (MRI), and ultrasound/photoacoustic imaging (US/PAI).

Design of Mechanical and Electrical Properties for Multidirectional Control of Microtubules

Microtubule (MT)-motor systems show promise as nanoscale actuator platforms for performing molecular manipulations in nanobiotechnology and micro total analysis systems. These systems have been demonstrated to exert a variety of functions, including the concentration, transportation, and detection of molecular cargos. Although gliding direction control of MTs is necessary for these applications, most direction control methods are currently conducted using micro/nanofabricated guiding structures and/or flow, magnetic, and electric field forces. These control methods force all MTs to exhibit identical gliding behaviors and destinations. In this chapter, we describe an active multidirectional control method for MT without guiding tracks. The bottom-up molecular design allowed MTs to be guided in designated directions under an electric field in a microfluidic device. By designing the stiffness and surface charge density of MTs, three types of MT (Stiff-MT, Soft-MT, and Charged soft-MT) with different mechanical and electrical properties are prepared. The gliding directions within an electric field are predicted according to the measured stiffness and electrophoretic mobility. Finally, the Stiff-MTs are separated from Soft-MTs and Charged soft-MTs with a microfluidic sorter.

Robotic end-to-end fusion of microtubules powered by kinesin

The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing the potential energy surface along the reaction coordinate, molecular machines expend energy to accelerate a reaction relative to the baseline provided by thermal motion and forces. Here, we design a nanorobotics system to accelerate end-to-end microtubule assembly by using kinesin motors and a circular confining chamber. We show that the mechanical interaction of kinesin-propelled microtubules gliding on a surface with the walls of the confining chamber results in a nonequilibrium distribution of microtubules, which increases the number of end-to-end microtubule fusion events 20-fold compared with microtubules gliding on a plane. In contrast to earlier nanorobots, where a nonequilibrium distribution was built into the initial state and drove the process, our nanorobotic system creates and actively maintains the building blocks in the concentrated state responsible for accelerated assembly through the adenosine triphosphate–fueled generation of force by kinesin-1 motor proteins. This approach can be used in the future to develop biohybrid or bioinspired nanorobots that use molecular machines to access nonequilibrium states and accelerate nanoscale assembly.

Revealing and Attenuating the Electrostatic Properties of Tubulin and Its Polymers

Tubulin is an electrostatically negative protein that forms cylindrical polymers termed microtubules, which are crucial for a variety of intracellular roles. Exploiting the electrostatic behavior of tubulin and microtubules within functional microfluidic and optoelectronic devices is limited due to the lack of understanding of tubulin behavior as a function of solvent composition. This work displays the tunability of tubulin surface charge using dimethyl sulfoxide (DMSO) for the first time. Increasing the DMSO volume fractions leads to the lowering of tubulin's negative surface charge, eventually causing it to become positive in solutions >80% DMSO. As determined by electrophoretic mobility measurements, this change in surface charge is directionally reversible, i.e., permitting control between -1.5 and + 0.2 cm²  (V s)^-1 . When usually negative microtubules are exposed to these conditions, the positively charged tubulin forms tubulin sheets and aggregates, as revealed by an electrophoretic transport assay. Fluorescence-based experiments also indicate that tubulin sheets and aggregates colocalize with negatively charged g-C₃ N₄ sheets while microtubules do not, further verifying the presence of a positive surface charge. This study illustrates that tubulin and its polymers, in addition to being mechanically robust, are also electrically tunable.

All Wired Up: An Exploration of the Electrical Properties of Microtubules and Tubulin

Microtubules are hollow, cylindrical polymers of the protein α, β tubulin, that interact mechanochemically with a variety of macromolecules. Due to their mechanically robust nature, microtubules have gained attention as tracks for precisely directed transport of nanomaterials within lab-on-a-chip devices. Primarily due to the unusually negative tail-like C-termini of tubulin, recent work demonstrates that these biopolymers are also involved in a broad spectrum of intracellular electrical signaling. Microtubules and their electrostatic properties are discussed in this Review, followed by an evaluation of how these biopolymers respond mechanically to electrical stimuli, through microtubule migration, electrorotation and C-termini conformation changes. Literature focusing on how microtubules act as nanowires capable of intracellular ionic transport, charge storage, and ionic signal amplification is reviewed, illustrating how these biopolymers attenuate ionic movement in response to electrical stimuli. The Review ends with a discussion on the important questions, challenges, and future opportunities for intracellular microtubule-based electrical signaling.

A bio-pen for direct writing of single molecules on user-functionalized surfaces

Advancing ultrahigh resolution (below 10 nm) direct writing technologies could lead to impacts in areas as diverse as disease detection, genetic analysis and nanomanufacturing. Current methods based on electron-beams and photo- or dip-pen nanolithography are laborious and lack flexibility when aiming to create single molecule patterns for application specific integration. We hypothesize that a novel strategy could be developed to allow for writing of parallel and yet individually addressable patterns of single molecules on user-controlled surfaces. The strategy is based on using in vitro self-recognition of tubulin protein to assemble rigid protofilaments of microtubules, with one such microtubule to be subsequently used as a "bio-pen" capable of writing "inks" of single kinesin molecules in user-defined environments. Our results show that single kinesin inks could be written under the energy of adenosine triphosphate hydrolysis and observed by both atomic force and optical microscopy. Upon extending ink functionalities, the integration of soft and hard materials for nanostructure assembly and complex single molecule pattern formation is envisioned.

Local direction change of surface gliding microtubules

In vitro gliding assay, microtubule translocation by kinesin motor proteins on a surface, has been used as an engineering tool in analyte detection, molecular cargo transport, and other applications. Although controlling the moving direction is often necessary to realize these applications, current direction control methods focus largely on lithographic microfabrication of tracks or external fields on the microtubules. These methods are effective, but are relatively complicated. In addition, they cannot target particular microtubules without affecting others. In this study, we propose a facile approach that can make local direction changes for selected microtubules using a polystyrene particle as a circular motion center and a DNA double helix with streptavidin as a capture arm. The DNA arm captures a microtubule in the close proximity of the immobilized particle via biotin-streptavidin interaction and changes the moving direction ~10° on average. In contrast, no significant direction changes are observed other than random variations with streptavidin-less DNA arms (normal distribution centered at 0°), similar to regular motility assay. The particle-assisted local direction change scheme is compared with a flow field-based ensemble method. The combination of flow and kinesin interactions with each microtubule exerts a force to change the direction, ultimately aligning it to the flow field, regardless of its initial direction. A simple model based on the force balance predicts the time needed for such an alignment. Overall, the particle-based local scheme is distinct and different from ensemble methods such as crossflow that changes directions of all microtubules in the field, thus offering unique utility in engineering applications.

Engineering with Biomolecular Motors

Biomolecular motors, such as the motor protein kinesin, can be used as off-the-shelf components to power hybrid nanosystems. These hybrid systems combine elements from the biological and synthetic toolbox of the nanoengineer and can be used to explore the applications and design principles of active nanosystems. Efforts to advance nanoscale engineering benefit greatly from biological and biophysical research into the operating principles of motor proteins and their biological roles. In return, the process of creating in vitro systems outside of the context of biology can lead to an improved understanding of the physical constraints creating the fitness landscape explored by evolution. However, our main focus is a holistic understanding of the engineering principles applying to systems integrating molecular motors in general. To advance this goal, we and other researchers have designed biomolecular motor-powered nanodevices, which sense, compute, and actuate. In addition to demonstrating that biological solutions can be mimicked in vitro, these devices often demonstrate new paradigms without parallels in current technology. Long-term trends in technology toward the deployment of ever smaller and more numerous motors and computers give us confidence that our work will become increasingly relevant. Here, our discussion aims to step back and look at the big picture. From our perspective, energy efficiency is a key and underappreciated metric in the design of synthetic motors. On the basis of an analogy to ecological principles, we submit that practical molecular motors have to have energy conversion efficiencies of more than 10%, a threshold only exceeded by motor proteins. We also believe that motor and system lifetime is a critical metric and an important topic of investigation. Related questions are if future molecular motors, by necessity, will resemble biomolecular motors in their softness and fragility and have to conform to the "universal performance characteristics of motors", linking the maximum force and mass of any motor, identified by Marden and Allen. The utilization of molecular motors for computing devices emphasizes the interesting relationship among the conversion of energy, extraction of work, and production of information. Our recent work touches upon these topics and discusses molecular clocks as well as a Landauer limit for robotics. What is on the horizon? Just as photovoltaics took advantage of progress in semiconductor fabrication to become commercially viable over a century, one can envision that engineers working with biomolecular motors leverage progress in biotechnology and drug development to create the engines of the future. However, the future source of energy is going to be electricity rather than fossil or biological fuels, a fact that has to be accounted for in our future efforts. In summary, we are convinced that past, ongoing, and future efforts to engineer with biomolecular motors are providing exciting demonstrations and fundamental insights as well as opportunities to wander freely across the borders of engineering, biology, and chemistry.

Controlled Surface Silanization for Actin-Myosin Based Nanodevices and Biocompatibility of New Polymer Resists

Molecular motor-based nanodevices require organized cytoskeletal filament guiding along motility-promoting tracks, confined by motility-inhibiting walls. One way to enhance motility quality on the tracks, particularly in terms of filament velocity but also the fraction of motile filaments, is to optimize the surface hydrophobicity. We have investigated the potential to achieve this for the actin-myosin II motor system on trimethylchlorosilane (TMCS)-derivatized SiO₂ surfaces to be used as channel floors in nanodevices. We have also investigated the ability to supress motility on two new polymer resists, TU7 (for nanoimprint lithography) and CSAR 62 (for electron beam and deep UV lithography), to be used as channel walls. We developed a chemical-vapor deposition tool for silanizing SiO₂ surfaces in a controlled environment to achieve different surface hydrophobicities (measured by water contact angle). In contrast to previous work, we were able to fabricate a wide range of contact angles by varying the silanization time and chamber pressure using only one type of silane. This resulted in a significant improvement of the silanization procedure, producing a predictable contact angle on the surface and thereby predictable quality of the heavy meromyosin (HMM)-driven actin motility with regard to velocity. We observed a high degree of correlation between the filament sliding velocity and contact angle in the range 10-86°, expanding the previously studied range. We found that the sliding velocity on TU7 surfaces was superior to that on CSAR 62 surfaces despite similar contact angles. In addition, we were able to suppress the motility on both TU7 and CSAR 62 by plasma oxygen treatment before silanization. These results are discussed in relation to previously proposed surface adsorption mechanisms of HMM and their relationship to the water contact angle. Additionally, the results are considered for the development of actin-myosin based nanodevices with superior performance with respect to actin-myosin functionality.

Magnetic Cytoskeleton Affinity Purification of Microtubule Motors Conjugated to Quantum Dots

We develop magnetic cytoskeleton affinity (MiCA) purification, which allows for rapid isolation of molecular motors conjugated to large multivalent quantum dots, in miniscule quantities, which is especially useful for single-molecule applications. When purifying labeled molecular motors, an excess of fluorophores or labels is usually used. However, large labels tend to sediment during the centrifugation step of microtubule affinity purification, a traditionally powerful technique for motor purification. This is solved with MiCA, and purification time is cut from 2 h to 20 min, a significant time-savings when it needs to be done daily. For kinesin, MiCA works with as little as 0.6 μg protein, with yield of ∼27%, compared to 41% with traditional purification. We show the utility of MiCA purification in a force-gliding assay with kinesin, allowing, for the first time, simultaneous determination of whether the force from each motor in a multiple-motor system drives or hinders microtubule movement. Furthermore, we demonstrate rapid purification of just 30 ng dynein-dynactin-BICD2N-QD (DDB-QD), ordinarily a difficult protein-complex to purify.

Motility of Microtubules on the Inner Surface of Water-in-Oil Emulsion Droplets

Water-in-oil emulsion systems have recently attracted much attention in various fields. However, functionalization of water-in-oil emulsion systems, which is required for expanding their applications in industries and research, has been challenging. We now demonstrate the functionalization of a water-in-oil emulsion system by anchoring a target protein molecule. A microtubule (MT)-associated motor protein kinesin-1 was successfully anchored to the inner surface of water-in-oil emulsion droplets by employing the specific interaction of nickel-nitrilotriacetic acid-histidine tag. The MTs exhibited a gliding motion on the kinesin-functionalized inner surface of the emulsion droplets, which confirmed the success of the functionalization of the water-in-oil emulsion system. This result would be beneficial in exploring the roles of biomolecular motor systems in the cellular events that take place at the cell membrane and might also contribute to expanding the nanotechnological applications of biomolecular motors and water-in-oil emulsion systems in the future.

Control of molecular shuttles by designing electrical and mechanical properties of microtubules

Kinesin-driven microtubules have been focused on to serve as molecular transporters, called "molecular shuttles," to replace micro/nanoscale molecular manipulations necessitated in micro total analysis systems. Although transport, concentration, and detection of target molecules have been demonstrated, controllability of the transport directions is still a major challenge. Toward broad applications of molecular shuttles by defining multiple moving directions for selective molecular transport, we integrated a bottom-up molecular design of microtubules and a 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, each with different gliding directions corresponding to their electrical and mechanical properties. The measured curvature of the gliding microtubules enabled us to optimize the size and design of the device for molecular sorting in a top-down approach. The integrated bottom-up and top-down design achieved separation of stiff microtubules from negatively charged, soft microtubules under an electric field. Our method guides multiple microtubules by integrating molecular control and microfluidic device design; it is not only limited to molecular sorters but is also applicable to various molecular shuttles with the high controllability in their movement directions.

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

Pick-and-Place Assembly of Single Microtubules

Intracellular transport is affected by the filament network in the densely packed cytoplasm. Biophysical studies focusing on intracellular transport based on microtubule-kinesin system frequently use in vitro motility assays, which are performed either on individual microtubules or on random (or simple) microtubule networks. Assembling intricate networks with high flexibility requires the manipulation of 25 nm diameter microtubules individually, which can be achieved through the use of pick-and-place assembly. Although widely used to assemble tiny objects, pick-and-place is not a common practice for the manipulation of biological materials. Using the high-level handling capabilities of microelectromechanical systems (MEMS) technology, tweezers are designed and fabricated to pick and place single microtubule filaments. Repeated picking and placing cycles provide a multilayered and multidirectional microtubule network even for different surface topographies. On-demand assembly of microtubules forms crossings at desired angles for biophysical studies as well as complex networks that can be used as nanotransport systems.

Mechanistic Challenges and Advantages of Biosensor Miniaturization into the Nanoscale

Over the past few decades, there has been tremendous interest in developing biosensing systems that combine high sensitivity and specificity with rapid sample-to-answer times, portability, low-cost operation, and ease-of-use. Miniaturizing the biosensor dimensions into the nanoscale has been identified as a strategy for addressing the functional requirements of point-of-care and wearable biosensors. However, it is important to consider that decreasing the critical dimensions of biosensing elements impacts the two most important performance metrics of biosensors: limit-of-detection and response time. Miniaturization into the nanoscale enhances signal-to-noise-ratio by increasing the signal density (signal/geometric surface area) and reducing background signals. However, there is a trade-off between the enhanced signal transduction efficiency and the longer time it takes to collect target analytes on sensor surfaces due to the increase in mass transport times. By carefully considering the signal transduction mechanisms and reaction-transport kinetics governing different classes of biosensors, it is possible to develop structure-level and device-level strategies for leveraging miniaturization toward creating biosensors that combine low limit-of-detection with rapid response times.

Spatiotemporal control of kinesin motor protein by photoswitches enabling selective single microtubule regulations

Artificial control of bio-nanomachines should have a major impact on the development of controllable transport systems for specific cargo transport on chips. Precise spatiotemporal control and local regulation of the bio-motor activity will, however, be necessary if we are to accomplish such a goal. In this study, we exploited the photoswitching properties of azobenzene-based high-energy molecules and inhibitors to control a single kinesin-driven microtubule that has potential to work as a nanocarrier for molecular cargos. In particular, we could influence the local concentration and dispersion of the microtubules at any desired position and time by irradiating a local area of the motility system at one wavelength, while irradiating the entire area at another wavelength, to enrich either cis or trans isomers of photoswitches in the selected region. Furthermore, various regulations (e.g., transporting, bending, breaking) of single microtubules were possible while almost arresting ambient microtubules-all without the need for any surface patterning.

Sensing surface mechanical deformation using active probes driven by motor proteins

Studying mechanical deformation at the surface of soft materials has been challenging due to the difficulty in separating surface deformation from the bulk elasticity of the materials. Here, we introduce a new approach for studying the surface mechanical deformation of a soft material by utilizing a large number of self-propelled microprobes driven by motor proteins on the surface of the material. Information about the surface mechanical deformation of the soft material is obtained through changes in mobility of the microprobes wandering across the surface of the soft material. The active microprobes respond to mechanical deformation of the surface and readily change their velocity and direction depending on the extent and mode of surface deformation. This highly parallel and reliable method of sensing mechanical deformation at the surface of soft materials is expected to find applications that explore surface mechanics of soft materials and consequently would greatly benefit the surface science.

Polymer surface properties control the function of heavy meromyosin in dynamic nanodevices

The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro- and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

Switching of actin-myosin motors by voltage-induced pH bias in vitro

ATP-driven motor proteins, which function in cell motility and organelle transport, have potential applications as bio-inspired micro-devices; however, their control remains unsatisfactory. Here, we show rapid-velocity control of actin filaments interacting with myosin motors using voltage applied to Pt electrodes in an in vitro motility system, by which immediate increases and decreases in velocity were induced beside the cathode and anode, respectively. Indicator dye revealed pH changes after voltage application, and alternate voltage switching allowed actin filaments to cyclically alter their velocity in response to these changes. This principle provides a basis for on-demand control of not only motor proteins but also pH-sensitive events at a microscopic level.

Steering microtubule shuttle transport with dynamically controlled magnetic fields

Nanoscale control of matter is critical to the design of integrated nanosystems. Here, we describe a method to dynamically control directionality of microtubule (MT) motion using programmable magnetic fields. MTs are combined with magnetic quantum dots (i.e., MagDots) that are manipulated by external magnetic fields provided by magnetic nanowires. MT shuttles thus undergo both ATP-driven and externally-directed motion with a fluorescence component that permits simultaneous visualization of shuttle motion. This technology is used to alter the trajectory of MTs in motion and to pin MT motion. Such an approach could be used to evaluate the MT-kinesin transport system and could serve as the basis for improved lab-on-a-chip technologies based on MT transport.

pH responsive ATP carriers to drive kinesin movement

Multilayer film coated CaCO3 microspheres were employed as pH responsive ATP carriers to drive kinesin movement. The production of oxygen scavengers in a kinesin-microtubule system induces the decomposition of ATP-loaded CaCO3 microspheres and then leads to the release of ATP.

On-chip microtubule gliding assay for parallel measurement of tau protein species

Tau protein is a well-established biomarker for a group of neurodegenerative diseases collectively called tauopathies. So far, clinically relevant detection of tau species in cerebrospinal fluid (CSF) cannot be achieved without immunological methods. Recently, it was shown that different tau isoforms including the ones carrying various types of mutations affect microtubule (MT)-kinesin binding and velocity in an isoform specific manner. Here, based on these observations, we developed a microfluidic device to analyze tau mutations, isoforms and their ratios. The assay device consists of three regions: a MT reservoir which captures MTs from a solution to a kinesin-coated surface, a microchannel which guides gliding MTs, and an arrowhead-shaped collector which concentrates MTs. Tau-bound fluorescently labeled MTs (tau-MTs) were assayed, and the increase in fluorescence intensity (FI) corresponding to the total number of MTs accumulated was measured at the collector. We show that our device is capable of differentiating 3R and 4R tau isoform ratios and effects of point mutations within 5 minutes. Furthermore, radially oriented collector regions enable simultaneous FI measurements for six independent assays. Performing parallel assays in the proposed device with minimal image processing provides a cost-efficient, easy-to-use and fast tau detection platform.

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

Kinesin-1 Expressed in Insect Cells Improves Microtubule in Vitro Gliding Performance, Long-Term Stability and Guiding Efficiency in Nanostructures

The cytoskeletal motor protein kinesin-1 has been successfully used for many nanotechnological applications. Most commonly, these applications use a gliding assay geometry where substrate-attached motor proteins propel microtubules along the surface. So far, this assay has only been shown to run undisturbed for up to 8 h. Longer run times cause problems like microtubule shrinkage, microtubules getting stuck and slowing down. This is particularly problematic in nanofabricated structures where the total number of microtubules is limited and detachment at the structure walls causes additional microtubule loss. We found that many of the observed problems are caused by the bacterial expression system, which has so far been used for nanotechnological applications of kinesin-1. We strive to enable the use of this motor system for more challenging nanotechnological applications where long-term stability and/or reliable guiding in nanostructures is required. Therefore, we established the expression and purification of kinesin-1 in insect cells which results in improved purity and--more importantly--long-term stability > 24 h and guiding efficiencies of > 90% in lithographically defined nanostructures.

Negative differential electrical resistance of a rotational organic nanomotor

A robust, nanoelectromechanical switch is proposed based upon an asymmetric pendant moiety anchored to an organic backbone between two C60 fullerenes, which in turn are connected to gold electrodes. Ab initio density functional calculations are used to demonstrate that an electric field induces rotation of the pendant group, leading to a nonlinear current-voltage relation. The nonlinearity is strong enough to lead to negative differential resistance at modest source-drain voltages.

Simulating an Actomyosin in Vitro Motility Assay: Toward the Rational Design of Actomyosin-Based Microtransporters

We present a simulation study of an actomyosin in vitro motility assay. In vitro motility assays have served as an essential element facilitating the application of actomyosin in nanotechnology; such applications include biosensors and biocomputation. Although actomyosin in vitro motility assays have been extensively investigated, some ambiguities remain, as a result of the limited spatio-temporal resolution and unavoidable uncertainties associated with the experimental process. These ambiguities hamper the rational design of nanodevices for practical applications. Here, with the aim of moving toward a rational design process, we developed a 3D computer simulation method of an actomyosin in vitro motility assay, based on a Brownian dynamics simulation. The simulation explicitly included the ATP hydrolysis cycle of myosin. The simulation was validated by the reproduction of previous experimental results. More importantly, the simulation provided new insights that are difficult to obtain experimentally, including data on the number of myosin motors actually binding to actin filaments, the mechanism responsible for the guiding of actin filaments by chemical edges, and the effect of the processivity of motor proteins on the guiding probabilities. The simulations presented here will be useful in interpreting experimental results, and also in designing future nanodevices integrated with myosin motors.

Helical alignment inversion of microtubules in accordance with a structural change in their lattice

Giant helical (oriented chiral nematic) alignments of microtubules of nanometer to centimeter lengths are known to form over a temperature gradient during anisotropic spiral propagation via tubulin dimer addition in a capillary cell. Such helical alignments may be modified by the addition of either paclitaxel or dimethyl sulfoxide, which induces a lattice (helical) structural change in the microtubule itself. In this study, we found that the lattice structural change of microtubules brings about inversion of microtubule alignments in the helical ordering. Based on microscopy and scattering data, a mechanism for the helical ordering of microtubules is discussed in relation to their lattice (helical) structure.

Dynamic formation of a microchannel array enabling kinesin-driven microtubule transport between separate compartments on a chip

Microtubules driven by kinesin motors have been utilised as "molecular shuttles" in microfluidic environments with potential applications in autonomous nanoscale manipulations such as capturing, separating, and/or concentrating biomolecules. However, the conventional flow cell-based assay has difficulty in separating bound target molecules from free ones even with buffer flushing because molecular manipulations by molecular shuttles take place on a glass surface and molecular binding occurs stochastically; this makes it difficult to determine whether molecules are carried by molecular shuttles or by diffusion. To address this issue, we developed a microtubule-based transport system between two compartments connected by a single-micrometre-scale channel array that forms dynamically via pneumatic actuation of a polydimethylsiloxane membrane. The device comprises three layers-a control channel layer (top), a microfluidic channel layer (middle), and a channel array layer (bottom)-that enable selective injection of assay solutions into a target compartment and dynamic formation of the microchannel array. The pneumatic channel also serves as a nitrogen supply path to the assay area, which reduces photobleaching of fluorescently labelled microtubules and deactivation of kinesin by oxygen radicals. The channel array suppresses cross-contamination of molecules caused by diffusion or pressure-driven flow between compartments, facilitating unidirectional transport of molecular shuttles from one compartment to another. The method demonstrates, for the first time, efficient and unidirectional microtubule transport by eliminating diffusion of target molecules on a chip and thus may constitute one of the key aspects of motor-driven nanosystems.

Control of microtubule trajectory within an electric field by altering surface charge density

One of challenges for using microtubules (MTs) driven by kinesin motors in microfluidic environments is to control their direction of movement. Although applying physical biases to rectify MTs is prevalent, it has not been established as a design methodology in conjunction with microfluidic devices. In the future, the methodology is expected to achieve functional motor-driven nanosystems. Here, we propose a method to guide kinesin-propelled MTs in multiple directions under an electric field by designing a charged surface of MT minus ends labeled with dsDNA via a streptavidin-biotin interaction. MTs labeled with 20-bp or 50-bp dsDNA molecules showed significantly different trajectories according to the DNA length, which were in good agreement with values predicted from electrophoretic mobilities measured for their minus ends. Since the effective charge of labeled DNA molecules was equal to that of freely dispersed DNA molecules in a buffer solution, MT trajectory could be estimated by selecting labeling molecules with known charges. Moreover, the estimated trajectory enables to define geometrical sizes of a microfluidic device. This rational molecular design and prediction methodology allows MTs to be guided in multiple directions, demonstrating the feasibility of using molecular sorters driven by motor proteins.

Transporting a tube in a tube

LbL-assembled tubes were employed for micro/nanoscale cargo transportation through the kinesin-microtubule system. Selectively modified with kinesins onto the inner tube walls through Ni-NTA complexes, these tubes can work as channels for microtubules. A motility assay shows the smooth movement of microtubules along the tube inner wall powered by the inside immobilized kinesins. It could be envisioned that cargoes with different sizes can be transported through these tubular channels with little outside interruption.

Understanding the guiding of kinesin/microtubule-based microtransporters in microfabricated tracks

Microtransporters using cargo-laden microtubules propelled by kinesin motors are attractive for numerous applications in nanotechnology. To improve the efficiency of transport, the movement of microtubules must be guided by microfabricated tracks. However, the mechanisms of the guiding methods used are not fully understood. Here, using computer simulation, we systematically studied the guiding of such microtransporters by three different types of guiding methods: a chemical boundary, a physical barrier, and their combination. The simulation reproduced the probabilities of guiding previously observed experimentally for the three methods. Moreover, the simulation provided further insight into the mechanisms of guiding, which overturn previous assumptions and models.

Nanoshuttles propelled by motor proteins sequentially assemble molecular cargo in a microfluidic device

Nanoshuttles powered by the molecular motor kinesin have the potential to capture and concentrate rare molecules from solution as well as to transport, sort and assemble them in a high-throughput manner. One long-thought-of goal has been the realisation of a molecular assembly line with nanoshuttles as workhorses. To harness them for this purpose might allow the community to engineer novel materials and nanodevices. The central milestone towards this goal is to expose nanoshuttles to a series of different molecules or building blocks and load them sequentially to build hierarchical structures, macromolecules or materials. Here, we addressed this challenge by exploiting the synergy of two so far mostly complementary techniques, nanoshuttle-mediated active transport and pressure-driven passive transport, integrated into a single microfluidic device to demonstrate the realisation of a molecular assembly line. Multiple step protocols can thus be miniaturised to a highly parallelised and autonomous working lab-on-a-chip: in each reaction chamber, analytes or building blocks are captured from solution and are then transported by nanoshuttles across fluid flow boundaries in the next chamber. Cargo can thus be assembled, modified, analysed and eventually unloaded in a procedure that requires only one step by its operator.

Tug-of-war of microtubule filaments at the boundary of a kinesin- and dynein-patterned surface

Intracellular cargo is transported by multiple motor proteins. Because of the force balance of motors with mixed polarities, cargo moves bidirectionally to achieve biological functions. Here, we propose a microtubule gliding assay for a tug-of-war study of kinesin and dynein. A boundary of the two motor groups is created by photolithographically patterning gold to selectively attach kinesin to the glass and dynein to the gold surface using a self-assembled monolayer. The relationship between the ratio of two antagonistic motor numbers and the velocity is derived from a force-velocity relationship for each motor to calculate the detachment force and motor backward velocity. Although the tug-of-war involves >100 motors, values are calculated for a single molecule and reflect the collective dynein and non-collective kinesin functions when they work as a team. This assay would be useful for detailed in vitro analysis of intracellular motility, e.g., mitosis, where a large number of motors with mixed polarities are involved.

Complete ON/OFF photoswitching of the motility of a nanobiomolecular machine

To apply motor proteins as natural nanomolecular machines to transporting systems in nanotechnology, complete temporal control over ON/OFF switching of the motility is necessary. We have studied the photoresponsive inhibition properties of azobenzene-tethered peptides for regulation of kinesin-microtubule motility. Although a compound containing a peptide having an amino acid sequence derived from the kinesin's C-terminus (a known inhibitor of kinesin's motor domain) and also featuring a terminal azobenzene unit exhibited an inhibition effect, the phototunability of this behavior upon irradiation with UV or visible light was only moderate. Unexpectedly, newly synthesized peptides featuring the reverse sequence of amino acids of the C-terminus of kinesin exhibited excellent photoresponsive inhibition. In particular, azobenzene-CONH-IPKAIQASHGR completely stopped and started the motility of kinesin-microtubules in its trans- and cis-rich states, respectively, obtained after irradiation with visible and UV light, respectively. A gliding motility system containing this photoresponsive inhibitor allowed in situ control of the motion of microtubules on a kinesin-coated glass substrate. It is expected that the present results on the photoresponsive nanomotor system open up new opportunities to design nanotransportation systems.

Microtubule-Cyclodextrin Conjugate: Functionalization of Motile Filament with Molecular Inclusion Ability

A microtubule-beta-cyclodextrin conjugate was prepared on a kinesin-adsorbed glass surface by chemical and biochemical means. Fluorescence microscope observation and a motility assay indicated that the conjugate simultaneously expressed an inherent motor function and an inclusion property.

Utilization and control of bioactuators across multiple length scales

In this review, we summarize the recent developments in the emerging field of bioactuators across a multitude of length scales. First, we discuss the use and control of biomolecules as nanoscale actuators. Molecular motors, such as DNA, kinesin, myosin, and F1-ATPase, have been shown to exert forces in the range between 1 pN to 45 pN. Second, we discuss the use and control of single and small clusters of cells to power microscale devices. Microorganisms, such as flagellated bacteria, protozoa, and algae, can naturally swim at speeds between 20 μm s(-1) to 2 mm s(-1) and produce thrust forces between 0.3 pN to 200 pN. Individual and clustered mammalian cells, such as cardiac and skeletal cells, can produce even higher contractile forces between 80 nN to 3.5 μN. Finally, we discuss the use and control of 2D- and 3D-assembled muscle tissues and muscle tissue explants as bioactuators to power devices. Depending on the size, composition, and organization of these hierarchical tissue constructs, contractile forces have been demonstrated to produce between 25 μN to 1.18 mN.

Molecular motor-powered shuttles along multi-walled carbon nanotube tracks

As a complementary tool to nanofluidics, biomolecular-based transport is envisioned for nanotechnological devices. We report a new method for guiding microtubule shuttles on multi-walled carbon nanotube tracks, aligned by dielectrophoresis on a functionalized surface. In the absence of electric field and in fluid flow, alignment is maintained. The directed translocation of kinesin propelled microtubules has been investigated using fluorescence microscopy. To our knowledge, this is the first demonstration of microtubules gliding along carbon nanotubes.

Transport and self-organization across different length scales powered by motor proteins and programmed by DNA

In eukaryotic cells, cargo is transported on self-organized networks of microtubule trackways by kinesin and dynein motor proteins. Synthetic microtubule networks have previously been assembled in vitro, and microtubules have been used as shuttles to carry cargoes on lithographically defined tracks consisting of surface-bound kinesin motors. Here, we show that molecular signals can be used to program both the architecture and the operation of a self-organized transport system that is based on kinesin and microtubules and spans three orders of magnitude in length scale. A single motor protein, dimeric kinesin-1, is conjugated to various DNA nanostructures to accomplish different tasks. Instructions encoded into the DNA sequences are used to direct the assembly of a polar array of microtubules and can be used to control the loading, active concentration and unloading of cargo on this track network, or to trigger the disassembly of the network.

Plasma treatment of PDMS for applications of in vitro motility assays

In vitro motility assays are readily used to simplify the complex environments within the cell and in muscle tissue. These assays have afforded considerable insight into the fundamentals of their underlying biophysics, interactions with cargo, intracellular regulation, and motor cooperation/competition. Extension of the standard in vitro motility assay into a more automated and cost-effective fluidic design while providing availability to the scientific community without expertise in lithographic fabrication is critical for the continued advancement of the field. In this work, we utilized a standard plasma cleaner to oxidize the widely prevalent material polydimethylsiloxane (PDMS) to create flow cells that could be used for in vitro motility assays. Our analysis indicated that a 40 min pre-treatment of the PDMS with plasma exposure resulted in optimal bundle motility. This finding was attributed to the condition at which the least amount of oxygen permeates the PDMS slab, enters the motility buffer, and oxidizes the motor proteins. Based on these findings, we developed a method for constructing microfluidic devices from glass and plasma-treated PDMS molds in which motility could be observed.

Self-organized optical device driven by motor proteins

Protein molecules produce diverse functions according to their combination and arrangement as is evident in a living cell. Therefore, they have a great potential for application in future devices. However, it is currently very difficult to construct systems in which a large number of different protein molecules work cooperatively. As an approach to this challenge, we arranged protein molecules in artificial microstructures and assembled an optical device inspired by a molecular system of a fish melanophore. We prepared arrays of cell-like microchambers, each of which contained a scaffold of microtubule seeds at the center. By polymerizing tubulin from the fixed microtubule seeds, we obtained radially arranged microtubules in the chambers. We subsequently prepared pigment granules associated with dynein motors and attached them to the radial microtubule arrays, which made a melanophore-like system. When ATP was added to the system, the color patterns of the chamber successfully changed, due to active transportation of pigments. Furthermore, as an application of the system, image formation on the array of the optical units was performed. This study demonstrates that a properly designed microstructure facilitates arrangement and self-organization of molecules and enables assembly of functional molecular systems.