Microtubule transport, concentration and alignment in enclosed microfluidic channels

Adaptation of Patterns of Motile Filaments under Dynamic Boundary Conditions

Boundary conditions are important for pattern formation in active matter. However, it is still not well-understood how alterations in the boundary conditions (dynamic boundary conditions) impact pattern formation. To elucidate the effect of dynamic boundary conditions on the pattern formation by active matter, we investigate an in vitro gliding assay of microtubules on a deformable soft substrate. The dynamic boundary conditions were realized by applying mechanical stress through stretching and compression of the substrate during the gliding assay. A single cycle of stretch-and-compression (relaxation) of the substrate induces perpendicular alignment of microtubules relative to the stretch axis, whereas repeated cycles resulted in zigzag patterns of microtubules. Our model shows that the orientation angles of microtubules correspond to the direction to attain smooth movement without buckling, which is further amplified by the collective migration of the microtubules. Our results provide an insight into understanding the rich dynamics in self-organization arising in active matter subjected to time-dependent boundary conditions.

Collective dynamics of microtubule-based 3D active fluids from single microtubules

Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains unclear. In this work, the motion of single microtubules was characterized by means of 2D gliding assays and compared with the flows of 3D active fluids. While the scales of the two systems differ by ∼1000×, both were driven by processive, non-processive or an equal mixture of both molecular motor proteins. To search for the dynamic correlation between both systems, the motor activities were tuned by varying temperature and ATP concentration, and the changes in both systems were compared. Motor processivity played an important role in active fluid flows but only when the fluids were nearly motionless; otherwise, flows were dominated by hydrodynamic resistance controlled by sample size. Furthermore, while the motors' thermal reaction led active fluids to flow faster with increasing temperature, such temperature dependence could be reversed by introducing temperature-varying depletants, emphasizing the potential role of the depletant in designing an active fluid's temperature response. The temperature response of active fluids was nearly immediate (⪅10 s). Such a characteristic enables active fluids to be controlled with a temperature switch. Overall, this work not only clarifies the role of temperature in active fluid activity, but also sheds light on the underlying principles of the relationship between the collective dynamics of active fluids and the dynamics of their constituent single microtubules.

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.

Microtubule guiding in a multi-walled carbon nanotube circuit

In nanotechnological devices, mass transport can be initiated by pressure driven flow, diffusion or by employing molecular motors. As the scale decreases, molecular motors can be helpful as they are not limited by increased viscous resistance. Moreover, molecular motors can move against diffusion gradients and are naturally fitted for nanoscale transportation. Among motor proteins, kinesin has particular potential for lab-on-a-chip applications. It can be used for sorting, concentrating or as a mechanical sensor. When bound to a surface, kinesin motors propel microtubules in random directions, depending on their landing orientation. In order to circumvent this complication, the microtubule motion should be confined or guided. To this end, dielectrophoretically aligned multi-walled-carbon nanotubes (MWCNT) can be employed as nanotracks. In order to control more precisely the spatial repartition of the MWCNTs, a screening method has been implemented and tested. Polygonal patterns have been fabricated with the aim of studying the guiding and the microtubule displacement between MWCNT segments. Microtubules are observed to transfer between MWCNT segments, a prerequisite for the guiding of microtubules in MWCNT circuit-based biodevices. The effect of the MWCNT organization (crenellated or hexagonal) on the MT travel distance has been investigated as well.

Sensing protein antigen and microvesicle analytes using high-capacity biopolymer nano-carriers

Lab-on-a-chip systems with molecular motor driven transport of analytes attached to cytoskeletal filament shuttles (actin filaments, microtubules) circumvent challenges with nanoscale liquid transport. However, the filaments have limited cargo-carrying capacity and limitations either in transportation speed (microtubules) or control over motility direction (actin). To overcome these constraints we here report incorporation of covalently attached antibodies into self-propelled actin bundles (nanocarriers) formed by cross-linking antibody conjugated actin filaments via fascin, a natural actin-bundling protein. We demonstrate high maximum antigen binding activity and propulsion by surface adsorbed myosin motors. Analyte transport capacity is tested using both protein antigens and microvesicles, a novel class of diagnostic markers. Increased incubation concentration with protein antigen in the 0.1-100 nM range (1 min) reduces the fraction of motile bundles and their velocity but maximum transportation capacity of >1 antigen per nm of bundle length is feasible. At sub-nanomolar protein analyte concentration, motility is very well preserved opening for orders of magnitude improved limit of detection using motor driven concentration on nanoscale sensors. Microvesicle-complexing to monoclonal antibodies on the nanocarriers compromises motility but nanocarrier aggregation via microvesicles shows unique potential in label-free detection with the aggregates themselves as non-toxic reporter elements.

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.

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.

In silico evolution of guiding track designs for molecular shuttles powered by kinesin motors

Molecular shuttles powered by kinesin motors require guiding tracks to perform specific tasks in nanoscale devices. Here, using our simulation of molecular shuttle movements, we describe an in silico evolutionary design method that makes it possible to automatically design the guiding tracks in accordance with their functions defined by designers. With this design method, we designed two types of pre-existing guiding track modules with improved performances, as well as one with a novel function.

Transportation of nanoscale cargoes by myosin propelled actin filaments

Myosin II propelled actin filaments move ten times faster than kinesin driven microtubules and are thus attractive candidates as cargo-transporting shuttles in motor driven lab-on-a-chip devices. In addition, actomyosin-based transportation of nanoparticles is useful in various fundamental studies. However, it is poorly understood how actomyosin function is affected by different number of nanoscale cargoes, by cargo size, and by the mode of cargo-attachment to the actin filament. This is studied here using biotin/fluorophores, streptavidin, streptavidin-coated quantum dots, and liposomes as model cargoes attached to monomers along the actin filaments (“side-attached”) or to the trailing filament end via the plus end capping protein CapZ. Long-distance transportation (>100 µm) could be seen for all cargoes independently of attachment mode but the fraction of motile filaments decreased with increasing number of side-attached cargoes, a reduction that occurred within a range of 10–50 streptavidin molecules, 1–10 quantum dots or with just 1 liposome. However, as observed by monitoring these motile filaments with the attached cargo, the velocity was little affected. This also applied for end-attached cargoes where the attachment was mediated by CapZ. The results with side-attached cargoes argue against certain models for chemomechanical energy transduction in actomyosin and give important insights of relevance for effective exploitation of actomyosin-based cargo-transportation in molecular diagnostics and other nanotechnological applications. The attachment of quantum dots via CapZ, without appreciable modulation of actomyosin function, is useful in fundamental studies as exemplified here by tracking with nanometer accuracy.

High-performance microfluidic rectifier based on sudden expansion channel with embedded block structure

A high-performance microfluidic rectifier incorporating a microchannel and a sudden expansion channel is proposed. In the proposed device, a block structure embedded within the expansion channel is used to induce two vortex structures at the end of the microchannel under reverse flow conditions. The vortices reduce the hydraulic diameter of the microchannel and, therefore, increase the flow resistance. The rectification performance of the proposed device is evaluated by both experimentally and numerically. The experimental and numerical values of the rectification performance index (i.e., the diodicity, Di) are found to be 1.54 and 1.76, respectively. Significantly, flow rectification is achieved without the need for moving parts. Thus, the proposed device is ideally suited to the high pressure environment characteristic of most micro-electro-mechanical-systems (MEMS)-based devices. Moreover, the rectification performance of the proposed device is superior to that of existing valveless rectifiers based on Tesla valves, simple nozzle/diffuser structures, or cascaded nozzle/diffuser structures.

Biomolecular-motor-based autonomous delivery of lipid vesicles as nano- or microscale reactors on a chip

We aimed to create an autonomous on-chip system that performs targeted delivery of lipid vesicles (liposomes) as nano- or microscale reactors using machinery from biological systems. Reactor-liposomes would be ideal model cargoes to realize biomolecular-motor-based biochemical analysis chips; however, there are no existing systems that enable targeted delivery of cargo-liposomes in an autonomous manner. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA (ssDNA)-labeled microtubules (MTs), gliding on kinesin-coated surfaces, acted as cargo transporters and that ssDNA-labeled cargo-liposomes were loaded/unloaded onto/from gliding MTs without bursting at loading reservoirs/micropatterned unloading sites specified by DNA base sequences. Our results contribute to the development of an alternative strategy to pressure-driven or electrokinetic flow-based microfluidic devices.

In silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors

We present an extended computer simulation method which allows in silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors. The simulation reproduced molecular shuttle movements under external forces and dissociation of shuttles from guiding track surfaces. The simulation was validated by comparing the simulation results with the corresponding experimental ones. Using the simulation, track designers can change guiding track designs, choose guiding methods, tune the strength of external forces, and test the module performance. This simulation would significantly reduce the effort expended in designing guiding tracks for molecular shuttles powered by kinesin motors.

Molecular Motors as Components of Future Medical Devices and Engineered Materials

A new frontier in the development of prosthetic devices is the design of nanoscale systems which replace, augment, or support individual cells. Similar to cells, such devices will require the ability to generate mechanical movement, either for transport or actuation. Here, the development of nanoscale transport systems, which integrate biomolecular motors, is reviewed. To date, close to 100 publications have explored the design of such “molecular shuttles” based on the integration of synthetic molecules, nano- and microparticles, and micropatterned structures with kinesin and myosin motors and their associated cytoskeletal filaments, microtubules, and actin filaments. Tremendous progress has been made in addressing the key challenges of guiding, loading, and controlling the shuttles, providing a foundation for the exploration of applications in medicine and engineering.

Surface manipulation of microtubules using self-assembled monolayers and electrophoresis

We integrate microtubule (MT)-resistant self-assembled monolayers (SAMs) with lithographically patterned electrodes to control MTs in a cell-free environment. Formed through a facile, one-step assembly method, the poly(ethylene glycol) trimethoxysilane SAM prevents MT adsorption on both silicon substrates and Au microstructures without casein. We characterize the SAM using ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy and compare it with other MT passivation techniques. The SAM retains its passivating ability when used as a substrate for electron beam lithography, a key feature that allows us to pattern microtubules on lithographically defined Au structures. Moreover, by combining the SAM-passivated Au microelectrodes and DC electrophoresis, we demonstrate reversible trapping of MTs as well as capture and alignment of individual MTs.

Surface-bound casein modulates the adsorption and activity of kinesin on SiO2 surfaces

Conventional kinesin is routinely adsorbed to hydrophilic surfaces such as SiO(2). Pretreatment of surfaces with casein has become the standard protocol for achieving optimal kinesin activity, but the mechanism by which casein enhances kinesin surface adsorption and function is poorly understood. We used quartz crystal microbalance measurements and microtubule gliding assays to uncover the role that casein plays in enhancing the activity of surface-adsorbed kinesin. On SiO(2) surfaces, casein adsorbs as both a tightly bound monolayer and a reversibly bound second layer that has a dissociation constant of 500 nM and can be desorbed by washing with casein-free buffer. Experiments using truncated kinesins demonstrate that in the presence of soluble casein, kinesin tails bind well to the surface, whereas kinesin head binding is blocked. Removing soluble casein reverses these binding profiles. Surprisingly, reversibly bound casein plays only a moderate role during kinesin adsorption, but it significantly enhances kinesin activity when surface-adsorbed motors are interacting with microtubules. These results point to a model in which a dynamic casein bilayer prevents reversible association of the heads with the surface and enhances association of the kinesin tail with the surface. Understanding protein-surface interactions in this model system should provide a framework for engineering surfaces for functional adsorption of other motor proteins and surface-active enzymes.

Biomolecular-motor-based nano- or microscale particle translocations on DNA microarrays

We aimed to create autonomous on-chip systems that perform targeted translocations of nano- or microscale particles in parallel using machinery that mimics biological systems. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA-labeled microtubules gliding on kinesin-coated surfaces acted as cargo translocators and that single-stranded DNA-labeled cargoes were loaded/unloaded onto/from gliding microtubules at micropatterned loading/unloading sites specified by DNA base sequences. Our results will help to create autonomous molecular sorters and sensors.

Biomolecular motor-driven molecular sorter

We have developed a novel, microfabricated, stand-alone microfluidic device that can efficiently sort and concentrate (bio-)analyte molecules by using kinesin motors and microtubules as a chemo-mechanical transduction machine. The device removes hundreds of targeted molecules per second from an analyte stream by translocating functionalized microtubules with kinesin across the stream and concentrating them at a horseshoe-shaped collector. Target biomolecule concentrations increase up to three orders of magnitude within one hour of operation.

Setting up roadblocks for kinesin-1: mechanism for the selective speed control of cargo carrying microtubules

Motor-driven cytoskeletal filaments are versatile transport platforms for nanosized cargo in molecular sorting and nano-assembly devices. However, because cargo and motors share the filament lattice as a common substrate for their activity, it is important to understand the influence of cargo-loading on transport properties. By performing single-molecule stepping assays on biotinylated microtubules we found that individual kinesin-1 motors frequently stopped upon encounters with attached streptavidin molecules. Consequently, we attribute the deceleration of cargo-laden microtubules in gliding assays to an obstruction of kinesin-1 paths on the microtubule lattice rather than to 'frictional' cargo-surface interactions. We propose to apply this obstacle-caused slow-down of gliding microtubules in a novel molecular detection scheme: Using a mixture of two distinct microtubule populations that each bind a different kind of protein, the presence of these proteins can be detected via speed changes in the respective microtubule populations.

Microtubule alignment and manipulation using AC electrokinetics

The kinesin-microtubule system plays an important role in intracellular transport and is a model system for integrating biomotor-driven transport into microengineered devices. AC electrokinetics provides a novel tool for manipulating and organizing microtubules in solution, enabling new experimental geometries for investigating and controlling the interactions of microtubules and microtubule motors in vitro. By fabricating microelectrodes on glass substrates and generating AC electric fields across solutions of microtubules in low-ionic-strength buffers, bundles of microtubules are collected and aligned and the electrical properties of microtubules in solution are measured. The AC electric fields result in electro-osmotic flow, electrothermal flow, and dielectrophoresis of microtubules, which can be controlled by varying the solution conductivity, AC frequency, and electrode geometry. By mapping the solution conductivity and AC frequency over which positive dielectrophoresis occurs, the apparent conductivity of taxol-stabilized bovine-brain microtubules in PIPES buffer is measured to be 250 mS m(-1). By maximizing dielectrophoretic forces and minimizing electro-osmotic and electrothermal flow, microtubules are assembled into opposed asters. These experiments demonstrate that AC electrokinetics provides a powerful new tool for kinesin-driven transport applications and for investigating the role of microtubule motors in development and maintenance of the mitotic spindle.

Comparing guiding track requirements for myosin- and kinesin-powered molecular shuttles

The design of nanoscale transport systems utilizing motor proteins as engines has advanced rapidly. Here, actin/myosin- and microtubule/kinesin-based molecular shuttles are compared with respect to their requirements for track designs. To this end, the trajectory persistence length of actin filaments gliding on myosin-coated surfaces has been experimentally determined to be equal to 8.8 +/- 2 microm. This measurement complements an earlier determination of the trajectory persistence length of microtubules gliding on kinesin-coated surfaces and enables a comparison of the accessible track designs for kinesin and myosin motor-powered systems. Despite the 200-fold smaller stiffness of actin filaments compared to that of microtubules, the dimensions of myosin tracks for actin filaments have to be quite similar to the dimensions of kinesin tracks for microtubules (radii larger than 200 nm and widths smaller than 0.9 microm compared to 600 nm and 19 microm). The difference in gliding speed is shown to require additional consideration in the design of track modules.

Transport and detection of unlabeled nucleotide targets by microtubules functionalized with molecular beacons

Shrinking biosensors down to microscale dimensions enables increases in sensitivity and the ability to analyze minute samples such as the contents of individual cells. The goal of the present study is to create mobile microscale biosensors by attaching molecular beacons to microtubules and using kinesin molecular motors to transport these functionalized microtubules across two-dimensional surfaces. Previous work has shown that microfluidic channels can be functionalized with kinesin motors such that microtubules can be transported and directed through these channels without the need for external power or pressure-driven pumping. In this work, we show that molecular beacons can be attached to microtubules such that both the fluorescence reporting capability of the beacon and the motility of the microtubules are retained. These molecular beacon-functionalized microtubules were able to bind ssDNA target sequences, transport them across surfaces, and report their presence by an increase in fluorescence that was detected by fluorescence microscopy. This work is an important step toward creating hybrid microdevices for sensitive virus detection or analyzing mRNA profiles of individual cells.

Enhancing the stability of kinesin motors for microscale transport applications

Biomolecular motors, such as kinesins, have great potential for micro-actuation and micro- or nanoscale active transport when integrated into microscale devices. However, the stability and limited shelf life of these motor proteins and their associated protein filaments is a barrier to their implementation. Here we demonstrate that freeze-drying or critical point-drying kinesins adsorbed to glass surfaces extends their lifetime from days to more than four months. Further, photoresist deposition and removal can be carried out on these motor-adsorbed surfaces without loss of motor function. The methods developed here are an important step towards realizing the integration of biological motors into practical devices, and these approaches can be extended to patterning and preserving other proteins immobilized on surfaces.