Transport of semiconductor nanocrystals by kinesin molecular motors

In Vitro Synthesis and Design of Kinesin Biomolecular Motors by Cell-Free Protein Synthesis

Kinesin is a biomolecular motor that generates force and motility along microtubule cytoskeletons in cells. Owing to their ability to manipulate cellular nanoscale components, microtubule/kinesin systems show great promise as actuators of nanodevices. However, classical in vivo protein production has some limitations for the design and production of kinesins. Designing and producing kinesins is laborious, and conventional protein production requires specific facilities to create and contain recombinant organisms. Here, we demonstrated the in vitro synthesis and editing of functional kinesins using a wheat germ cell-free protein synthesis system. The synthesized kinesins propelled microtubules on a kinesin-coated substrate and showed a higher binding affinity with microtubules than E. coli-produced kinesins. We also successfully incorporated affinity tags into the kinesins by extending the original sequence of the DNA template by PCR. Our method will accelerate the study of biomolecular motor systems and encourage their wider use in various nanotechnology applications.

Biomolecular interfaces based on self-assembly and self-recognition form biosensors capable of recording molecular binding and release

This research proposed to create the next generation of versatile electrochemical-based biosensors capable of monitoring target capture and release as dictated by molecular binding or unbinding. The biosensor integrates cellular machines (i.e., microtubules, structural elements of cells and kinesin molecular motors involved in cellular transport) as functional units; its assembly is based on molecular self-assembly and self-recognition. Our results demonstrate that the designed biosensor was capable of allowing detection of binding and unbinding events based on redox reactions at user-controlled electrode interfaces. The analysis also showed that the sensitivity of the designed biosensor or its ability to record such events could be user-controlled at any given time by adjusting the energy source that "fuels" the system.

A review on optical imaging of DNA nanostructures and dynamic processes

DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.

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.

High-Resolution Vertical Observation of Intracellular Structure Using Magnetically Responsive Microplates

A vertical confocal observation system capable of high-resolution observation of intracellular structure is demonstrated. The system consists of magnet-active microplates to rotate, incline, and translate single adherent cells in the applied magnetic field. Appended to conventional confocal microscopes, this system enables high-resolution cross-sectional imaging with single-molecule sensitivity in single scanning.

Constructing 3D microtubule networks using holographic optical trapping

Developing abilities to assemble nanoscale structures is a major scientific and engineering challenge. We report a technique which allows precise positioning and manipulation of individual rigid filaments, enabling construction of custom-designed 3D filament networks. This approach uses holographic optical trapping (HOT) for nano-positioning and microtubules (MTs) as network building blocks. MTs are desirable engineering components due to their high aspect ratio, rigidity, and their ability to serve as substrate for directed nano-transport, reflecting their roles in the eukaryotic cytoskeleton. The 3D architecture of MT cytoskeleton is a significant component of its function, however experimental tools to study the roles of this geometric complexity in a controlled environment have been lacking. We demonstrate the broad capabilities of our system by building a self-supporting 3D MT-based nanostructure and by conducting a MT-based transport experiment on a dynamically adjustable 3D MT intersection. Our methodology not only will advance studies of cytoskeletal networks (and associated processes such as MT-based transport) but will also likely find use in engineering nanostructures and devices.

Behavior of Kinesin Driven Quantum Dots Trapped in a Microtubule Loop

We report the observation of kinesin driven quantum dots (QDs) trapped in a microtubule loop, allowing the investigation of moving QDs for a long time and an unprecedented long distance. The QD conjugates did not depart from our observational field of view, enabling the tracking of specific conjugates for more than 5 min. The unusually long run length and the periodicity caused by the loop track allow comparing and studying the trajectory of the kinesin driven QDs for more than 2 full laps, i.e., about 70 μm, enabling a statistical analysis of interactions of the same kinesin driven object with the same obstacle. The trajectories were extracted and analyzed from kymographs with a newly developed algorithm. Despite dispersion, several repetitive trajectory patterns can be identified. A method evaluating the similarity is introduced allowing a quantitative comparison between the trajectories. The velocity variations appear strongly correlated to the presence of obstacles. We discuss the reasons making this long continuous travel distances on the loop track possible.

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.

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.

Colocalization of quantum dots by reactive molecules carried by motor proteins on polarized microtubule arrays

The field of microfluidics has drastically contributed to downscale the size of benchtop experiments to the dimensions of a chip without compromising results. However, further miniaturization and the ability to directly manipulate individual molecules require a platform that permits organized molecular transport. The motor proteins and microtubules that carry out orderly intracellular transport are ideal for driving in vitro nanotransport. Here, we demonstrate that a reconstruction of the cellular kinesin/dynein-microtubule system in nanotracks provides a molecular total analysis system (MTAS) to control massively parallel chemical reactions. The mobility of kinesin and a microtubule dissociation method enable orientation of a microtubule in an array for directed transport of reactive molecules carried by kinesin or dynein. The binding of glutathione S-transferase (GST) to glutathione (GSH) and the binding of streptavidin to biotin are visualized as colocalizations of quantum dots (Q-dots) when motor motilities bring them into contact. The organized nanotransport demonstrated here suggests the feasibility of using our platform to perform parallel biochemical reactions focused at the molecular level.

Engineering of a novel Ca²⁺-regulated kinesin molecular motor using a calmodulin dimer linker

The kinesin-microtubule system holds great promise as a molecular shuttle device within biochips. However, one current barrier is that such shuttles do not have "on-off" control of their movement. Here we report the development of a novel molecular motor powered by an accelerator and brake system, using a kinesin monomer and a calmodulin (CaM) dimer. The kinesin monomer, K355, was fused with a CaM target peptide (M13 peptide) at the C-terminal part of the neck region (K355-M13). We also prepared CaM dimers using CaM mutants (Q3C), (R86C), or (A147C) and crosslinkers that react with cysteine residues. Following induction of K355-M13 dimerization with CaM dimers, we measured K355-M13 motility and found that it can be reversibly regulated in a Ca(2+)-dependent manner. We also found that velocities of K355-M13 varied depending on the type and crosslink position of the CaM dimer used; crosslink length also had a moderate effect on motility. These results suggest Ca(2+)-dependent dimerization of K355-M13 could be used as a novel molecular shuttle, equipped with an accelerator and brake system, for biochip applications.

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.

A nano-needle/microtubule composite gliding on a kinesin-coated surface for target molecule transport

An alternative method of micro/nano-transport has been achieved by using motor proteins. Microtubules on a kinesin-coated surface have potential to act as a nano-transport system. When microtubules are used as carriers, either cargo or cargo linkers are attached on the microtubule surface. Such cargo attachments can significantly affect kinesin motion. To deal with the difficulty caused by molecular attachment to the microtubule surface, the cargo loading and transport mechanism should be separated. In this work, we propose to use micromachined needles as cargo carriers which then can be transported on microtubules. Because of the separation of needle functionalization and transport mechanism, functionalization of the needles can proceed without any effect on the microtubule structure, significantly increasing the possible types of cargo. We have fabricated silicon needles in mass numbers using a simple and effective method and have shown that the microtubule-needle composites are transported without affecting the kinesin activity.

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.

Active transport of oil droplets along oriented microtubules by kinesin molecular motors

We demonstrate the active transport of liquid cargos in the form of oil-in-water emulsion droplets loaded on kinesin motor proteins moving along oriented microtubules. We analyze the motility properties of the kinesin motors (velocity and run length) and find that the liquid cargo in the form of oil droplets does not alter the motor function of the kinesin molecules. This work provides a novel method for handling only a few molecules/particles encapsulated inside the oil droplets and represents a key finding for the integration of kinesin-based active transport into nanoscale lab-on-a-chip devices. We also investigate the effect of the diameter of the droplets on the motility properties of the kinesin motors. The velocity is approximately constant irrespective of the diameter of the droplets whereas we highlight a strong increase of the run length when the diameter of the droplets increases. We correlate these results with the number of kinesin motors involved in the transport process and find an excellent agreement between our experimental result and a theoretical model.

Resolving sub-diffraction limit encounters in nanoparticle tracking using live cell plasmon coupling microscopy

We use plasmon coupling between individual gold nanoparticle labels to monitor subdiffraction limit distances in live cell nanoparticle tracking experiments. While the resolving power of our optical microscope is limited to approximately 500 nm, we improve this by more than an order of magnitude by detecting plasmon coupling between individual gold nanoparticle labels using a ratiometric detection scheme. We apply this plasmon coupling microscopy to resolve the interparticle separations during individual encounters of gold nanoparticle labeled fibronectin-integrin complexes in living HeLa cells.

Harnessing biological motors to engineer systems for nanoscale transport and assembly

Living systems use biological nanomotors to build life's essential molecules--such as DNA and proteins--as well as to transport cargo inside cells with both spatial and temporal precision. Each motor is highly specialized and carries out a distinct function within the cell. Some have even evolved sophisticated mechanisms to ensure quality control during nanomanufacturing processes, whether to correct errors in biosynthesis or to detect and permit the repair of damaged transport highways. In general, these nanomotors consume chemical energy in order to undergo a series of shape changes that let them interact sequentially with other molecules. Here we review some of the many tasks that biomotors perform and analyse their underlying design principles from an engineering perspective. We also discuss experiments and strategies to integrate biomotors into synthetic environments for applications such as sensing, transport and assembly.

Functional characterization and atomic force microscopy of a DNA repair protein conjugated to a quantum dot

Quantum dots (QDs) possess highly desirable optical properties that make them ideal fluorescent labels for studying the dynamic behavior of proteins. However, a lack of characterization methods for reliably determining protein-quantum dot conjugate stoichiometry and functionality has impeded their widespread use in single-molecule studies. We used atomic force microscopic (AFM) imaging to demonstrate the 1:1 formation of UvrB-QD conjugates based on an antibody-sandwich method. We show that an agarose gel-based electrophoresis mobility shift assay and AFM can be used to evaluate the DNA binding function of UvrB-QD conjugates. Importantly, we demonstrate that quantum dots can serve as a molecular marker to unambiguously identify the presence of a labeled protein in AFM images.

The mitotic kinesin CENP-E is a processive transport motor

In vivo studies suggest that centromeric protein E (CENP-E), a kinesin-7 family member, plays a key role in the movement of chromosomes toward the metaphase plate during mitosis. How CENP-E accomplishes this crucial task, however, is not clear. Here we present single-molecule measurements of CENP-E that demonstrate that this motor moves processively toward the plus end of microtubules, with an average run length of 2.6 +/- 0.2 mum, in a hand-over-hand fashion, taking 8-nm steps with a stall force of 6 +/- 0.1 pN. The ATP dependence of motor velocity obeys Michaelis-Menten kinetics with K(M,ATP) = 35 +/- 5 muM. All of these features are remarkably similar to those for kinesin-1-a highly processive transport motor. We, therefore, propose that CENP-E transports chromosomes in a manner analogous to how kinesin-1 transports cytoplasmic vesicles.

Polarity orientation of microtubules utilizing a dynein-based gliding assay

The motor protein dynein was introduced into a nanotransport system. We oriented microtubules by their polarity, and immobilized them based on a dynein-microtubule gliding assay system. This system achieved unidirectional transport of kinesin-coated microbeads. In contrast to conventional kinesin-based orientation systems, the dynein-based system allowed the reverse motion of microtubules, resulting in an inversion of the orientation of microtubule polarity and thus reverse transport of kinesin-coated microbeads. This combined kinesin- and dynein-based system constitutes a new means to facilitate the bidirectional orientation of microtubules and transport of cargos in a nanofluidic system.

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.

Guidance of actin filament elongation on filament-binding tracks

Biomolecular motors, which convert chemical energy into mechanical work in intracellular processes, have high potential in bionanotechnology in vitro as molecular shuttles or nanoscale actuators. In this context, guided elongation of actin filaments in vitro could be used to lay tracks for myosin motor-based shuttles or to direct nanoscale actuators based on actin filament end-tracking motors. To guide the direction of filament polymerization on surfaces, microcontact printing was used to create tracks of chemically modified myosin, which binds to, but cannot exert force on, filaments. These filament-binding tracks captured nascent filaments from solution and guided the direction of their subsequent elongation. The effect of track width and protein surface density on filament alignment and elongation rate was quantified. These results indicate that microcontact printing is a useful method for guiding actin filament polymerization in vitro for biomolecular motor-based applications.

Cargo pick-up from engineered loading stations by kinesin driven molecular shuttles

Exploiting biological motors ex vivo to transport and distribute cargo with high spatial control, as done by cells, requires that we learn how molecular shuttles (microtubules propelled by kinesins) can pick up cargo from defined surface regions (loading stations). The main challenge of building microfabricated cargo loading stations is to adjust the sum of non-covalent interactions such that the station stably holds on to the cargo under static conditions, but allows for transfer when a gliding microtubule collides with station-bound cargo and starts to pull on it. Successful pick-up of cargo could be observed using biotin-anti-biotin interactions and hybridized oligonucleotides. The effect of different tethering chemistries on the efficiency of cargo pick-up was tested.

Protein Linear Molecular Motor-Powered Nanodevices

Myosin–actin and kinesin–microtubule linear protein motor systems and their application in hybrid nanodevices are reviewed. Research during the past several decades has provided a wealth of understanding about the fundamentals of protein motors that continues to be pursued. It has also laid the foundations for a new branch of investigation that considers the application of these motors as key functional elements in laboratory-on-a-chip and other micro/nanodevices. Current models of myosin and kinesin motors are introduced and the effects of motility assay parameters, including temperature, toxicity, and in particular, surface effects on motor protein operation, are discussed. These parameters set the boundaries for gliding and bead motility assays. The review describes recent developments in assay motility confinement and unidirectional control, using micro- and nano-fabricated structures, surface patterning, microfluidic flow, electromagnetic fields, and self-assembled actin filament/microtubule tracks. Current protein motor assays are primitive devices, and the developments in governing control can lead to promising applications such as sensing, nano-mechanical drivers, and biocomputation.