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

Functionalization of Tubulin: Approaches to Modify Tubulin with Biotin and DNA

The filamentous cytoskeletal protein microtubule, a polymer of α and β heterodimers of tubulin, plays major roles in intracellular transport as well as in vitro molecular actuation and transportation. Functionalization of tubulin dimers through covalent linkage facilitates utilization of microtubule in the nanobioengineering. Here we present a detailed description of the methodologies used to modify tubulin dimers with DNA strand and biotin through covalent interaction.

Linking path and filament persistence lengths of microtubules gliding over kinesin

Microtubules and kinesin motor proteins are involved in intracellular transports in living cells. Such intracellular material transport systems can be reconstructed for utilisation in synthetic environments, and they are called molecular shuttles driven by kinesin motors. The performance of the molecular shuttles depends on the nature of their trajectories, which can be characterized by the path persistence length of microtubules. It has been theoretically predicted that the path persistence length should be equal to the filament persistence length of the microtubules, where the filament persistence length is a measure of microtubule flexural stiffness. However, previous experiments have shown that there is a significant discrepancy between the path and filament persistence lengths. Here, we showed how this discrepancy arises by using computer simulation. By simulating molecular shuttle movements under external forces, the discrepancy between the path and filament persistence lengths was reproduced as observed in experiments. Our close investigations of molecular shuttle movements revealed that the part of the microtubules bent due to the external force was extended more than it was assumed in the theory. By considering the extended length, we could elucidate the discrepancy. The insights obtained here are expected to lead to better control of molecular shuttle movements.

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.

DNA-assisted swarm control in a biomolecular motor system

In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

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.

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.

Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism

The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.

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.

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.

Diamagnetic repulsion of particles for multilaminar flow assays

A continuous multilaminar flow reaction was performed on functionalised polymer particlesviadiamagnetic repulsion forces, using a simple, inexpensive setup.