Mole c Machines V

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Annu. Rev. Biomed. Eng. 2004. 6:363–95doi: 10.1146/annurev.bioeng.6.040803.140143

Copyright c© 2004 by Annual Reviews. All rights reserved

MOLECULAR MACHINES

C. Mavroidis,1 A. Dubey,2 and M.L. Yarmush31Department of Mechanical and Industrial Engineering, Northeastern University,Boston, Massachusetts 02115; email: [email protected] of Mechanical and Aerospace Engineering, Rutgers University,Piscataway, New Jersey 08854; email: [email protected] of Biomedical Engineering, Rutgers University, Piscataway,New Jersey 08854; email: [email protected]

Key Words molecular motors, nanomachines, nanodevices, nanomotors,bionanotechnology

� Abstract Molecular machines are tiny energy conversion devices on the mole-cular-size scale. Whether naturally occurring or synthetic, these machines are generallymore efficient than their macroscale counterparts. They have their own mechanochem-istry, dynamics, workspace, and usability and are composed of nature’s building blocks:namely proteins, DNA, and other compounds, built atom by atom. With modern sci-entific capabilities it has become possible to create synthetic molecular devices andinterface them with each other. Countless such machines exist in nature, and it is pos-sible to build artificial ones by mimicking nature. Here we review some of the knownmolecular machines, their structures, features, and characteristics. We also look at cer-tain devices in their early development stages, as well as their future applications andchallenges.

CONTENTS

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364ATP-BASED PROTEIN MOLECULAR MACHINES . . . . . . . . . . . . . . . . . . . . . . . . 364

The F0F1-ATP Synthase Motors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365The Kinesin, Myosin, Dynein, and Flagella Molecular Motors . . . . . . . . . . . . . . . . 368

DNA-BASED MOLECULAR MOTORS/DEVICES . . . . . . . . . . . . . . . . . . . . . . . . . . 375The DNA Tweezers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377Rotary DNA Actuator Concept . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377

INORGANIC (CHEMICAL) MOLECULAR MACHINES . . . . . . . . . . . . . . . . . . . . 378The Rotaxanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378The Catenanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379Other Inorganic Molecular Machines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381

OTHER PROTEIN-BASED MOTORS UNDER DEVELOPMENT . . . . . . . . . . . . . . 382Viral Protein Linear Motors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382Synthetic Contractile Polymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382

CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383

1523-9829/04/0815-0363$14.00 363

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364 MAVROIDIS � DUBEY � YARMUSH

INTRODUCTION

Molecular machines can be defined as devices that can produce useful work throughthe interaction of individual molecules at the molecular scale of length. A conve-nient unit of measurement at the molecular scale would be a nanometer. Hence,molecular machines also fall into the category of nanomachines. Molecular ma-chines depend on inter- and intramolecular interactions for their function. Theseinteractions include forces such as the ionic and Van der Waal’s forces and are afunction of the geometry of the individual molecules. The interaction between twogiven molecules can be well understood by a set of laws governing them, whichbrings in a definite level of predictability and controllability of the underlyingmechanics. Mother Nature has her own set of molecular machines that have beenworking for centuries and have become optimized for performance and designover the ages. As our knowledge and understanding of these numerous machinescontinues to increase, we now see a possibility of using the natural machines, orcreating synthetic ones from scratch, by mimicking nature. In this review, we tryto understand the principles, theory, and utility of the known molecular machinesand look into the design and control issues for creation and modification of suchmachines. A majority of natural molecular machines are protein based, whereas theDNA-based molecular machines are mostly synthetic. Nature deploys proteins toperform various cellular tasks, from moving cargo to catalyzing reactions, whereasDNA has been retained as an information carrier. Hence, it is understandable thatmost of the natural machinery is built from proteins. With the powerful crystal-lographic techniques now available, protein structures are clearer than ever. Theever-increasing computing power makes it possible to dynamically model proteinfolding processes and predict the conformations and structure of lesser knownproteins. These findings help unravel the mysteries associated with the molecularmachinery and pave the way for the production and application of these miniaturemachines in various fields, including medicine, space exploration, electronics andmilitary. We divide the molecular machines into three broad categories—proteinbased, DNA-based, and chemical molecular motors.

ATP-BASED PROTEIN MOLECULAR MACHINES

Three naturally existing rotary motors have been identified and studied in detailso far. Two form the F0F1-ATP synthase, and the third one is the bacterial flagel-lar motor. The protein-based molecular motors rely on an energy-rich moleculeknown as adenosine triphosphate (ATP), which is basically a nucleotide havingthree phosphate molecules that play a vital role in its energetics, and make itan indispensable commodity of life. The machines described in this section, theF0F1-ATPase, the kinesin, myosin, and dynein superfamily of protein molecularmachines, and bacteria flagellar motors all depend, directly or indirectly, on ATPfor their input energy. These machines, which have been carrying out vital life


MOLECULAR MACHINES 365

functions both inside and outside cells for millions of years, have now been segre-gated out of their natural environment and are seen as energy conversion devicesto obtain forces, torques, and motion. One disadvantage associated with ATP de-pendence is that the ATP creation machinery itself could be many times heavierand bulkier than the motors, thereby making the assembly more complex. Thesemachines perform best in their natural environment, and in the near future it maynot be possible to have them as a part of feasible biomimetic molecular machinery.

The F0F1-ATP Synthase Motors

ATP is regarded as the energy currency of biological systems (1). The ATP moleculeowes much of its energy to the terminal three phosphate ions attached to an adeno-sine base (2). In 1941 the role of ATP in the energy conversion process in livingbeings was recognized (3). However, the mode of transfer and structure of the en-zyme was unknown. When this currency is utilized (i.e., the energy of the moleculethat is used to drive a biological process), the terminal anhydride bond in the ATPmolecule has to be split. This leaves adenosine diphosphate (ADP) and a phosphateion (Pi) as the products, which are recombined to form ATP by a super efficient(4) enzyme motor assembly called the F0F1-ATP synthase (F0F1-ATPase). ATPsynthase is present inside the mitochondria of animal cells, in plant chloroplasts,in bacteria, and some other organisms. ATP synthase was first seen in 1962 in anelectron microscopy experiment on bovine heart mitochondria, as 10 nm diameterknobs (5). Their importance in energy conversion was realized, but their function-ing was still unknown. In 1966 the relation of the thus far unknown knobs to theproduction of ATP was established (6), which provided one of the first structuresof the enzyme.

The ATP synthase is actually a combination of two motors functioning to-gether, the hydrophobic transmembrane F0-ATPase motor and the globular F1-ATPase motor (7). Both motors have distinct structures and functions. There aredifferent abbreviations used for the F1-ATPase based on their sources; the heartmitochondrial motors are called mF1, chloroplast motors are cF1, those obtainedfrom Escherichia coli are termed EcF1, and the ones from Kagawa’s thermophilicbacterium are known as TF1 (2). The F0 motor has organism-dependant structuralvariations. In addition, the regulation of catalysis in ATP synthase depends on theorganism’s source (1). In animal mitochondria, this motor is embedded in the innermitochondrial membrane and uses an ion-motive force for its function. Initially,however, it was believed that the force was proton-motive (8) only until it wasshown that, in some cases, Na+ ions induce the motive force for the F0 motor (9);hence the term ion-motive force. The proton-motive force can be defined as thework per unit charge that a proton traveling through a membrane can perform.

STRUCTURE: F1-ATPase MOTOR The F1 motor, powered by hydrolysis of ATP, iscomposed of a central protein stalk, called the γ -subunit, surrounded by threecopies each of α- and β-subunits. The α- and β-subunits are arranged



Figure 1 The F0F1-ATPase motors. The F0 motor is embedded in the inner mitochon-drial membrane of the mitochondria. F0 is typically composed of a, b, and c subunitsas shown. The F1 motor is the soluble region composed of three α-, three β-, one eachof γ -, δ- and ε-subunits.

alternately so that they make a symmetric circular pattern when viewed fromthe top. There are δ-subunits attached to the periphery of the α-β cylinder and theε-subunits are present at the base of the γ -subunits, as shown in Figure 1. Hence,the F1 motor is composed of nine polypeptides (10). The α- and the β-subunitscontain nucleotide-binding sites that bind ATP/ADP molecules. The nucleotide-binding sites in the α-subunits simply bind the nucleotide, whereas those in theβ-subunit actually perform the catalysis. The a, b, and the c subunits shown inFigure 1 are a part of the F0 motor discussed below.

FUNCTION: F1-ATPase MOTOR The binding-change mechanism to explain the func-tion of F1-ATPase was proposed in 1973 (11). The mechanism, as known today,shows that each of the β-subunits take three forms: O (open), L (loose), andT (tight) binding site. When the subunit is in the O form, it is catalytically inactiveand has very low affinity to bind substrates. In the L form, the subunit loosely bindssubstrates (ADP and Pi), although it is catalytically inactive. In the T form, theADP and Pi are converted into a tightly bound ATP until a conformational changeconverts the T-site into an O-site, thereby allowing the release of the newly formedATP (12). The mechanism is shown in Figure 2.

The conformational change in the β-subunits is triggered by the rotation ofthe 4.5 nm long γ -subunit, which acts as a link connecting the F1-ATPase to the



Figure 2 The binding-change mechanism of F1-ATPase. The three catalytic sitesbind ADP/ATP alternately in L (loose), T (tight) and O (open) fashion. ADP and Pi areinitially loosely bound, then the binding becomes tight, with the conversion of ADP +Pi into ATP, which is finally released when the open conformation is achieved.

F0-ATPase. This was shown experimentally in 1997 (13). In this experiment, the F1-ATPase was attached to a nickel-coated glass surface; a 1–3 µm long fluorescentlylabeled actin filament was attached to the other end of the γ -subunit. The rotationcould then be observed through a fluorescence microscope, which was extremelyinteresting because the motor has a diameter of about 10 nm, whereas it couldsupport and rotate a structure about one hundred times larger! However, the rate ofrotation was reduced by 50 times to 1 rotation per second. The experimental setupis shown in Figure 3. F1-ATPase can produce 80–100 pN-nm of rotary torque (4).

STRUCTURE: F0-ATPase MOTOR Since the rotation of the γ -subunit has been shownto play the essential role in ATP creation, it is now imperative to see what causes the

Figure 3 Rotation of the ATPase motor as shown experimentally in (13).A 1–4 µm long fluorescently tagged actin filament was attached to the F0-ATPase using streptavidin to observe the rotation of the ATP synthase motor.



γ -subunit to rotate. The answer lies in the functioning of the F0-ATPase motor. Al-though the structure of the F0-ATPase is not as well known as that of the F1-ATPase,findings indicate that its structure depends on its source. The F0 domain from theeubacterial enzymes, exemplified by E. coli. (14), has three types of subunitstermed a, b, and c with 1 unit of a, 2 units of b, and 9 to 12 (15) units of c subunits(16, 17). Hence the subunit a, the two b, and the twelve c subunits in Figure 1belong to the F0-ATPase motor. In yeast, the F0 has only 10 c subunits (18). The F0

“turbine” from plant chloroplasts was found to have 14 c subunits (19), whereasa Na+-driven specimen from bacteria was found to have 14 such subunits (20).

FUNCTION: F0-ATPase MOTOR A flow of ions through the membrane propels theobserved reversible (21) rotation of F0-ATPase (22). As mentioned above, F0 isthe membrane-spanning unit of the ATPase motor. It remains embedded in themitochondrial or cellular membrane. In 1978, it was discovered that a chemicalpotential gradient for protons is formed across the inner mitochondrial membraneor the proton-motive force (8). This force is utilized by the ATPase enzyme toproduce ATP. The structure of F0-ATPase is not as well known as its F1 counterpart,which has been fully resolved (18, 23–28). The mechanochemical and quantitativemodels that explain how the ion-motive force is converted into the rotation of theγ -subunit were described in (15, 29–33).

The first hybrid nanoassembly structures powered by F1-ATPase was proposedin (34). Nano-fabricated Ni posts, about 80 nm in diameter and 200 nm in height,each separated by about 2.5 µm were built. Upon these posts they attached speciallyproduced recombinant biotinylated F1-ATPases using histidine tags into their β-subunit coding sequences. A streptavidin molecule was bound to the γ -subunit,and finally Ni propellers of lengths 750 to 1400 nm were attached to them. Inan action that is reverse of its ATP-producing cycle, the F1-ATPase consumedexternally provided ATP and produced anticlockwise rotation with a speed ofabout eight rotations per second. To date, this achievement remains a landmark inbionanotechnology.

The Kinesin, Myosin, Dynein, and Flagella Molecular Motors

With modern microscopic tools, we view a cell as a set of many different movingcomponents powered by molecular machines rather than a static environment.Molecular motors that move unidirectionally along protein polymers (actin ormicrotubules) drive the motions of muscles, as well as much smaller intracellularcargoes. In addition to the F0F1-ATPase motors inside the cell, there are lineartransport motors present, tiny vehicles known as motor proteins, that transportmolecular cargoes (35) and also require ATP for functioning. These minute cellularmachines exist in three families: kinesins, myosins, and dyneins (36). The cargoescan be organelles, lipids, or proteins, etc. They play an important role in celldivision and motility.

There are over 250 kinesin-like proteins, and they are involved in processes asdiverse as the movement of chromosomes and the dynamics of cell membranes. The



only part they have in common is the catalytic portion known as the motor domain.They have significant differences in their location within cells, their structuralorganization, and the movement they generate (37). Muscle myosin, whose studydates back to 1864, has served as a model system for understanding motility fordecades. Kinesin, however was not discovered until 1985, using in vitro motilityassays (38). Conventional kinesin is a highly processive motor that can take severalhundred steps on a microtubule without detaching (39, 40), whereas muscle myosinexecutes a single stroke and then dissociates (41). Detailed analysis and modelingof these motors has been done (38, 42).

Kinesin and myosin make for an interesting comparison. Kinesin is microtubulebased; it binds to and carries cargoes along microtubules, whereas myosin is actinbased. The motor domain of kinesin weighs one third that of myosin and onetenth of that of dynein (43). Before the advent of modern microscopic and analytictechniques, it was believed that these two had little in common. However, thecrystal structures available today indicate that they probably originated from acommon ancestor (44).

THE MYOSIN LINEAR MOTOR Myosin is a diverse superfamily of motor proteins(45). Myosin-based molecular machines transport cargoes along actin filaments,the two-stranded helical polymers of the protein actin that are about 5–9 nm indiameter. They do this by hydrolyzing ATP and utilizing the released energy (46).In addition to transport, they are also involved in the process of force genera-tion during muscle contraction, wherein thin actin filaments and thick myosinfilaments slide past each other. Not all members of the myosin superfamily havebeen characterized. However, much is known about their structure and function.Myosin molecules were first seen (in the late 1950s) through electron microscopeprotruding out from thick filaments and interacting with the thin actin filaments(47–49). Since that time, ATP has been known to play a role in myosin-relatedmuscle movement along actin (50); however, the exact mechanism was unknown,until it was explained in (51).

STRUCTURE: MYOSIN MOLECULAR MOTOR A myosin molecule binding to an actinpolymer is shown in Figure 4a (52). A myosin molecule has a size of about 520kDa, including two 220-kDa heavy chains and light chains of sizes between 15–22 kDa (53, 54). They can be visualized as two identical globular motor heads,also known as motor domains, each having a catalytic domain (actin, nucleotide,and light chain binding sites) and ∼8 nm long lever arms. One of the heads,sometimes referred to as S1 regions (subfragment 1), is shown in green (onlythe active head is visible); the lever arms or the light chains, in red and yellow.Both heads are connected via a coiled coil made of two α-helical coils (green)to the thick base filament. The light chains have considerable sequence similaritywith the protein calmodulin and troponin C and are sometimes referred to ascalmodulin-like chains. They act as links to the motor domains and do not playany role in their ATP binding activity (55) except for some exceptions (56, 57).



The motor domain in itself is sufficient for moving actin filaments (58). Three-dimensional structures of a myosin head revealed that it is a pear-shaped domain,about 19 nm long and 5 nm in maximum diameter (58, 59).

FUNCTION: MYOSIN MOLECULAR MOTOR A crossbridge-cycle model for the ac-tion of myosin on actin has been widely accepted since 1957 (47, 60, 61). Sincethe time the atomic structures of actin monomer (62, 63) and myosin (59) wereresolved, this model has been refined into a lever-arm model which is now accept-able (64). Only one motor head is able to connect to the actin filament at a time,the other head remains passive. Initially, the catalytic domain in the head has ADPand Pi bound to it and, as a result, its binding with actin was weak. With the activemotor head docking properly to the actin-binding site, the Pi has to be released.As soon as this happens, the lever arm swings counterclockwise (65) owing toa conformational change (49, 66–71), which pushes the actin filament down byabout 10 nm along its longitudinal axis (38). The active motor head now releasesits bound ADP, and another ATP molecule, by way of Brownian motion, quicklyreplaces it, making the binding of the head to the actin filament weak again. Themyosin motor then dissociates from the actin filament, and a new cycle starts.However, nano-manipulation of single S1 molecules (motor domains) shows thatmyosin can take multiple steps per ATP molecule hydrolyzed, moving in 5.3 nmsteps and resulting in displacements of 11 to 30 nm (72).

THE KINESIN LINEAR MOTOR The kinesin (43) and dynein families of proteinsare involved in cellular cargo transport along microtubules, in contrast to myosin,which transports along actin (73). Microtubules are 25-nm diameter tubes made ofprotein tubulin and are present in the cells in an organized manner. Microtubuleshave polarity; one end being the plus (fast-growing) end while the other end is theminus (slow-growing) end (74). Kinesins move from the minus end to the plusend of the microtubule, whereas dyneins move from the plus end to the minusend. Microtubule arrangement varies in different cell systems. In nerve axons,they are arranged longitudinally such that their plus ends point away from thecell body and into the axon. In epithelial cells, their plus ends point toward thebasement membrane. They extend radially out of the cell center in fibroblastsand macrophages with the plus end protruding outward (75). Similar to myosin,kinesin is also an ATP-driven motor. One unique characteristic of the kinesinfamily proteins is their processivity; they bind to microtubules and literally walkon it for many enzymatic cycles before detaching (76, 77). Also, each of theglobular heads/motor domains of kinesin is made of a single polypeptide unlikemyosin (heavy and light chains and dynein heavy, intermediate, and light chains).

STRUCTURE: KINESIN MOLECULAR MOTOR Much structural information about ki-nesin is now available through the crystal structures (44, 78, 79). The motor domaincontains a folding motif similar to that of myosin and G proteins (36). The twoheads or the motor domains of kinesin are linked via neck linkers to a long coiled



coil, which extends up to the cargo (Figure 4b). These heads interact with the α-and β-subunits of the tubulin hetrodimer along the microtubule protofilament. Theheads contain nucleotide- and microtubule-binding domains.

FUNCTION: KINESIN MOLECULAR MOTOR Although kinesin is also a two-headedlinear motor, its modus operandi is different from myosin in the sense that bothof its heads work together in a coordinated manner in contrast to one being leftout in the case of myosin. Figure 4b shows the kinesin walk. Each of the motorheads is near the microtubule in the initial state, with each motor head carrying anADP molecule. When one of the heads loosely binds to the microtubule, it losesits ADP molecule to facilitate a stronger binding. Another ATP molecule replacesthe ADP, which facilitates a conformational change such that the neck regionof the bound head snaps forward and zips on to the head (37). In the process, itpulls the other ADP-carrying motor head forward by about 16 nm so that it can bindto the next microtubule-binding site. This results in the net movement of the cargoby about 8 nm (80). The second head now binds to the microtubule by losing itsADP, which is promptly replaced by another ATP molecule (Brownian motion).The first head, meanwhile hydrolyzes the ATP and loses the resulting Pi. It isthen snapped forward by the second head while it carries its ADP forward. Hencecoordinated hydrolysis of ATP in the two motor heads is the key to the kinesinprocessivity (81, 82). Kinesin is able to take about 100 steps before detaching fromthe microtubule (39, 76, 83), while moving at 1000 nm/s and exerting forces ofthe order of 5–6 pN at rest (84, 85).

THE DYNEIN MOTOR The dynein superfamily of proteins was discovered in 1965(86). Dyneins exist in two isoforms: cytoplasmic and axonemal. Cytoplasmicdyneins are involved in cargo movement, whereas axonemal dyneins are involvedin producing bending motions of cilia and flagella (87–97). Figure 5 shows a typicalcytoplasmic dynein molecule.

STRUCTURE: DYNEIN MOLECULAR MOTOR The structure consists of two heavychains in the form of globular heads, three intermediate chains, and four light inter-mediate chains (98, 99). Recent studies have exposed a linker domain connectingthe stem region below the heads to the head itself (100). Also the microtubule-binding domains (the stalk region, not visible in the figure) protrude from the topof the heads (101). The ends of these stalks have smaller ATP-sensitive globulardomains that bind to the microtubules. Cytoplasmic dynein is associated with aprotein complex known as dynactin, which contains 10 subunits (102). Some areshown in the Figure 5 as p150, p135, actin-related protein 1 (Arp1), actin, dyna-mitin, capping protein, and p62 subunit. These play an important regulatory rolein the binding ability of dynein to the microtubules. The heavy chains forming thetwo globular heads contain the ATPase and microtubule motor domains (103).

One striking difference between dynein and the kinesins and myosins is thatdynein has AAA (ATPases associated with a variety of cellular activities) modules



Figure 5 A dynein molecule. Shown are the globular heads (heavy chains) connectedto the intermediate chains and the light chains. Dynactin complex components p150,p135, dynamitin, p62, capping proteins, Arp1, and Actin are also shown.

(104–106), which indicate that its mode of working will be entirely different fromkinesins and myosins. This puts dyneins into the AAA superfamily of mechanoen-zymes. The dynein heavy chains contain six tandemly linked AAA modules (107,108), with the head having a ring-like domain organization, which is typical of aAAA superfamily. Four of these are nucleotide-binding motifs, named P1–P4, butonly P1 (AAA1) is able to hydrolyze ATP.

FUNCTION: DYNEIN MOLECULAR MOTOR Because dynein is a larger and morecomplex structure than other motor proteins, its mode of operation is not as wellknown. However, electron microscopy and image processing was used (100) toshow the structure of a flagellar dynein at the start and end of its power stroke, whichgives some insight into its possible mode of force generation. When the dyneincontains bound ADP and Vi (vandate), it is in the prepower stroke conformation.



The state when it has lost the two, known as the apo-state, is the more compactpost-power stroke state. There is a distinct conformational change involving thestem, linker, head, and the stalk that produces about 15 nm of translation onto themicrotubule bound to the stalk (100).

THE FLAGELLA MOTORS Unicellular organisms such as E. coli have an interestingmode of motility (see 109–111). They have a number of molecular motors, about45 nm in diameter, that drive their feet or the flagella, which help the cell to swim.Motility is critical for cells, as they often have to travel from a less favorable toa more favorable environment. The flagella are helical filaments that extend outof the cell into the medium and perform a function analogous to what the oarsperform to a boat. The flagella and the motor assembly are called a flagellum. Themotor assembly imparts a rotary motion into the flagella (112, 113). In additionto a rotary mechanism, the flagellar machines consist of components such as ratemeters, particle counters, and gearboxes (114). These are necessary to help the celldecide which way to go, depending on the change of concentration of nutrients inthe surroundings. The rotary motion imparted to the flagella needs to be modulatedto ensure the cell is moving in the proper direction, as well as to ensure that allflagella of the given cell are providing a concerted effort toward it (115). Whenthe motors rotate the flagella in a counterclockwise direction, as viewed along theflagella filament from outside, the helical flagella create a wave away from the cellbody. Adjacent flagella subsequently intertwine in a propulsive corkscrew mannerand propel the bacteria. When the motors rotate clockwise, the flagella fly apart,causing the bacteria to tumble or change its direction (116). These reversals occurirregularly, giving the bacterium a random walk, unless, of course, there is a pref-erential direction of motility due to reasons mentioned earlier. The flagella motorsallow the bacteria to move at speeds of as much as 25 µm/s, with directional rever-sals occurring approximately 1 per second (117). A number of bacterial species inaddition to E. coli depend on flagella motors for motility: e.g., Salmonella enter-ica serovar, Typhimurium (Salmonella), Streptococcus, Vibrio spp., Caulobacter,Leptospira, Aquaspirrilum serpens, and Bacillus. The rotation of flagella motorsis stimulated by a flow of ions through them, which is a result of a build-up ofa transmembrane ion gradient. There is no direct ATP-involvement; however, theproton gradient needed for the functioning of flagella motors can be produced byATPase.

STRUCTURE: THE FLAGELLA MOTORS A complete part list of the flagella motorsis not yet available. Continued efforts dating back to early 1970s have, however,revealed much of their structure, composition, genetics, and function. Newer mod-els of the motor function are still being proposed with an aim to explain observedexperimental phenomena (118, 119) because we still do not fully understand thefunctioning of this motor (110). A typical flagella motor from E. coli. consistsof ∼20 different proteins (110), and many more are involved in its assemblyand operation. There are 14 Flg-type proteins, FlgA–FlgN; 5 Flh-type proteins,



Figure 6 A typical flagellum. A filament (FliC) is connected to the hook (FlgE),which connects to the transmembrane motor unit through a shaft. Hook-related proteins(FlgK, FlgL, and FliD) help in assembly and stability of the hook and filament. TheL-ring is embedded in the outer cell membrane, the P-ring in the peptidoglycan layer,and the MS-ring (FliF) along with FliG (rotor) and parts of stator (MotA and MotB)are embedded in the inner cell membrane. The C-ring and the transport apparatus arelocated inside the cell.

FlhA–FlhE; 19 Fli-type proteins, FliA–FliT; with MotA and MotB making a totalof 40 related proteins. The group names Flg, Flh, Fli, and Mot correspond to therelated genes (120). Within the main structural proteins are other proteins: FliCor the filament; FliD (filament cap); FliF or the MS-ring; FliG, FliM, and FliN(C-ring); FlgB, FlgC, and FlgF (proximal rod); FlgG (distal rod); FlgH (L-ring);FlgI (P-ring); FlgK and FlgL (hook-filament junction); and MotA-MotB (torque-generating units) (see Figure 6). It was initially believed that the M and S weretwo separate rings (M, membrane; S, supramembranous) (121). However, theyare now called the MS-ring because they were found to be two domains of thesame protein, FliF (122, 123). The C-ring stands for cytoplasmic (124–126); thee names for the P and L-rings come from peptidoglycan and lipopolysaccharide,respectively, indicating their location as seen in Figure 6. FlhA, B, FliH, I, O, P,Q, and R constitute the transport apparatus.

The hook and filament part of the flagellum is located outside the cell body. Themotor portion is embedded in the cell membrane, with the C-ring and the transport



apparatus inside the inner membrane in the cytoplasmic region. MotA and MotBare arranged in a circular array embedded in the inner membrane, with the MS-ringat the center. Connected to the MS-ring is the proximal end of a shaft, to which theP-ring, embedded in the peptidoglycan layer, is attached. Moving further outward,is the L-ring, which is embedded in the outer cell membrane, followed by the distalshaft end that protrudes out of the cell. To this end there is an attachment of thehook and the filament, both of which are polymers of hook-protein and flagellinrespectively.

Function: the flagella motors The flagellar motors in most cases are powered byprotons flowing through the cell membrane (proton-motive force) barring excep-tions such as certain marine bacteria, for example, the Vibrio spp., which are drivenby Na+ ions (127). There are about 1200 protons required to rotate the motor byone rotation (128). A complete explanation of how this proton flow is able to gen-erate torque is not yet available. From what is known, the stator units of MotAand MotB play an important role in torque generation. They form a MotA/MotBcomplex that when oriented properly binds to the peptidoglycan and opens protonchannels through which protons can flow (129). It is believed that there are eightsuch channels per motor (130). The proton-motive force is a result of the differenceof pH between the outside and inside of the cell. The E. coli cells like to main-tain an internal pH of 7.6–7.8, so depending on the pH of the surroundings, theproton-motive force will vary, and hence the speed of rotation of their motors. Totest how the speed of rotation depends on the proton-motive force, the motors werepowered by external voltage with attached markers acting as heavy loads (131).As expected, the rotation was found to depend directly on the proton-motive force.According to the most widely accepted model, MotA/MotB complex interacts withthe rotor via binding sites. The passage of protons through a MotA/MotB complex(stator or torque generator) moves it so that the protons bind to the next availablebinding site on the rotor, thereby stretching their linkage. When the linkage recoils,the rotor assembly has to rotate by one step. Hence whichever complex receivesprotons from the flux will rotate the rotor and generate torque. The torque-speeddependence of the motor has been studied in detail (132, 133) and indicates thetorque range of about 2700 to 4600 pN-nm.

DNA-BASED MOLECULAR MOTORS/DEVICES

As mentioned above, nature chose DNA mainly as an information carrier. Therewas no mechanical work assigned to it. Energy conversion, trafficking, and sens-ing, for example, were the tasks assigned mainly to proteins. Probably for thisreason, DNA turns out to be a simpler structure, with only four kinds of nucleotidebases, adenosine, thiamine, guanine, and cytosine (A, T, G, and C), attached in alinear fashion that takes a double-helical conformation when paired with a com-plementary strand. Such structural simplicity vis-a-vis proteins, made of some20 amino acids with complex folding patterns, results in a simpler structure and



predictable behavior. There are certain qualities that make DNA an attractive choicefor the construction of artificial nanomachines. In recent years, DNA has founduse not only in mechanochemical but also in nanoelectronic systems (134–137).A DNA double-helical molecule is about 2 nm in diameter and has 3.4–3.6-nmhelical pitch no matter what its base composition is, a structural uniformity notachievable with protein structures if one changes their sequence. Furthermore,double-stranded DNA (ds-DNA) has a respectable persistence length of about50 nm (138), which provides it enough rigidity to be a candidate component ofmolecular machinery. Single-stranded DNA (ss-DNA) is very flexible and cannotbe used where rigidity is required; however, this flexibility allows its application inmachine components such as hinges or nanoactuators (139). Its persistence lengthis about 1 nm, covering up to 3 base pairs (140) at 1M salt concentration.

Other than the above structural features, two important and exclusive propertiesmake DNA suitable for molecular level constructions: molecular recognition andself-assembly. The nucleotide bases A and T on two different ss-DNA have affinityfor each other, so do G and C. Effective and stable ds-DNA structures are formedonly if the base orders of the individual strands are complementary. Hence, iftwo complementary single strands of DNA are in a solution, they will eventuallyrecognize each other and hybridize, or zip-up, forming a ds-DNA. This property ofmolecular recognition and self-assembly has been exploited in a number of waysto build complex molecular structures (141–148). From a mechanical perspective,if the free energy released by hybridization of two complementary DNA strandsis used to lift a hypothetical load, a force capacity of 15 pN can be achieved (F.C.Simmel & B.Yurke, unpublished data), comparable to that of other molecularmachines such as kinesin (5 pN) (150).

The first artificial DNA-based structure in the form of a cube in 1991 waspresented in (143, 151). More complex structures such as knots (152, 153) andBorromean rings (147) were also developed. In addition to these individual con-structs, two-dimensional arrays (145, 154, 155) were made with the help of thedouble-crossover (DX) DNA molecule (156–158). This DX molecule gave thestructural rigidity required to create a dynamic molecular device, the B-Z switch(159). DNA double helices can be of three types: A-, B-, or Z-DNA. The B-DNA isthe natural, right-handed helical form of DNA, whereas the A-DNA is a shrunken,low-humidity form of the B-DNA. Z-DNA, obtained from certain CG base re-peat sequences occurring in B-DNA, can take a left-handed double helical form(160). The CG-repeated base pair regions can be switched between the left and theright-handed conformations by changing ionic concentration (161). The switchwas designed in such a way that it had three cyclic strands of DNA, two of themwrapped around a central strand that had the CG repeat region in the middle. Onthe two free ends of the side strands fluorescent dyes were attached in order tomonitor the conformational change. With the change in ionic concentration thecentral CG repeat sequence could alternate between the B and the Z modes bidi-rectionally, which was observed through fluorescence resonance energy transfer(FRET) spectroscopy.



The DNA Tweezers

An artificial DNA-based molecular machine that also accepted DNA as a fuel wasrecently developed (162). The machine, called DNA tweezers, consisted of threestrands of DNA labeled A, B and C. Strands B and C are partially hybridized on tothe central strand A with overhangs on both ends (Figure 7). This conformation ofthe machine is the open conformation. When F, an auxiliary fuel strand designedto hybridize with both overhang regions, is introduced, the machine attains aclosed conformation. The fuel strand is then removed from the system by theintroduction of its exact complement, leaving the system to go back to its originalopen conformation. In this way a reversible motion is produced, which can beobserved by attaching fluorescent tags to the two ends of the strand A. In this casethe 5′ end was labeled with the dye TET (tetrachloro-fluorescein phosphoramidite),and the 3′ end was labeled with TAMRA (carboxy-tertamethylrhodamine). Asidefrom the creation of a completely new molecular machine, this showed a way ofselective fueling of such machines. The fuel strands are sequence specific, so theywill work on only those machines toward which they are directed and will nottrigger other machines surrounding them.

This machine was later improved to form a three-state device (163), which hadtwo robust states and one flexible intermediate state. A variation of the tweezerscame about as the DNA-scissors (164).

Rotary DNA Actuator Concept

Based on the principle of branch migration and targeted fueling as achieved in theDNA tweezers, a rotary machine element made of DX-DNA (double-crossoverDNA) molecules was introduced. This element was based on the reversible transi-tion between two states, the paranemic crossover (PX) (165) DNA, and its topoi-somer, JX2 (Figure 8a).

The PX-DNA is known to play a role in recombination process. As seen inFigure 8b, the PX-DNA is formed by brown, green, and blue DNA strands. How-ever, the top and bottom double-helical regions of the brown and green strands areconnected to each other by a single-stranded region. These single-stranded regionsare partially hybridized by blue strands with overhangs that will act as ‘sticky ends’to adhere to incoming fuel strands. When exact complements of the blue strandsare supplied (i), the blue strands are displaced from the PX motif and bind withtheir complements. This makes possible the addition of a different set of strandsinto the gap. In stage ii, when the purple strands are added into the gap, the PXmolecule changes conformation to JX2 state with the lower double helices C andD rotating by 180◦. The purple strands can then be removed in a fashion similarto displacing the blue ones, and fresh blue strands can be added to the remainingintermediate, which will result in another rotation such that the C and D portionscome back to their PX-positions. In a very smart complex molecular construction,the researchers attached half-hexagonal DNA structures formed by DX and ds-DNA onto one of the ds regions (brown or green, Figure 8) of PX motifs arranged



in a linear array (166). Because of the larger size of the structures, they could bevisualized using an atomic force microscope to prove that the rotary device indeedrotates. A possible application of two DNA rotary machines to rotate a central discis shown in Figure 9.

INORGANIC (CHEMICAL) MOLECULAR MACHINES

In the past two decades, chemists have been able to create, modify, and controlnumerous types of chemical molecular machines. Many of these machines carrya striking resemblance to our everyday macroscale machines such as gears, pro-pellers, shuttles, etc. In addition, all of these molecular machines are easy to synthe-size artificially and are generally more robust than the natural molecular machines.Most of these machines are organic compounds of carbon, nitrogen, and hydrogen,with the presence of a metal ion being required occasionally. Electrostatic interac-tions and covalent and hydrogen bonding play essential roles in the performanceof these machines. Such artificial chemical machines can be controlled in variousways—chemically, electrochemically, and photochemically (through irradiationby light). Some are even controlled in several ways, rendering them more flexi-ble, which enhances their utility. A scientist can have more freedom with respectto the design of chemical molecular machines depending on the performance re-quirements and conditions. Rotaxanes (167–169) and catenanes (170, 171) makethe basis of many of the molecular machines described in this section. These arefamilies of interlocked organic molecular compounds with a distinctive shape andproperties that guide their performance and control.

The Rotaxanes

Rotaxane family of molecular machines is characterized by two parts: a dumbbell-shaped compound with two heavy chemical groups at the ends and a light, cycliccomponent, called a macrocycle, interlocked between the heads (Figure 10).

A reversible switch can be made with a rotaxane setup (172). For this, one needsto have two chemically active recognition sites in the neck region of the dumbbell.In this particular example, the thread was made of polyether, marked by recogni-tion sites of hydroquinol units and terminated at the ends by large triisoproplylsilylgroups. A tetracationic bead was designed and self-assembled into the system thatinteracts with the recognition sites. The macrocycle has a natural, low-energy stateon the first recognition site, but can be switched reversibly between the two sitesupon application of suitable stimuli. Depending on the type of rotaxane setup,the stimuli can be chemical, electrochemical, or photochemical (173, 174). Thestereo-electronic properties of the recognition sites can be altered by protonationor deprotonation, or by oxidation or reduction, thereby changing the affinity of thesites toward the macrocycle. In a recent example, light-induced acceleration of ro-taxane motion was achieved by photoisomerization (175). Similar controls throughalternating current (oscillating electric fields) had previously been shown (176).



Figure 10 A typical rotaxane shuttle setup. The macrocycle encircles the thread-likeportion of the dumbbell with heavy groups at its ends. The thread has two recognitionsites that can be altered reversibly so as to make the macrocycle shuttle between thetwo sites.

There are various ways for making rotaxanes by supramolecular synthesis (177).They can be self-assembled (178) using template-directed synthesis (179) methodssuch as threading, clipping, and slippage (180–182). In addition, various other ro-taxane shuttles and means of controlling the switching motion have been described(183–192).

The Catenanes

The catenanes are also a special type of interlocked structures that represent agrowing family of molecular machines. They are synthesized by supramolecularassistance to molecular synthesis (177). The general structure of a catenane isthat of two interlocked ring-like components that are noncovalently linked via amechanical bond, i.e., they are held together without any valence forces. Bothmacrocyclic components have recognition sites composed of atoms or groups ofatoms that are redox active or photochemically reactive. It is possible to have bothrings with similar recognition sites. In such a scenario, one of the rings may rotateinside the other with the conformations stabilized by noncovalent interactions, butthe two states of the inner ring, differing by 180◦, will be undistinguishable (de-generate) (193). For better control and distinguishable molecular conformations,it is desirable to have different recognition sites within the macrocycles. Then theycan be controlled independently through their own specific stimuli. The stereo-electronic property of a recognition site within a macrocycle can be varied suchthat at one point it has more affinity for the sites on the other ring. At this instant,the force balance will guide the rotating macrocycle for a stable conformation,which requires that particular site to be inside the other macrocycle. Similarly,with other stimuli, this affinity can be turned off, or even reversed, along with an



Figure 11 A nondegenerate catenane. One of the rings (the moving ring) has twodifferent recognition sites in it. Both sites can be turned off or on with different stimuli.When the trapezoidal-shaped site is activated, the force and energy balance resultsin the first conformation, whereas when the disc-shaped site is activated, the secondconformation results. They can be called states 0 and 1, analogous to binary machinelanguage.

increase of the affinity of the second recognition site on the rotating macrocycletoward those on the static one. There is a need for computational modeling, simu-lation, and analysis of such molecular machine motion (194). Catenanes can alsobe designed for chemical, photochemical, or electrochemical control (195–199).Figure 11 describes one such catenane molecular motor.

For both rotaxane- and catenane-based molecular machines, it is desirable tohave recognition sites such that they can be easily controlled externally. Hence, it ispreferable to build sites that are either redox active or photo active (173). Catenanescan also be self-assembled (200). An example of a catenane-assembled molecularmotor is the electronically controllable bistable switch (201). An intuitive way of



looking at catenanes is to think of them as molecular equivalents of ball and socketand universal joints (196, 202, 203).

Pseudorotaxanes are structures that contain a ring-like element and a thread-likeelement that can be threaded or dethreaded onto the ring upon application of vari-ous stimuli. Again, the stimuli can be chemical, photochemical, or electrochemical(204). These contain a promise of forming molecular machine components anal-ogous to switches and nuts and bolts from the macroscopic world.

Other Inorganic Molecular Machines

Many other molecular devices reported in the past four decades bear a strikingresemblance to macroscopic machinery. Chemical compounds behaving as bevelgears and propellers that were reported in the late 1960s and early 1970s are stillbeing studied today (205–208). A molecular propeller can be formed when twobulky rings such as the aryl rings (209) are connected to one central atom, oftencalled the focal atom. Clockwise rotation of one such ring induces a counterclock-wise rotation of the opposite ring about the bond connecting it to the central atom.It is possible to have a three-propeller system as well (210–212). Triptycyl andamide ring systems have been shown to observe a coordinated gear-like rotation(213–217). “Molecular turnstiles,” which are rotating plates inside a macrocycle,have been created (218, 219). However, such rotations are not controllable. A ro-tation of a molecular ring about a bond could be controlled by chemical stimuli,as was shown for the case of a molecular brake (220). A propeller-like rotationof a 9-triptycyl ring system, which was used in gears, this time connected to a2,2′-bipyridine unit, could be controlled by the addition and subsequent removalof a metal. Thus free rotations along single bonds can be stopped and released atwill. Soon after demonstrating the brake, A similar structure, called the molec-ular ratchet, was also proposed (221, 222). Again, the polycyclic structure wasallowed only one degree of rotational freedom about a single bond connecting trip-tycene and benzophenantherene (223). On similar lines and by the same group, achemically powered unidirectional rotary machine was introduced (224–226). Thedemonstrations, as for most chemical machines, were done by 1H NMR techniques.

An additional type of molecular switch is the chiroptical molecular switch(227). Another large cyclic compound was found to be switchable between itstwo stable isomeric forms P and M′ (right- and left-handed) stimulated by light.Depending on the frequency of the bombarded light, the cis and trans confor-mations of the compound 4-[9′(2′-meth-oxythioxanthylidene)]-7-methyl-1,2,3,4-tetrahydrophenanthrene can be interconverted. Allowing a slight variation to thisswitch, a striking molecular motor driven by light and/or heat was introduced in(228). In contrast to the rotation around a single bond in the ratchet described above,this rotation was achieved around a carbon-carbon double bond in a helical alkene.Ultraviolet light or the change in temperature could trigger a rotation involvingfour isomerization steps in the compound (3R,3′R)-(P,P)-trans-1,1′,2,2′,3,3′,4,4′-octahydro-3,3′-dimethyl-4,4′,-biphenanthrylidene. A second-generation motor



along with eight other motors from the same material is now operational (229).This redesigned motor has distinct upper and lower portions, and it operates ata higher speed. It also provides a good example of how controlled motion at themolecular level can be used to produce a macroscopic change in a system thatis visible to the naked eye. The light-driven motors when inside liquid crystal(LC) films can produce a color change by inducing a reorganization of mesogenicmolecules (230).

OTHER PROTEIN-BASED MOTORSUNDER DEVELOPMENT

In this section we present two protein-based motors that are at initial developmentalstages and yet possess some very original and interesting characteristics.

Viral Protein Linear Motors

The idea of viral protein linear motors (231) stems from the fact that a family ofretroviruses like the influenza virus (232) and HIV-1 (233) has a typical mechanismof infecting a human cell. When such a virus comes near the cell, it is believedthat it experiences a drop in pH of its surroundings owing to the environmentsurrounding the cell. This is a sort of signal to the virus that its future host is near.The drop of pH changes the energetics of the outer (envelope glycoprotein) proteinof the viral membrane in such a way that there is a distinct conformational changein a part of it (234, 235). A triple-stranded coiled coil domain of the membraneprotein changes conformation from a loose random structure to a distinctive α-helical conformation (236). It is proposed to isolate this domain from the virus andtrigger the conformational change by variation of pH in vitro. Once this is realized,attachments can be added to the N or C (or both) terminals of the peptide, and areversible linear motion can be achieved. Figure 12 shows a triple-stranded coiledcoil structure at a pH of 7.0; the inverted hairpin-like coils shown in the front viewin Figure 12a and top view shown in Figure 12b that change conformation intoextended helical coils as seen in Figure 12b.

Synthetic Contractile Polymers

In a recent development, large plant proteins that can change conformation whenstimulated by positively charged ions were separated from their natural environ-ment and shown to exert forces in orthogonal directions (237, 238). Proteins fromsieve elements of higher plants that are a part of the microfluidics system of theplant were chosen to build a new protein molecular machine element. These ele-ments change conformations in the presence of Ca2+ ions and organize themselvesinside the tubes to stop the fluid flow in case there is a rupture downstream. Thisis a natural defense mechanism seen in such plants. The change in conformation



is akin to a balloon inflating and extending in its lateral as well as longitudinaldirections. These elements, designated as forisomes, adhered to glass tubes, wereshown to reversibly swell in the presence of Ca2+ ions and shrink in their ab-sence, hence performing a pulling/pushing action in both directions. Artificiallyprepared protein bodies such as the forisomes could be a useful molecular machinecomponent in a future molecular assembly, producing forces of the order of mi-cronewtons (237). Unlike the ATP-dependant motors discussed previously, thesemachine elements are more robust because they can perform well in the absenceof their natural environment.

CONCLUSIONS

The recent explosion of research in nanotechnology, combined with important dis-coveries in molecular biology, has created a new interest in biomolecular machinesand robots. The main goal in the field of biomolecular machines is to use variousbiological elements—whose function at the cellular level creates a motion, force,or a signal—as machine components that perform the same function in responseto the same biological stimuli but in an artificial setting. In this way, proteins andDNA could act as motors, mechanical joints, transmission elements, or sensors. Ifall these components were assembled together they could form nanodevices with

Figure 12 (a) VPL motor at neutral pH. Front view of the partially α-helical triplestranded coiled coil. VPL motor is in the closed conformation. (b) VPL Motor in theopen conformation at acidic pH. The random coil regions are converted into well-defined helices and an extension occurs at lower pH.



Figure 12 (Continued)



multiple degrees of freedom, able to apply forces and manipulate objects in thenanoscale world, transfer information from the nano- to the macroscale world, andeven travel in a nanoscale environment.

The future of molecular machinery is bright. We are at the dawn of a new erain which many disciplines will merge, including robotics, mechanical, chemical,and biomedical engineering, chemistry, biology, physics, and mathematics, so thatfully functional systems will be developed. However, challenges toward such agoal abound. Developing a complete database of different biomolecular machinecomponents and the ability to interface or assemble different machine componentsare some of the challenges to be faced in the near future. The problems involvedin controlling and coordinating several biomolecular machines will come next.

ACKNOWLEDGMENTS

This work was supported by the National Science Foundation (DMI-02,28103and DMI-03,03950). Any opinions, findings, conclusions, or recommendationsexpressed in this publication are those of the authors and do not necessarily reflectthe views of the National Science Foundation. The authors thank Kevin Nikitczukof the Department of Biomedical Engineering at Rutgers University for providingassistance in the creation of the graphics for this paper.

The Annual Review of Biomedical Engineering is online athttp://bioeng.annualreviews.org

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MOLECULAR MACHINES C-1

Figure 4 The kinesin-myosin walks. (a) Myosin motor mechanism. (i) Motor headloosely docking to the actin-binding site; (ii) the binding becomes tighter along withthe release of Pi; (iii) lever arm swings to the left with the release of ADP; and(iv) replacement of the lost ADP with a fresh ATP molecule results in dissociation ofthe head. (b) Kinesin heads working in conjunction. (i) Both ADP-carrying headscome near the microtubule and one (black neck) binds; (ii) loss of bound ADP andaddition of fresh ATP in the bound head moves the other (red neck) to the right;(iii) the second head (red) binds to microtubule while losing its ADP, and replacingit with a new ATP molecule, whereas the first head hydrolyzes its ATP and loses Pi;(iv) the ADP-carrying black neck will now be snapped forward, and the cycle willbe repeated.

HI-RES-BE06-15-Mavroidis.qxd 7/13/04 9:10 PM Page 1

C-2 MAVROIDIS � DUBEY � YARMUSH

Figure 7 The DNA tweezers. (a) The machine is in the open conformation with thecentral strand (black) partially hybridized to the two side strands (red and green);(b) a fuel strand (white) is introduced; and (c) the fuel strand hybridizes with the twofree ends to bring the device into a closed conformation. With the addition of com-plement to the fuel strand, it can be removed to leave the system back to state (a).Figure reprinted with permission from Bernard Yurke, Lucent Technologies.


MOLECULAR MACHINES C-3

Fig

ure

8(a

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C-4 MAVROIDIS � DUBEY � YARMUSH

Figure 9 A possible application of two DNA rotary machines to rotate a central discby half a rotation at a time to achieve one full rotation. Red tags on the disc are stop-pers that will allow linkage to the motifs.


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