Behavior of polycatalytic assemblies in a substrate-displaying matrix

Biased motion and molecular motor properties of bipedal spiders

Molecular spiders are synthetic molecular motors featuring multiple legs that each can interact with a substrate through binding and cleavage. Experimental studies suggest the motion of the spider in a matrix is biased toward uncleaved substrates and that spider properties such as processivity can be altered by changing the binding strength of the legs to substrate [R. Pei, S. K. Taylor, D. Stefanovic, S. Rudchenko, T. E. Mitchell, and M. N. Stojanovic, J. Am. Chem. Soc. 128, 12693 (2006)]. We investigate the origin of biased motion and molecular motor properties of bipedal spiders using Monte Carlo simulations. Our simulations combine a realistic chemical kinetic model, hand-over-hand or inchworm modes of stepping, and the use of a one-dimensional track. We find that stronger binding to substrate, cleavage and spider detachment from the track are contributing mechanisms to population bias. We investigate the contributions of stepping mechanism to speed, randomness parameter, processivity, coupling, and efficiency, and comment on how these molecular motor properties can be altered by changing experimentally tunable kinetic parameters.

A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies

Recent improvements in methods of single-particle fluorescence tracking have permitted detailed studies of molecular motion on the nanometer scale. In a quest to introduce these tools to the burgeoning field of DNA nanotechnology, we have exploited fluorescence imaging with one-nanometer accuracy (FIONA) and single-molecule high-resolution colocalization (SHREC) to monitor the diffusive behavior of synthetic molecular walkers, dubbed "spiders," at the single-molecule level. Here we discuss the imaging methods used, results from tracking individual spiders on pseudo-one-dimensional surfaces, and some of the unique experimental challenges presented by the low velocities (approximately 3 nm/min) of these nanowalkers. These experiments demonstrate the promise of fluorescent particle tracking as a tool for the detailed characterization of synthetic molecular nanosystems at the single-molecule level.

A synthetic small molecule that can walk down a track

Although chemists have made small-molecule rotary motors, to date there have been no reports of small-molecule linear motors. Here we describe the synthesis and operation of a 21-atom two-legged molecular unit that is able to walk up and down a four-foothold molecular track. High processivity is conferred by designing the track-binding interactions of the two feet to be labile under different sets of conditions such that each foot can act as a temporarily fixed pivot for the other. The walker randomly and processively takes zero or one step along the track using a 'passing-leg' gait each time the environment is switched between acid and base. Replacing the basic step with a redox-mediated, disulfide-exchange reaction directionally transports the bipedal molecules away from the minimum-energy distribution by a Brownian ratchet mechanism. The ultimate goal of such studies is to produce artificial, linear molecular motors that move directionally along polymeric tracks to transport cargoes and perform tasks in a manner reminiscent of biological motor proteins.

The Tumbleweed: towards a synthetic proteinmotor

Biomolecular motors have inspired the design and construction of artificial nanoscale motors and machines based on nucleic acids, small molecules, and inorganic nanostructures. However, the high degree of sophistication and efficiency of biomolecular motors, as well as their specific biological function, derives from the complexity afforded by protein building blocks. Here, we discuss a novel bottom-up approach to understanding biological motors by considering the construction of synthetic protein motors. Specifically, we present a design for a synthetic protein motor that moves along a linear track, dubbed the "Tumbleweed." This concept uses three discrete ligand-dependent DNA-binding domains to perform cyclically ligand-gated, rectified diffusion along a synthesized DNA molecule. Here we describe how de novo peptide design and molecular biology could be used to produce the Tumbleweed, and we explore the fundamental motor operation of such a design using numerical simulations. The construction of this and more sophisticated protein motors is an exciting challenge that is likely to enhance our understanding of the structure-function relationship in biological motors.

A bipedal DNA Brownian motor with coordinated legs

A substantial challenge in engineering molecular motors is designing mechanisms to coordinate the motion between multiple domains of the motor so as to bias random thermal motion. For bipedal motors, this challenge takes the form of coordinating the movement of the biped's legs so that they can move in a synchronized fashion. To address this problem, we have constructed an autonomous DNA bipedal walker that coordinates the action of its two legs by cyclically catalyzing the hybridization of metastable DNA fuel strands. This process leads to a chemically ratcheted walk along a directionally polar DNA track. By covalently cross-linking aliquots of the walker to its track in successive walking states, we demonstrate that this Brownian motor can complete a full walking cycle on a track whose length could be extended for longer walks. We believe that this study helps to uncover principles behind the design of unidirectional devices that can function without intervention. This device should be able to fulfill roles that entail the performance of useful mechanical work on the nanometer scale.

Directed evolution of streptavidin variants using in vitro compartmentalization

We have developed and implemented an in vitro compartmentalization (IVC) selection scheme for the identification of streptavidin (SA) variants with altered specificities for the biotin analog desthiobiotin. Wild-type SA and selected variants bind desthiobiotin with similar affinities (approximately 10(-13) M), but the variants have off rates almost 50 times slower and a half-life for dissociation of 24 hr at 25 degrees C. The utility of streptavidin variants with altered specificities and kinetic properties was shown by constructing protein microarrays that could be used to differentially organize and immobilize DNAs bearing these ligands. The methods we have developed should prove to be generally useful for generating a variety of novel SA reagents and for evolving other extremely high-affinity protein:ligand couples.

Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding

An important goal of nanotechnology is to assemble multiple molecules while controlling the spacing between them. Of particular interest is the phenomenon of multivalency, which is characterized by simultaneous binding of multiple ligands on one biological entity to multiple receptors on another. Various approaches have been developed to engineer multivalency by linking multiple ligands together. However, the effects of well-controlled inter-ligand distances on multivalency are less well understood. Recent progress in self-assembling DNA nanostructures with spatial and sequence addressability has made deterministic positioning of different molecular species possible. Here we show that distance-dependent multivalent binding effects can be systematically investigated by incorporating multiple-affinity ligands into DNA nanostructures with precise nanometre spatial control. Using atomic force microscopy, we demonstrate direct visualization of high-affinity bivalent ligands being used as pincers to capture and display protein molecules on a nanoarray. These results illustrate the potential of using designer DNA nanoscaffolds to engineer more complex and interactive biomolecular networks.

Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme

Many sequence variations of the 8–17 RNA-cleaving deoxyribozyme have been isolated through in vitro selection. In an effort to understand how these sequence variations affect cleavage site selectivity, we systematically mutated the catalytic core of 8–17 and measured the cleavage activity of each mutant deoxyribozyme against all 16 possible chimeric (RNA/DNA) dinucleotide junctions. We observed sequence-function relationships that suggest how the following non-conserved positions in the catalytic core influence selectivity at the dinucleotide (5′ rN₁₈-N_1.1 3′) cleavage site: (i) positions 2.1 and 12 represent a primary determinant of the selectivity at the 3′ position (N_1.1) of the cleavage site; (ii) positions 15 and 15.0 represent a primary determinant of the selectivity at the 5′ position (rN₁₈) of the cleavage site and (iii) the sequence of the 3-bp intramolecular stem has relatively little influence on cleavage site selectivity. Furthermore, we report for the first time that 8–17 variants have the collective ability to cleave all dinucleotide junctions with rate enhancements of at least 1000-fold over background. Three optimal 8–17 variants, identified from ∼75 different sequences that were examined, can collectively cleave 10 of 16 junctions with useful rates of ≥0.1 min⁻¹, and exhibit an overall hierarchy of reactivity towards groups of related junctions according to the order NG > NA > NC > NT.

Engineering entropy-driven reactions and networks catalyzed by DNA

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.

Molecular Spiders in One Dimension

Molecular spiders are synthetic bio-molecular systems which have "legs" made of short single-stranded segments of DNA. Spiders move on a surface covered with single-stranded DNA segments complementary to legs. Different mappings are established between various models of spiders and simple exclusion processes. For spiders with simple gait and varying number of legs we compute the diffusion coefficient; when the hopping is biased we also compute their velocity.

An autonomous polymerization motor powered by DNA hybridization

We present a synthetic molecular motor capable of autonomous nanoscale transport in solution. Inspired by bacterial pathogens such as Rickettsia rickettsii, which locomote by inducing the polymerization of the protein actin at their surfaces to form 'comet tails', the motor operates by polymerizing a double-helical DNA tail2. DNA strands are propelled processively at the living end of the growing polymers, demonstrating autonomous locomotion powered by the free energy of DNA hybridization.

Rise of the nanomachine: the evolution of a revolution in medicine

Although the current array of nanomachines mostly comprises simple devices (at least from a mechanical viewpoint), the underlying physical and chemical interactions that play key roles in the ‘assembly’ of these machines have required decades of research to ascertain a fundamental understanding of how such processes can be manipulated at the nanoscale. In this review, we wish to convey a realistic picture of the current developments in the design and implementation of nanomachines, with an emphasis on how these developments are leading to practical applications in medicine, including a sense of how such simple devices are rapidly becoming the building blocks for assembling the nanorobots of tomorrow.

Molecular spiders with memory

Synthetic biomolecular spiders with "legs" made of single-stranded segments of DNA can move on a surface which is also covered by single-stranded segments of DNA complementary to the leg DNA. In experimental realizations, when a leg detaches from a segment of the surface for the first time it alters that segment, and legs subsequently bind to these altered segments more weakly. Inspired by these experiments, we investigate spiders moving along a one-dimensional substrate, whose legs leave newly visited sites at a slower rate than revisited sites. For a random walk (one-leg spider), the slowdown does not affect the long time behavior. For a bipedal spider, however, the slowdown generates an effective bias toward unvisited sites, and the spider behaves similarly to the excited walk. Surprisingly, the slowing down of the spider at new sites increases the diffusion coefficient and accelerates the growth of the number of visited sites.

Is there a future for DNA-based molecular devices in diabetes management?

We provide a thought experiment in advanced molecular engineering leading to the construction of a molecular robot acting as a DNA-based closed-loop device for the management of diabetes mellitus. The key components of this robot are nucleic acid enzymes regulated allosterically by glucose. In the presence of glucose above a threshold level the robot moves, releasing insulin from a lawn covered with insulin, but stops in its tracks whenever glucose decreases to a level below threshold; thus, the robot could provide an insulin release response to spikes in glucose concentration in real time.