Rizal F. Hariadi

Programming DNA Tube Circumferences

Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices.

Cellular chirality arising from the self-organization of the actin cytoskeleton

Cellular mechanisms underlying the development of left–right asymmetry in tissues and embryos remain obscure. Here, the development of a chiral pattern of actomyosin was revealed by studying actin cytoskeleton self-organization in cells with isotropic circular shape. A radially symmetrical system of actin bundles consisting of α-actinin-enriched radial fibres (RFs) and myosin-IIA-enriched transverse fibres (TFs) evolved spontaneously into the chiral system as a result of the unidirectional tilting of all RFs, which was accompanied by a tangential shift in the retrograde movement of TFs. We showed that myosin-IIA-dependent contractile stresses within TFs drive their movement along RFs, which grow centripetally in a formin-dependent fashion. The handedness of the chiral pattern was shown to be regulated by α-actinin-1. Computational modelling demonstrated that the dynamics of the RF–TF system can explain the pattern transition from radial to chiral. Thus, actin cytoskeleton self-organization provides built-in machinery that potentially allows cells to develop left–right asymmetry.

Integrating DNA strand-displacement circuitry with DNA tile self-assembly

DNA nanotechnology has emerged as a reliable and programmable way of controlling matter at the nanoscale through the specificity of Watson–Crick base pairing, allowing both complex self-assembled structures with nanometer precision and complex reaction networks implementing digital and analog behaviors. Here we show how two well-developed frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically integrated to provide programmable kinetic control of self-assembly. We demonstrate the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network. Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures.

Myosin lever arm directs collective motion on cellular actin network

Significance Myosins function as groups of motors anchored to a cellular scaffold that interacts with neighboring actin filaments patterned in complex three-dimensional networks. Although much is known about the function of individual myosin molecules, the contribution of intermotor interactions to collective movement is poorly understood. We used a precisely engineered biomimetic system to investigate how the mechanics of a structural element in the individual myosin influences the collective motion of groups of motors. Stochastic simulations suggest that the interplay between intramolecular strain on the motor lever arm and intermotor tension dictates trajectory shapes in groups of identical and antagonistic motors. Our study provides a general approach to dissecting emergence in cellular processes with applications for the efficient synthetic design of molecular transport systems. The molecular motor myosin teams up to drive muscle contraction, membrane traffic, and cell division in biological cells. Myosin function in cells emerges from the interaction of multiple motors tethered to a scaffold, with surrounding actin filaments organized into 3D networks. Despite the importance of myosin function, the influence of intermotor interactions on collective motion remains poorly understood. In this study, we used precisely engineered myosin assemblies to examine emergence in collective myosin movement. We report that tethering multiple myosin VI motors, but not myosin V motors, modifies their movement trajectories on keratocyte actin networks. Single myosin V and VI dimers display similar skewed trajectories, albeit in opposite directions, when traversing the keratocyte actin network. In contrast, tethering myosin VI motors, but not myosin V motors, progressively straightens the trajectories with increasing myosin number. Trajectory shape of multimotor scaffolds positively correlates with the stiffness of the myosin lever arm. Swapping the flexible myosin VI lever arm for the relatively rigid myosin V lever increases trajectory skewness, and vice versa. A simplified model of coupled motor movement demonstrates that the differences in flexural rigidity of the two myosin lever arms is sufficient to account for the differences in observed behavior of groups of myosin V and VI motors. In accordance with this model trajectory, shapes for scaffolds containing both myosin V and VI are dominated by the myosin with a stiffer lever arm. Our findings suggest that structural features unique to each myosin type may confer selective advantages in cellular functions.

Mechanical coordination in motor ensembles revealed using engineered artificial myosin filaments

The sarcomere of muscle is composed of tens of thousands of myosin motors that self-assemble into thick filaments and interact with surrounding actin-based thin filaments in a dense, near-crystalline hexagonal lattice. Together, these actin-myosin interactions enable large-scale movement and force generation, two primary attributes of muscle. Research on isolated fibres has provided considerable insight into the collective properties of muscle, but how actin-myosin interactions are coordinated in an ensemble remains poorly understood. Here, we show that artificial myosin filaments, engineered using a DNA nanotube scaffold, provide precise control over motor number, type and spacing. Using both dimeric myosin V- and myosin VI-labelled nanotubes, we find that neither myosin density nor spacing has a significant effect on the gliding speed of actin filaments. This observation supports a simple model of myosin ensembles as energy reservoirs that buffer individual stochastic events to bring about smooth, continuous motion. Furthermore, gliding speed increases with cross-bridge compliance, but is limited by Brownian effects. As a first step to reconstituting muscle motility, we demonstrate human β-cardiac myosin-driven gliding of actin filaments on DNA nanotubes.

Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.

Tuning myosin-driven sorting on cellular actin networks

Myosin V and VI are antagonistic motors that cohabit membrane vesicles in cells. A systematic study of their collective function, however, is lacking and forms the focus of this study. We functionally reconstitute a two-dimensional actin-myosin interface using myosin V and VI precisely patterned on DNA nanostructures, in combination with a model keratocyte actin meshwork. While scaffolds display solely unidirectional movement, their directional flux is modulated by both actin architecture and the structural properties of the myosin lever arm. This directional flux can be finely-tuned by the relative number of myosin V and VI motors on each scaffold. Pairing computation with experimental observations suggests that the ratio of motor stall forces is a key determinant of the observed competitive outcomes. Overall, our study demonstrates an elegant mechanism for sorting of membrane cargo using equally matched antagonistic motors, simply by modulating the relative number of engagement sites for each motor type. DOI: http://dx.doi.org/10.7554/eLife.05472.001

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics

Significance The hydrodynamic forces within bursting bubbles are of interest for their relevance to small-scale fluid mechanics, bioreactor efficiency, pollutant degradation, and the origin of life. However, despite the 150-year history of their study, the strengths of flows within bursting bubbles are only hypothetically known. Here, we show that DNA nanotubes––architecturally similar to biological microtubules—are fragmented during the bubble bursting process. Further, by analyzing the resulting fragment lengths, we characterize the spectrum of elongational flow rates, revealing that surprisingly strong tensile forces can be generated––in principle sufficient to fragment filamentous cyanobacterial chains, lipid vesicle protocells, genomic DNA, and other long polymeric molecules residing within or near the disintegrating liquid film. Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean’s environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension–driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates in commonly encountered ocean conditions. By using DNA nanotubes as a novel fluid flow sensor, we investigate the elongational rates generated in bursting films within aqueous bubble foams using both laboratory buffer and ocean water. To characterize the elongational rate distribution associated with a bursting bubble, we introduce the concept of a fragmentation volume and measure its form as a function of elongational flow rate. We find that substantial volumes experience surprisingly large flow rates: during the bursting of a bubble having an air volume of 10 mm3, elongational rates at least as large as ϵ˙=1.0×108 s−1 are generated in a fragmentation volume of ∼2×10−6 μL. The determination of the elongational strain rate distribution is essential for assessing how effectively fluid motion within bursting bubbles at the ocean surface can shear microscopic particles and microorganisms, and could have driven the self-replication of a protobiont.

A scanning force microscope study of detachment of nanometer‐sized particles from glass surfaces

The nominal shear stress required to detach nanometer‐scale, single‐crystal salt particles from a soda lime glass substrate is a strong function of particle size and relative humidity. We use the tip of an atomic force microscope to detach these particles from a glass substrate under controlled atmospheres of known humidity. The peak lateral force at detachment was divided by the nominal particle area to yield an effective interfacial shear strength. We describe the variation of shear strength with particle area and humidity in terms of detachment by chemically assisted crack growth along the salt–glass interface.

SCANNING FORCE MICROSCOPE OBSERVATIONS OF PARTICLE DETACHMENT FROM SUBSTRATES : THE ROLE OF WATER VAPOR IN TRIBOLOGICAL DEBONDING

The tip of a scanning force microscope was used to detach nanometer-scale, single crystal NaCl particles from a glass substrate under controlled atmospheres of known humidity. After characterizing a particle at low contact force, a single line scan at high contact force was used to apply stresses to the attached particle. The lateral force during the line scan showed a sharp discontinuity associated with detachment of the particle from the substrate. The peak lateral force during this procedure is a strong function of particle contact area and humidity. As the relative humidity is raised from low values, the strength of the particle-substrate bond decreases dramatically. We interpret these results in terms of detachment by chemically assisted crack growth along the NaCl-glass interface.