Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor.

ABSTRACT: DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements.

SUBMITTER: Wang L

PROVIDER: S-EPMC5716610 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor.

Wang Liying L Meng Zhenyu Z Martina Felicia F Shao Huilin H Shao Fangwei F

Nucleic acids research 20171201 21

DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotati ...[more]

PMID: 29126166

Similar Datasets

A DNA origami rotary ratchet motor.

Project description:To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6-8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9-12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.

| S-EPMC9300469 | biostudies-literature

Dynamic Assemblies of Molecular Motor Amphiphiles Control Macroscopic Foam Properties.

Project description:Stimuli-responsive supramolecular assemblies controlling macroscopic transformations with high structural fluidity, i.e., foam properties, have attractive prospects for applications in soft materials ranging from biomedical systems to industrial processes, e.g., textile coloring. However, identifying the key processes for the amplification of molecular motion to a macroscopic level response is of fundamental importance for exerting the full potential of macroscopic structural transformations by external stimuli. Herein, we demonstrate the control of dynamic supramolecular assemblies in aqueous media and as a consequence their macroscopic foam properties, e.g., foamability and foam stability, by large geometrical transformations of dual light/heat stimuli-responsive molecular motor amphiphiles. Detailed insight into the reversible photoisomerization and thermal helix inversion at the molecular level, supramolecular assembly transformations at the microscopic level, and the stimuli-responsive foam properties at the macroscopic level, as determined by UV-vis absorption and NMR spectroscopies, electron microscopy, and foamability and in situ surface tension measurements, is presented. By selective use of external stimuli, e.g., light or heat, multiple states and properties of macroscopic foams can be controlled with very dilute aqueous solutions of the motor amphiphiles (0.2 weight%), demonstrating the potential of multiple stimuli-responsive supramolecular systems based on an identical molecular amphiphile and providing opportunities for future soft materials.

| S-EPMC7273467 | biostudies-literature

Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor.

Project description:V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20??M ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2?mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.

| S-EPMC5095293 | biostudies-literature

Dynamic DNA assemblies mediated by binding-induced DNA strand displacement.

Project description:Dynamic DNA assemblies, including catalytic DNA circuits, DNA nanomachines, molecular translators, and reconfigurable nanostructures, have shown promising potential to regulate cell functions, deliver therapeutic reagents, and amplify detection signals for molecular diagnostics and imaging. However, such applications of dynamic DNA assembly systems have been limited to nucleic acids and a few small molecules, due to the limited approaches to trigger the DNA assemblies. Herein, we describe a binding-induced DNA strand displacement strategy that can convert protein binding to the release of a predesigned output DNA at room temperature with high conversion efficiency and low background. This strategy allows us to construct dynamic DNA assembly systems that are able to respond to specific protein binding, opening an opportunity to initiate dynamic DNA assembly by proteins.

| S-EPMC3580983 | biostudies-literature

A rotary motor drives Flavobacterium gliding.

Project description:Cells of Flavobacterium johnsoniae, a rod-shaped bacterium devoid of pili or flagella, glide over glass at speeds of 2-4 ?m/s [1]. Gliding is powered by a protonmotive force [2], but the machinery required for this motion is not known. Usually, cells move along straight paths, but sometimes they exhibit a reciprocal motion, attach near one pole and flip end over end, or rotate. This behavior is similar to that of a Cytophaga species described earlier [3]. Development of genetic tools for F. johnsoniae led to discovery of proteins involved in gliding [4]. These include the surface adhesin SprB that forms filaments about 160 nm long by 6 nm in diameter, which, when labeled with a fluorescent antibody [2] or a latex bead [5], are seen to move longitudinally down the length of a cell, occasionally shifting positions to the right or the left. Evidently, interaction of these filaments with a surface produces gliding. To learn more about the gliding motor, we sheared cells to reduce the number and size of SprB filaments and tethered cells to glass by adding anti-SprB antibody. Cells spun about fixed points, mostly counterclockwise, rotating at speeds of 1 Hz or more. The torques required to sustain such speeds were large, comparable to those generated by the flagellar rotary motor. However, we found that a gliding motor runs at constant speed rather than at constant torque. Now, there are three rotary motors powered by protonmotive force: the bacterial flagellar motor, the Fo ATP synthase, and the gliding motor.

| S-EPMC4319542 | biostudies-literature

Structure and dynamics of rotary V1 motor.

Project description:Rotary ATPases are unique rotary molecular motors that function as energy conversion machines. Among all known rotary ATPases, F1-ATPase is the best characterized rotary molecular motor. There are many high-resolution crystal structures and the rotation dynamics have been investigated in detail by extensive single-molecule studies. In contrast, knowledge on the structure and rotation dynamics of V1-ATPase, another rotary ATPase, has been limited. However, recent high-resolution structural studies and single-molecule studies on V1-ATPase have provided new insights on how the catalytic sites in this molecular motor change its conformation during rotation driven by ATP hydrolysis. In this review, we summarize recent information on the structural features and rotary dynamics of V1-ATPase revealed from structural and single-molecule approaches and discuss the possible chemomechanical coupling scheme of V1-ATPase with a focus on differences between rotary molecular motors.

| S-EPMC5910484 | biostudies-literature

Dynamic motor imagery mentally simulates uncommon real locomotion better than static motor imagery both in young adults and elderly.

Project description:A new form of Motor Imagery (MI), called dynamic Motor Imagery (dMI) has recently been proposed. The dMI adds to conventional static Motor Imagery (sMI) the presence of simultaneous actual movements partially replicating those mentally represented. In a previous research conducted on young participants, dMI showed to be temporally closer than sMI in replicating the real performance for some specific locomotor conditions. In this study, we evaluated if there is any influence of the ageing on dMI. Thirty healthy participants were enrolled: 15 young adults (27.1±3.8 y.o.) and 15 older adults (65.9±9.6y.o.). The performance time and the number of steps needed to either walk to a target (placed at 10m from participants) or to imagine walking to it, were assessed. Parameters were measured for sMI, dMI and real locomotion (RL) in three different locomotor conditions: forward walking (FW), backward walking (BW), and lateral walking (LW). Temporal performances of sMI and dMI did not differ between RL in the FW, even if significantly different to each other (p = 0.0002). No significant differences were found for dMI with respect to RL for LW (p = 0.140) and BW (p = 0.438), while sMI was significantly lower than RL in LW (p<0.001). The p-value of main effect of age on participants' temporal performances was p = 0.055. The interaction between age and other factors such as the type of locomotion (p = 0.358) or the motor condition (p = 0.614) or third level interaction (p = 0.349) were not statistically significant. Despite a slight slowdown in the performance of elderly compared to young participants, the temporal and spatial accuracy was better in dMI than sMI in both groups. Motor imagery processes may be strengthened by the feedback generated through dMI, and this effect appears to be unaffected by age.

| S-EPMC6594612 | biostudies-literature

The dynamic stator stalk of rotary ATPases.

Project description:Rotary ATPases couple ATP hydrolysis/synthesis with proton translocation across biological membranes and so are central components of the biological energy conversion machinery. Their peripheral stalks are essential components that counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Here we present a 2.25-Å resolution crystal structure of the peripheral stalk from Thermus thermophilus A-type ATPase/synthase. We identify bending and twisting motions inherent within the structure that accommodate and complement a radial wobbling of the ATPase headgroup as it progresses through its catalytic cycles, while still retaining azimuthal stiffness necessary to counteract rotation of the central stalk. The conformational freedom of the peripheral stalk is dictated by its unusual right-handed coiled-coil architecture, which is in principle conserved across all rotary ATPases. In context of the intact enzyme, the dynamics of the peripheral stalks provides a potential mechanism for cooperativity between distant parts of rotary ATPases.

| S-EPMC3293630 | biostudies-literature

Multiscale molecular dynamics simulations of rotary motor proteins.

Project description:Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

| S-EPMC5899732 | biostudies-literature

Noise characteristics of the Escherichia coli rotary motor.

Project description:BackgroundThe chemotaxis pathway in the bacterium Escherichia coli allows cells to detect changes in external ligand concentration (e.g. nutrients). The pathway regulates the flagellated rotary motors and hence the cells' swimming behaviour, steering them towards more favourable environments. While the molecular components are well characterised, the motor behaviour measured by tethered cell experiments has been difficult to interpret.ResultsWe study the effects of sensing and signalling noise on the motor behaviour. Specifically, we consider fluctuations stemming from ligand concentration, receptor switching between their signalling states, adaptation, modification of proteins by phosphorylation, and motor switching between its two rotational states. We develop a model which includes all signalling steps in the pathway, and discuss a simplified version, which captures the essential features of the full model. We find that the noise characteristics of the motor contain signatures from all these processes, albeit with varying magnitudes.ConclusionsOur analysis allows us to address how cell-to-cell variation affects motor behaviour and the question of optimal pathway design. A similar comprehensive analysis can be applied to other two-component signalling pathways.

| S-EPMC3224245 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data