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The evolution of dynamic DNA nanostructures has propelled DNA nanotechnology into a robust and versatile field, offering groundbreaking applications in nanoscale communication, drug delivery, and molecular computing. Yet, the full potential of this technology awaits further enhancement through optimization of kinetic properties governing conformational changes. In this work, we introduce a mean-field theory to characterize the kinetic behavior of a dynamic DNA origami hinge where each arm bears complementary single-stranded DNA overhangs of different lengths, which can latch the hinge at a closed conformation. This device is currently being investigated for multiple applications, being of particular interest the development of DNA-based rapid diagnostic tests for coronavirus. Drawing from classical statistical mechanics theories, we derive analytical expressions for the mean binding time of these overhangs within a constant hinge. This analysis is then extended to flexible hinges, where the angle diffuses within a predetermined energy landscape. We validate our model by comparing it with experimental measurements of the closing rates of DNA nanocalipers with different energy landscapes and overhang lengths, demonstrating excellent agreement and suggesting fast angular relaxation relative to binding. These findings offer insights that can guide the optimization of devices for specific state lifetimes. Moreover, the framework introduced here lays the groundwork for further advancements in modeling the kinetics of dynamic DNA nanostructures. [ABSTRACT FROM AUTHOR]

The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model. [ABSTRACT FROM AUTHOR]

Reconfigurable chiral plasmonic complexes are fabricated by planar assembly of multiple individual gold nanorod dimers using DNA origami templates. Additionally, each chiral center can be controlled to switch among achiral, left-handed, and right-handed states. We demonstrate that their overall circular dichroism is determined by the coupling of individual chiral centers and is heavily influenced by the precise number and arrangement of these centers. Our study offers a novel self-assembly method for constructing intricate and dynamic chiral plasmonics as well as investigating the interactions among several plasmonic chiral centers. [ABSTRACT FROM AUTHOR]

Emerging nano-kirigami/origami technology enables the flexible transformations of 2D planar patterns into exquisite 3D structures in situ and has aroused great interest in the areas of nanophotonics and optoelectronics. This paper briefly reviews some milestone research and breakthrough progresses in nano-kirigami/origami from the aspects of stimuli approaches and application directions. Versatile stimuli for kirigami/origami, including capillary force, residual stress, mechanical force, and irradiation-induced stress, are introduced in the micro/nanoscale region. Appealing optical applications and reconfigurable schemes of nano-kirigami/origami structures are summarized, offering effective routes to realize tunable nanophotonic and optoelectronic devices. Future challenges and promising pathways are also envisioned, including design methods, innovative materials, multi-physics field driving, and reprogrammable devices. [ABSTRACT FROM AUTHOR]

Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces—base stacking, counterion-induced backbone self-interactions, and base pairing—via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach. [ABSTRACT FROM AUTHOR]

Model patchy particles have been shown to be able to form a wide variety of structures, including symmetric clusters, complex crystals, and even two-dimensional quasicrystals. Here, we investigate whether we can design patchy particles that form three-dimensional quasicrystals, in particular targeting a quasicrystal with dodecagonal symmetry that is made up of stacks of two-dimensional quasicrystalline layers. We obtain two designs that are able to form such a dodecagonal quasicrystal in annealing simulations. The first is a one-component system of seven-patch particles but with wide patches that allow them to adopt both seven- and eight-coordinated environments. The second is a ternary system that contains a mixture of seven- and eight-patch particles and is likely to be more realizable in experiments, for example, using DNA origami. One interesting feature of the first system is that the resulting quasicrystals very often contain a screw dislocation. [ABSTRACT FROM AUTHOR]

Quantum dot (QD) biological imaging and sensing applications often require surface modification with single-stranded deoxyribonucleic acid (ssDNA) oligonucleotides. Furthermore, ssDNA conjugation can be leveraged for precision QD templating via higher-order DNA nanostructures to exploit emergent behaviors in photonic applications. Use of ssDNA-QDs across these platforms requires compact, controlled conjugation that engenders QD stability over a wide pH range and in solutions of high ionic strength. However, current ssDNA-QD conjugation approaches suffer from limitations, such as the requirement for thick coatings, low control over ssDNA labeling density, requirement of large amounts of ssDNA, or low colloidal or photostability, restraining implementation in many applications. Here, we combine thin, multidentate, phytochelatin-3 (PC3) QD passivation techniques with strain-promoted copper-free alkyne-azide click chemistry to yield functional ssDNA-QDs with high stability. This process was broadly applicable across QD sizes (i.e., λem = 540, 560, 600 nm), ssDNA lengths (i.e., 10–16 base pairs, bps), and sequences (poly thymine, mixed bps). The resulting compact ssDNA-QDs displayed a fluorescence quenching efficiency of up to 89% by hybridization with complementary ssDNA-AuNPs. Furthermore, ssDNA-QDs were successfully incorporated with higher-order DNA origami nanostructure templates. Thus, this approach, combining PC3 passivation with click chemistry, generates ssDNA-PC3-QDs that enable emergent QD properties in DNA-based devices and applications. [ABSTRACT FROM AUTHOR]

The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that strikes a balance between these two criteria by representing these systems on a lattice at the level of binding domains. The free energy of hybridization between individual binding domains is estimated with a nearest-neighbour model. Double helical segments are treated as being rigid, but we allow flexibility at points where the backbone of one of the strands is interrupted, which provides a reasonably realistic representation of partially and fully assembled states. Particular attention is paid to the constraints imposed by the double helical twist, as they determine where strand crossovers between adjacent helices can occur. To improve the efficiency of sampling configuration space, we develop Monte Carlo methods for sampling scaffold conformations in near-assembled states, and we carry out simulations in the grand canonical ensemble, enabling us to avoid considering states with unbound staples. We demonstrate that our model can quickly sample assembled configurations of a small origami design previously studied with the oxDNA model, as well as a design with staples that span longer segments of the scaffold. The sampling ability of our method should allow for good statistics to be obtained when studying the assembly pathways and is suited to investigating, in particular, the effects of design and assembly conditions on these pathways and their resulting final assembled structures. [ABSTRACT FROM AUTHOR]

Double-stranded DNA translocates through sufficiently large nanopores either in a linear single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be controlled by changing the electrolyte concentration, pH, and polyethylene glycol content of the measurement buffer. At pH 8 in 1M LiCl or 0.35M KCl, single-file translocations make up more than 90% of the total. We attribute the effect to the onset of electro-osmotic flow from the pore at low ionic strength. Our hypothesis on the critical role of flows is supported by the preferred orientation of entry of a strand that has been folded into a multi-helix structure at one end. Control over DNA folding is critical for nanopore sensing approaches that use modifications along a DNA strand and the associated secondary current drops to encode information. [ABSTRACT FROM AUTHOR]

We built and characterised a macroscopic self-assembly reactor that agitates magnetic, centimeter- sized particles with a turbulent water flow. By scaling up the self-assembly processes to the centimeter-scale, the characteristic time constants also drastically increase. This makes the system a physical simulator of microscopic self-assembly, where the interaction of inserted particles is easily observable. Trajectory analysis of single particles reveals their velocity to be a Maxwell-Boltzmann distribution and it shows that their average squared displacement over time can be modelled by a confined random walk model, demonstrating a high level of similarity to the Brownian motion. The interaction of two particles has been modelled and verified experimentally by observing the distance between two particles over time. The disturbing energy (analogue to temperature) that was obtained experimentally increases with sphere size and differs by an order of magnitude between single-sphere and two-sphere systems (approximately 80 µJ versus 6.5 µJ, respectively). [ABSTRACT FROM AUTHOR]

Shearing DNA to a certain size is the first step in many medical and biological applications, especially in next-generation gene sequencing technology. In this article, we introduced a highly efficient ultrasonic DNA fragmentation method enhanced by needle-induced air bubbles, which is easy to operate with high throughput. The principle of the bubble-enhanced sonication system is introduced and verified by flow field and acoustic simulations and experiments. Lambda DNA long chains and mouse genomic DNA short chains are used in the experiments for testing the performance of the bubble-enhanced ultrasonic DNA fragmentation system. Air bubbles are an effective enhancement agent for ultrasonic DNA fragmentation; they can obviously improve the sound pressure level in the whole solution, thus, achieving better absorption of ultrasound energy. Growing bubbles also have a stretched function on DNA molecule chains and form a huge pressure gradient in the solution, which is beneficial to DNA fragmentation. Purified λDNA is cut from 48.5 to 2 kbp in 5 min and cut to 300 bp in 30 min. Mouse genomic DNA (≈1400 bp) decreases to 400 bp in 5 min and then reduces to 200 bp in 30 min. This bubble-enhanced ultrasonic method enables widespread access to genomic DNA fragmentation in a standard ultrasonic water bath for many virus sequencing demands even without good medical facilities. [ABSTRACT FROM AUTHOR]

Recent experiments and simulation studies showed that protein/DNA folding barriers inferred from folding rates or from potentials of mean force are often much higher than the barriers estimated from the distributions of transition path times. Here a toy model is used to explain a possible origin of this effect: It is shown that when the transition in question involves an entropic barrier, the one-dimensional Langevin model commonly used to interpret experimental data, while adequately predicting the transition rate, fails to describe the properties of the subset of the trajectories that form the transition path ensemble; the latter may still be describable in terms of a one-dimensional model, but with a different potential, just as observed experimentally. [ABSTRACT FROM AUTHOR]

A cantilever beam with elastic hinge pulled antagonistically by two dielectric elastomer (DE) membranes in tension forms a foldable actuator if one DE membrane is subject to a voltage and releases part of tension. Simply placing parallel rigid bars on the prestressed DE membranes results in enhanced actuators working in a pure shear state. We report design, analysis, fabrication, and experiment of soft mobile robots that are moved by such foldable DE actuators. We describe systematic measurement of the foldable actuators and perform theoretical analysis of such actuators based on minimization of total energy, and a good agreement is achieved between model prediction and measurement. We develop two versions of prototypes of soft mobile robots driven either by two sets of DE membranes or one DE membrane and elastic springs. We demonstrate locomotion of these soft mobile robots and highlight several key design parameters that influence locomotion of the robots. A 45 g soft robot driven by a cyclic triangle voltage with amplitude 7.4 kV demonstrates maximal stroke 160 mm or maximal rolling velocity 42 mm/s. The underlying mechanics and physics of foldable DE actuators can be leveraged to develop other soft machines for various applications. [ABSTRACT FROM AUTHOR]

Utilizing self-assembled DNA structures in the development of nanoelectronic circuits requires transforming the DNA strands into highly conducting wires. Toward this end, we investigate the use of DNA self-assembled nanowires as templates for the deposition of a superconducting material. Nanowires formed by the deposition of superconducting NbN exhibit thermally activated and quantum phase slips as well as exceptionally large negative magnetoresistance. The latter effect can be utilized to suppress a significant part of the low temperature resistance caused by the quantum phase slips. [ABSTRACT FROM AUTHOR]

The DNA origami technique itself is considered a milestone of DNA nanotechnology and DNA origami nanorulers represent the first widespread application of this technique. DNA origami nanorulers are used to demonstrate the capabilities of techniques and are valuable training samples. They have meanwhile been developed for a multitude of microscopy methods including optical microscopy, atomic force microscopy, and electron microscopy, and their unique properties are further exploited to develop point-light sources, brightness references, nanophotonic test structures, and alignment tools for correlative microscopy. In this perspective, we provide an overview of the basics of DNA origami nanorulers and their increasing applications in fields of optical and especially super-resolution fluorescence microscopy. In addition, emerging applications of reference structures based on DNA origami are discussed together with recent developments. [ABSTRACT FROM AUTHOR]

Precise control over the morphologies of nanomaterials is of great importance in nanoscience, as the properties of nanomaterials are strongly dependent on their size, shape, and composition. Taking advantage of the strict base-pairing principle, DNA origami provides a simple way of fabricating complex architectures with nanoscale precision. DNA origami nanostructures have exhibited great potential in tuning the morphology and customizing the functions of various nanomaterials. In this paper, we briefly summarize the progress of shape-controllable fabrication of metal, metal oxide, inorganic nonmetallic nanomaterials, and polymer nanomaterials based on DNA origami. Furthermore, the remaining obstacles and prospects of shape-controllable nanomaterials fabrication directed by DNA origami are also discussed. [ABSTRACT FROM AUTHOR]

Three-dimensional tubular origami, fabricated by the self-rolling of functional nanomembranes, is of great interest due to its numerous opportunities for applications in photochemical sensing, intelligent actuators, microrobots, electronics, and many others. A continuing opportunity of this area is in the development of strategies for fabricating tubular origami, in solvent-free and low-cost conditions. This paper proposed a semidry release approach, allowing for the sacrificial layer-free, vapor-assisted self-rolling, and recyclable use of substrates, to create microscale tubular origami. Interface engineering designs that involve hydrophilic and hydrophobic material stacks are introduced to realize the semidry release of nanomembranes, which finally self-roll into multifunctional tubular structures. Systematic experimental and theoretical studies demonstrate the controllability of their dimensions. Finally, a bioresorbable microtube with potential for transient implantable devices is demonstrated. Our present work adds to the portfolio of routes for the construction of tubular origami, which can be utilized as functional platforms for fundamental studies and practical applications. [ABSTRACT FROM AUTHOR]

Origami, the ancient Japanese art of folding paper to create esthetic sculptures, has recently emerged in the scientific literature as an innovative means to build mechanical structures with tailorable properties. Along those lines, the Kresling origami pattern has been used to design and construct bi-stable bellows with tailorable stiffness. In this work, we exploit the inter-well dynamic behavior of such bellows to develop and characterize a cluster of mechanical binary switches that can be selectively operated using a single input. This input is in the form of a harmonic resonant excitation with a pre-selected frequency and magnitude applied at the base of the switch. Using a phenomenological model of the switch, we study its nonlinear dynamic behavior and approximate its activation frequency bandwidth. We also demonstrate that multiple binary switches of different geometric characteristics can be combined to create a mechanical memory board of multiple bits placed on a single harmonically excited platform. [ABSTRACT FROM AUTHOR]

A new design of a noncontact atomic force microscope (AFM) is introduced in this paper, based on a piezoelectric oscillator sensor (PEOS) for ambient and liquid environments. Because of the recent development of quartz technology, the PEOS sensor operates independently from conventional laser alignments. The sensor is based on the length extension resonator, which has high force sensitivity and can deliver high resolution AFM images in ultrahigh vacuum. The oscillator design was tested in different gas compositions and liquids to determine its oscillation stability. The scan performance was investigated in both air and liquid on the topography of an inorganic hard material, graphite. The usability of PEOS for soft organic materials was further proven by imaging biological samples of DNA origami. [ABSTRACT FROM AUTHOR]

The authors report the unusual thermal stability of deoxyribose nucleic acid (DNA) origami when adhered to a solid substrate. Even when heated to 150 C for 45 min, these DNA nanostructures retain their physical and chemical integrity. This result suggests that DNA origami could be integrated into applications requiring moderate substrate heating, such as photoresist baking or chemical vapor deposition processes. [ABSTRACT FROM AUTHOR]

DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by the presence of short, single stranded DNA sequences (staples), that hold together separate regions of the scaffold. In this paper, we modelize the annealing-melting properties of these DNA constructions. The model captures important features such as the hysteresis between melting and annealing, as well as the dependence upon the topology of the scaffold. We show that cooperativity between staples is critical to quantitatively explain the folding process of DNA origamis. [ABSTRACT FROM AUTHOR]