DNA Hydrogels with Programmable Condensation, Expansion, and Degradation for Molecular Carriers.

Molecular carriers are necessary for the controlled release of drugs and genes to achieve the desired therapeutic outcomes. DNA hydrogels can be a promising candidate in this application with their distinctive sequence-dependent programmability, which allows precise encapsulation of specific cargo molecules and stimuli-responsive release of them at the target. However, DNA hydrogels are inherently susceptible to the degradation of nucleases, making them vulnerable in a physiological environment. To be an effective molecular carrier, DNA hydrogels should be able to protect encapsulated cargo molecules until they reach the target and release them once they are reached. Here, we develop a simple way of controlling the enzyme resistance of DNA hydrogels for cargo protection and release by using cation-mediated condensation and expansion. We found that DNA hydrogels condensed by spermine are highly resistant to enzymatic degradation. They become degradable again if expanded back to their original, uncondensed state by sodium ions interfering with the interaction between spermine and DNA. These controllable condensation, expansion, and degradation of DNA hydrogels pave the way for the development of DNA hydrogels as an effective molecular carrier.

Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures.

DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.

Harnessing a paper-folding mechanism for reconfigurable DNA origami.

The paper-folding mechanism has been widely adopted in building of reconfigurable macroscale systems because of its unique capabilities and advantages in programming variable shapes and stiffness into a structure1-5. However, it has barely been exploited in the construction of molecular-level systems owing to the lack of a suitable design principle, even though various dynamic structures based on DNA self-assembly6-9 have been developed10-23. Here we propose a method to harness the paper-folding mechanism to create reconfigurable DNA origami structures. The main idea is to build a reference, planar wireframe structure24 whose edges follow a crease pattern in paper folding so that it can be folded into various target shapes. We realized several paper-like folding and unfolding patterns using DNA strand displacement25 with high yield. Orthogonal folding, repeatable folding and unfolding, folding-based microRNA detection and fluorescence signal control were demonstrated. Stimuli-responsive folding and unfolding triggered by pH or light-source change were also possible. Moreover, by employing hierarchical assembly26 we could expand the design space and complexity of the paper-folding mechanism in a highly programmable manner. Because of its high programmability and scalability, we expect that the proposed paper-folding-based reconfiguration method will advance the development of complex molecular systems.

Engineering DNA-based synthetic condensates with programmable material properties, compositions, and functionalities.

Biomolecular condensates participate in diverse cellular processes, ranging from gene regulation to stress survival. Bottom-up engineering of synthetic condensates advances our understanding of the organizing principle of condensates. It also enables the synthesis of artificial systems with novel functions. However, building synthetic condensates with a predictable organization and function remains challenging. Here, we use DNA as a building block to create synthetic condensates that are assembled through phase separation. The programmability of intermolecular interactions between DNA molecules enables the control over various condensate properties including assembly, composition, and function. Similar to the way intracellular condensates are organized, DNA clients are selectively partitioned into cognate condensates. We demonstrate that the synthetic condensates can accelerate DNA strand displacement reactions and logic gate operation by concentrating specific reaction components. We envision that the DNA-based condensates could help the realization of the high-order functions required to build more life-like artificial systems.

Peptide-DNA origami as a cryoprotectant for cell preservation.

Cryopreservation of cells is essential for the conservation and cold chain of bioproducts and cell-based medicines. Here, we demonstrate that self-assembled DNA origami nanostructures have a substantial ability to protect cells undergoing freeze-thaw cycles; thereby, they can be used as cryoprotectant agents, because their nanoscale morphology and ice-philicity are tailored. In particular, a single-layered DNA origami nanopatch functionalized with antifreezing threonine peptides enabled the viability of HSC-3 cells to reach 56% after 1 month of cryopreservation, surpassing dimethyl sulfoxide, which produced 38% viability. It also exhibited minimal dependence on the cryopreservation period and freezing conditions. We attribute this outcome to the fact that the peptide-functionalized DNA nanopatches exert multisite actions for the retardation of ice growth in both intra- and extracellular regions and the protection of cell membranes during cryopreservation. This discovery is expected to deepen our fundamental understanding of cell survival under freezing environment and affect current cryopreservation technologies.

Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers.

Programmability of DNA sequences enables the formation of synthetic DNA nanostructures and their macromolecular assemblies such as DNA hydrogels. The base pair-level interaction of DNA is a foundational and powerful mechanism to build DNA structures at the nanoscale; however, its temperature sensitivity and weak interaction force remain a barrier for the facile and scalable assembly of DNA structures toward higher-order structures. We conducted this study to provide an alternative, non-base-pairing approach to connect nanoscale DNA units to yield micrometer-sized gels based on the sequential phase transition of amphiphilic unit structures. Strong electrostatic interactions between DNA nanostructures and polyelectrolyte spermines led to the formation of giant phase-separated aggregates of monomer units. Gelation could be initiated by the addition of NaCl, which weakened the electrostatic DNA-spermine interaction while attractive interactions between cholesterols created stable networks by crosslinking DNA monomers. In contrast to the conventional DNA gelation techniques, our system used solid aggregates as a precursor for DNA microgels. Therefore, in situ gelation could be achieved by depositing aggregates on the desired substrate and subsequently initiating a phase transition. Our approach can expand the utility and functionality of DNA hydrogels by using more complex nucleic acid assemblies as unit structures and combining the technique with top-down microfabrication methods.

DeepPhaseCut: Deep Relaxation in Phase for Unsupervised Fourier Phase Retrieval.

Fourier phase retrieval is a classical problem of restoring a signal only from the measured magnitude of its Fourier transform. Although Fienup-type algorithms, which use prior knowledge in both spatial and Fourier domains, have been widely used in practice, they can often stall in local minima. Convex relaxation methods such as PhaseLift and PhaseCut may offer performance guarantees, but these algorithms are usually computationally expensive for practical use. To address this problem, here we propose a novel unsupervised feed-forward neural network for Fourier phase retrieval which generates high quality reconstruction immediately. Unlike the existing deep learning approaches that use a neural network as a regularization term or an end-to-end blackbox model for supervised training, our algorithm is a feed-forward neural network implementation of physics-driven constraints in an unsupervised learning framework. Specifically, our network is composed of two generators: one for the phase estimation using PhaseCut loss, followed by another generator for image reconstruction, all of which are trained simultaneously without matched data. The link to the classical Fienup-type algorithms and the recent symmetry-breaking learning approach is also revealed. Extensive experiments demonstrate that the proposed method outperforms all existing approaches in Fourier phase retrieval problems.

Characterizing and Harnessing the Mechanical Properties of Short Single-Stranded DNA in Structured Assemblies.

Precise engineering of DNA structures is of growing interest to solve challenging problems in biomolecular applications and beyond. The introduction of single-stranded DNA (ssDNA) into the DNA structure can play a pivotal role in providing high controllability of critical structural features. Herein, we present a computational model of ssDNA with structural applications to harness its characteristics. The nonlinear properties of nucleotide gaps are systematically characterized to construct a structural model of the ssDNA across length scales with the incorporation of a finite element framework. The proposed method shows the programmability of structural bending, twisting, and persistence length by implementing the ssDNA in various DNA structures with experimental validation. Our results have significant implications for DNA nanotechnology in expanding the boundary of design and analysis of structural shape and stiffness.

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules.

Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.

Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution.

Structural DNA nanotechnology plays an ever-increasing role in advanced biomolecular applications. Here, we present a computational method to analyze structured DNA assemblies rapidly at near-atomic resolution. Both high computational efficiency and molecular-level accuracy are achieved by developing a multiscale analysis framework. The sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atom molecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information. The proposed method can predict the three-dimensional shape, equilibrium dynamic properties, and mechanical rigidities of monomeric to hierarchically assembled DNA structures at near-atomic resolution without adjusting any model parameters. The calculation takes less than only 15 min for most origami-scale DNA nanostructures consisting of 7000-8000 base-pairs. Hence, it is expected to be highly utilized in an iterative design-analysis-revision process for structured DNA assemblies.

Tailoring the Mechanical Stiffness of DNA Nanostructures Using Engineered Defects.

As scaffolded DNA origami enables the construction of diverse DNA nanostructures with predefined shapes, precise modulation of their mechanical stiffness remains challenging. We demonstrate a modular design method to widely and precisely control the mechanical flexibility of scaffolded DNA origami nanostructures while maintaining their overall structural integrity and geometric characteristics. Individually engineered defects that are short single-stranded DNA (ssDNA) gaps could reduce up to 70% of the bending stiffness of DNA origami constructs with different cross-sectional shapes. We further developed a computational analysis platform predicting the bending stiffness of a defect-engineered DNA nanostructure quickly during the design process, to offer an efficient way of designing various DNA constructs with required mechanical stiffness in a desired shape for a targeted function.

Configurational Design of Mechanical Perturbation for Fine Control of Twisted DNA Origami Structures.

DNA origami nanotechnology allows us to rationally design molecular devices with arbitrary shapes and properties through programming the sequence of DNA bases for their directed self-assembly. Despite its remarkable shape programmability, it has not been fully explored yet how to precisely control the twisted shape of DNA origami structures shown to be important in controlling the physical properties of DNA devices, building DNA superstructures, and synthesizing macroscopic soft materials with targeted properties. Here, we demonstrate that designing the spatial configuration of mechanical strain energies induced by base pair (BP) insertions and deletions can effectively modulate the twist rate of DNA origami structures with a fine resolution. To illustrate, various six-helix bundles (6HB) were successfully constructed whose twist rate was precisely tuned with a mean increment of 1.8° per 21-BP-long unit block. We also show that locally relaxing the strain energy via engineered gaps, short unpaired nucleotides (NTs), can widen the range of achievable twist rate with fine controllability. The proposed configurational design approach is expected to expand the feasible design space of twisted DNA origami structures for their various potential applications with target functionalities.

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28-82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology.

Publisher Correction: Polymorphic design of DNA origami structures through mechanical control of modular components.

The originally published version of this Article contained an error in Figure 5. In panel f, the right y-axis 'Strain energy (kbT)' was labelled 'Probability' and the left y-axis 'Probability' was labelled 'Strain energy (kbT)'. This error has now been corrected in both the PDF and HTML versions of the Article.

Polymorphic design of DNA origami structures through mechanical control of modular components.

Scaffolded DNA origami enables the bottom-up fabrication of diverse DNA nanostructures by designing hundreds of staple strands, comprised of complementary sequences to the specific binding locations of a scaffold strand. Despite its exceptionally high design flexibility, poor reusability of staples has been one of the major hurdles to fabricate assorted DNA constructs in an effective way. Here we provide a rational module-based design approach to create distinct bent shapes with controllable geometries and flexibilities from a single, reference set of staples. By revising the staple connectivity within the desired module, we can control the location, stiffness, and included angle of hinges precisely, enabling the construction of dozens of single- or multiple-hinge structures with the replacement of staple strands up to 12.8% only. Our design approach, combined with computational shape prediction and analysis, can provide a versatile and cost-effective procedure in the design of DNA origami shapes with stiffness-tunable units.

Robust microzip fastener: repeatable interlocking using polymeric rectangular parallelepiped arrays.

We report a highly repeatable and robust microzip fastener based on the van der Waals force-assisted interlocking between rectangular parallelepiped arrays. To investigate zipperlike interlocking behaviors, various line arrays were fabricated with three different spacing ratios (1, 3, and 5 of 800 nm in width) and width of parallelepipeds (400 nm, 800 nm, and 5 µm with the spacing ratio of 1). In addition, the different rigidity of line arrays was inspected for a repeatable microzip fastener. The normal and shear locking forces were measured with variation of the material rigidity as well as geometry of the array, in good agreement with a proposed theory based on the contact area and force balance. The maximum adhesion forces as high as ∼8.5 N cm(-2) in the normal direction and ∼29.6 N cm(-2) in the shear direction were obtained with high stability up to 1000 cycles. High stability of our fastening system was confirmed for preventing critical failures such as buckling and fracture in practical applications.

Ultrasensitive mechanical crack-based sensor inspired by the spider sensory system.

Recently developed flexible mechanosensors based on inorganic silicon, organic semiconductors, carbon nanotubes, graphene platelets, pressure-sensitive rubber and self-powered devices are highly sensitive and can be applied to human skin. However, the development of a multifunctional sensor satisfying the requirements of ultrahigh mechanosensitivity, flexibility and durability remains a challenge. In nature, spiders sense extremely small variations in mechanical stress using crack-shaped slit organs near their leg joints. Here we demonstrate that sensors based on nanoscale crack junctions and inspired by the geometry of a spider's slit organ can attain ultrahigh sensitivity and serve multiple purposes. The sensors are sensitive to strain (with a gauge factor of over 2,000 in the 0-2 per cent strain range) and vibration (with the ability to detect amplitudes of approximately 10 nanometres). The device is reversible, reproducible, durable and mechanically flexible, and can thus be easily mounted on human skin as an electronic multipixel array. The ultrahigh mechanosensitivity is attributed to the disconnection-reconnection process undergone by the zip-like nanoscale crack junctions under strain or vibration. The proposed theoretical model is consistent with experimental data that we report here. We also demonstrate that sensors based on nanoscale crack junctions are applicable to highly selective speech pattern recognition and the detection of physiological signals. The nanoscale crack junction-based sensory system could be useful in diverse applications requiring ultrahigh displacement sensitivity.

Directional oil sliding surfaces with hierarchical anisotropic groove microstructures.

A robust directional oil sliding surface is presented by utilizing re-entrant micro-groove arrays inspired from the microgrooves of rice leaf. The overhang micro-groove arrays are shown to provide two primary goals of "omniphobicty" and "anisotropic sliding" with DI water (γlv = 72.1 mN/m) as well as mineral oil (γlv = 28 mN/m) and conventional photoresist.