DNA Origami Colloidal Crystals: Opportunities and Challenges.

Over the last three decades, colloidal crystallization has provided an easy-to-craft platform for mesoscale engineering of photonic and phononic crystals. Nevertheless, the crystal lattices achieved thus far with commodity colloids are largely limited to symmetric and densely packed structures, restricting their functionalities. To obtain non-close-packed crystals and the resulting complexity of the available structures, directional binding between "patchy" colloids has been pursued.

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays.

Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems.

Free-Standing DNA Origami Superlattice to Facilitate Cryo-EM Visualization of Membrane Vesicles.

Technological breakthroughs in cryo-electron microscopy (cryo-EM) methods open new perspectives for highly detailed structural characterizations of extracellular vesicles (EVs) and synthetic liposome-protein assemblies. Structural characterizations of these vesicles in solution under a nearly native hydrated state are of great importance to decipher cell-to-cell communication and to improve EVs' application as markers in diagnosis and as drug carriers in disease therapy. However, difficulties in preparing holey carbon cryo-EM grids with low vesicle heterogeneities, at low concentration and with kinetic control of the chemical reactions or assembly processes, have limited cryo-EM use in the EV study.

Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform.

Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery.

Mechanism of DNA origami folding elucidated by mesoscopic simulations.

Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure.

A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids.

Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters.

DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes.

The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations.

Dynamic Gold Nanostructures Based on DNA Self Assembly.

The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties.

Controlling Silicification on DNA Origami with Polynucleotide Brushes.

DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired.

Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand.

Molecular forces generated by cell receptors are infrequent and transient, and hence difficult to detect. Here we report an assay that leverages the CRISPR-associated protein 12a (Cas12a) to amplify the detection of cellular traction forces generated by as few as 50 adherent cells. The assay involves the immobilization of a DNA duplex modified with a ligand specific for a cell receptor.

Circular single-stranded DNA as switchable vector for gene expression in mammalian cells.

Synthetic gene networks in mammalian cells are currently limited to either protein-based transcription factors or RNA-based regulators. Here, we demonstrate a regulatory approach based on circular single-stranded DNA (Css DNA), which can be used as an efficient expression vector with switchable activity, enabling gene regulation in mammalian cells. The Css DNA is transformed into its double-stranded form via DNA replication and used as vectors encoding a variety of different proteins in a wide range of cell lines as well as in mice.

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures.

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability.

A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision.

Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures.

Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes.

Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway.

DNA origami-designed 3D phononic crystals.

Moulding the flow of phononic waves in three-dimensional (3D) space plays a critical role in controlling the sound and thermal properties of matter. To this end, 3D phononic crystals (PnCs) have been considered the gold standard because their complete phononic bandgap (PnBG) enables omnidirectional inhibition of phononic wave propagation. Nevertheless, achieving a complete PnBG in the high-frequency regime is still challenging, as attaining the correspondingly demanded mesoscale 3D crystals consisting of continuous frame networks with conventional fabrications is difficult.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications.

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before.

A bistable and reconfigurable molecular system with encodable bonds.

Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ's conformation and transformation is realized by programming the stacking bonds (quasi-blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms.

Cooperative binding of T cell receptor and CD4 to peptide-MHC enhances antigen sensitivity.

Antigen recognition by the T cell receptor (TCR) of CD4 T cells can be greatly enhanced by the coreceptor CD4. Yet, understanding of the molecular mechanism is hindered by the ultra-low affinity of CD4 binding to class-II peptide-major histocompatibility complexes (pMHC). Here we show, using two-dimensional (2D) mechanical-based assays, that the affinity of CD4-pMHC interaction is 3-4 logs lower than that of cognate TCR-pMHC interactions, and it is more susceptible to increased dissociation by forces (slip bond).

Structure-Dependent Electrical Conductance of DNA Origami Nanowires.

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated.

Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions.

DNA nanostructure-based responsive drug delivery has become an increasingly potent method in cancer therapy. However, a variety of important cancer biomarkers have not been explored in searching of new and efficient targeted delivery systems. Uracil degradation glycosylase and human apurinic/apyrimidinic endonuclease are significantly more active in cancer cells.

Stress in DNA Gridiron Facilitates the Formation of Two-Dimensional Crystalline Structures.

Programmable DNA nanotechnology has generated some of the most intricate self-assembled nanostructures and has been employed in a growing number of applications, including functional nanomaterials, nanofabrication, biophysics, photonics, molecular machines, and drug delivery. An important design rule for DNA nanostructures is to minimize the mechanical stress to reduce the potential energy in these nanostructures whenever it is possible. This work revisits the DNA gridiron design consisting of Holliday junctions and compares the self-assembly of the canonical DNA gridiron with a new design of DNA gridiron, which has a higher degree of mechanical stress because of the interweaving of DNA helices.

DNA Assembly of Modular Components into a Rotary Nanodevice.

The bacterial flagellar motor is a rotary machine composed of functional modular components, which can perform bidirectional rotations to control the migration behavior of the bacterial cell. It resembles a two-cogwheel gear system, which consists of small and large cogwheels with cogs at the edges to regulate rotations. Such gearset models provide elegant blueprints to design and build artificial nanomachinery with desired functionalities.

Programmable allosteric DNA regulations for molecular networks and nanomachines.

Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging.

Spatiotemporal Control of Molecular Cascade Reactions by a Reconfigurable DNA Origami Domino Array.

Inspired by efficient biomolecular reactions in the cell, versatile DNA nanostructures have been explored for manipulating the spatial position and regulating reactions at the molecular level. Spatially controlled arrangement of molecules on the artificial scaffolds generally leads to enhanced reaction activities. Especially, the rich toolset of dynamic DNA nanostructures provides a potential route towards more sophisticated and vigorous regulation of molecular reactions.

Blockade of glutamine-dependent cell survival augments antitumor efficacy of CPI-613 in head and neck cancer.

Background: Alterations in metabolism are one of the emerging hallmarks of cancer cells and targeting dysregulated cancer metabolism provides a new approach to developing more selective therapeutics. However, insufficient blockade critical metabolic dependencies of cancer allows the development of metabolic bypasses, thus limiting therapeutic benefits.

Methods: A series of head and neck squamous cell carcinoma (HNSCC) cell lines and animal models were used to determine the efficacy of CPI-613 and CB-839 when given alone or in combination.