Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Mechanical design of DNA nanostructures

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.

DNA-caged gold nanoparticles for controlled release of doxorubicin triggered by a DNA enzyme and pH

DNA polyhedron-caged AuNPs were self-assembled using four-point-star DNAs, with three strands hybridizing to each other and the fourth strand attaching to the AuNPs. The caged AuNPs can act as doxorubicin nanocarriers; a DNA enzyme and pH can trigger controlled release.

Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures

The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.

Ear decomposition of 3-regular polyhedral links with applications

In this paper, we introduce a notion of ear decomposition of 3-regular polyhedral links based on the ear decomposition of the 3-regular polyhedral graphs. As a result, we obtain an upper bound for the braid index of 3-regular polyhedral links. Our results may be used to characterize and analyze the structure and complexity of protein polyhedra and entanglement in biopolymers.

TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA

Biopolymers, the essential components of life, are able to form many complex nanostructures, and proteins in particular are the material of choice for most cellular processes. Owing to numerous cooperative interactions, rational design of new protein folds remains extremely challenging. An alternative strategy is to design topofolds-nanostructures built from polypeptide arrays of interacting modules that define their topology. Over the course of the last several decades DNA has successfully been repurposed from its native role of information storage to a smart nanomaterial used for nanostructure self-assembly of almost any shape, which is largely because of its programmable nature. Unfortunately, polypeptides do not possess the straightforward complementarity as do nucleic acids. However, a modular approach can nevertheless be used to assemble polypeptide nanostructures, as was recently demonstrated on a single-chain polypeptide tetrahedron. This review focuses on the current state-of-the-art in the field of topological polypeptide folds. It starts with a brief overview of the field of structural DNA and RNA nanotechnology, from which it draws parallels and possible directions of development for the emerging field of polypeptide-based nanotechnology. The principles of topofold strategy and unique properties of such polypeptide nanostructures in comparison to native protein folds are discussed. Reasons for the apparent absence of such folds in nature are also examined. Physicochemical versatility of amino acid residues and cost-effective production makes polypeptides an attractive platform for designed functional bionanomaterials.

Designer three-dimensional DNA architectures

The capability to de novo design molecular structures with precise weights, geometries, and functions provides an important avenue not only for scientific explorations, but also for technological applications. Owing largely to its rationalizable design strategies, super-molecular self-assembly with DNA has emerged as a powerful approach to assemble custom-shaped intricate three-dimensional nanostructures with molecular weights up to several megadaltons. Here, we summarize and discuss landmark achievements and important methodologies in three-dimensional DNA nanostructures.

Engineering DNA self-assemblies as templates for functional nanostructures

CONSPECTUS: DNA is a well-known natural molecule that carries genetic information. In recent decades, DNA has been used beyond its genetic role as a building block for the construction of engineering materials. Many strategies, such as tile assembly, scaffolded origami and DNA bricks, have been developed to design and produce 1D, 2D, and 3D architectures with sophisticated morphologies. Moreover, the spatial addressability of DNA nanostructures and sequence-dependent recognition enable functional elements to be precisely positioned and allow for the control of chemical and biochemical processes. The spatial arrangement of heterogeneous components using DNA nanostructures as the templates will aid in the fabrication of functional materials that are difficult to produce using other methods and can address scientific and technical challenges in interdisciplinary research. For example, plasmonic nanoparticles can be assembled into well-defined configurations with high resolution limit while exhibiting desirable collective behaviors, such as near-field enhancement. Conducting metallic or polymer patterns can be synthesized site-specifically on DNA nanostructures to form various controllable geometries, which could be used for electronic nanodevices. Biomolecules can be arranged into organized networks to perform programmable biological functionalities, such as distance-dependent enzyme-cascade activities. DNA nanostructures can carry multiple cytoactive molecules and cell-targeting groups simultaneously to address medical issues such as targeted therapy and combined administration. In this Account, we describe recent advances in the functionalization of DNA nanostructures in different fashions based on our research efforts in nanophotonics, nanoelectronics, and nanomedicine. We show that DNA origami nanostructures can guide the assembly of achiral, spherical, metallic nanoparticles into nature-mimicking chiral geometries through hybridization between complementary DNA strands on the surface of nanoparticles and DNA scaffolds, to generate circular dichroism (CD) response in the visible light region. We also show that DNA nanostructures, on which a HRP-mimicking DNAzyme acts as the catalyst, can direct the site-selective growth of conductive polymer nanomaterials with template configuration-dependent doping behaviors. We demonstrate that DNA origami nanostructures can act as an anticancer-drug carrier, loading drug through intercalation, and can effectively circumvent the drug resistance of cultured cancer cells. Finally, we show a label-free strategy for probing the location and stability of DNA origami nanocarriers in cellular environments by docking turn-off fluorescence dyes in DNA double helices. These functionalizations require further improvement and expansion for realistic applications. We discuss the future opportunities and challenges of DNA based assemblies. We expect that DNA nanostructures as engineering materials will stimulate the development of multidisciplinary and interdisciplinary research.

Wireframe and tensegrity DNA nanostructures

CONSPECTUS: Not only can triangulated wireframe network and tensegrity design be found in architecture, but it is also essential for the stability and organization of biological matter. Whether the scaffolding material is metal as in Buckminster Fuller's geodesic domes and Kenneth Snelson's floating compression sculptures or proteins like actin or spectrin making up the cytoskeleton of biological cells, wireframe and tensegrity construction can provide great stability while minimizing the material required. Given the mechanical properties of single- and double-stranded DNA, it is not surprising to find many variants of wireframe and tensegrity constructions in the emerging field of DNA nanotechnology, in which structures of almost arbitrary shape can be built with nanometer precision. The success of DNA self-assembly relies on the well-controlled hybridization of complementary DNA strands. Consequently, understanding the fundamental physical properties of these molecules is essential. Many experiments have shown that double-stranded DNA (in its most commonly occurring helical form, the B-form) behaves in a first approximation like a relatively stiff cylindrical beam with a persistence length of many times the length of its building blocks, the base pairs. However, it is harder to assign a persistence length to single-stranded DNA. Here, normally the Kuhn length is given, a measure that describes the length of individual rigid segments in a freely jointed chain. This length is on the order of a few nucleotides. Two immediate and important consequences arise from this high flexibility: single-stranded DNA is almost always present in a coiled conformation, and it behaves, just like all flexible polymers in solution, as an entropic spring. In this Account, we review the relation between the mechanical properties of DNA and design considerations for wireframe and tensegrity structures built from DNA. We illustrate various aspects of the successful evolution of DNA nanotechnology starting with the construction of four-way junctions and then allude to simple geometric objects such as the wireframe cube presented by Nadrian Seeman along with a variety of triangulated wireframe constructions. We examine DNA tensegrity triangles that self-assemble into crystals with sizes of several hundred micrometers as well as prestressed DNA origami tensegrity architecture, which uses single-stranded DNA with its entropic spring behavior as tension bearing components to organize stiff multihelix bundles in three dimensions. Finally, we discuss emerging applications of the aforementioned design principles in diverse fields such as diagnostics, drug delivery, or crystallography. Despite great advances in related research fields like protein and RNA engineering, DNA self-assembly is currently the most accessible technique to organize matter on the nanoscale, and we expect many more exciting applications to emerge.

Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT

DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons. We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 megadaltons), a triangular prism (30 megadaltons), a cube (40 megadaltons), a pentagonal prism (50 megadaltons), and a hexagonal prism (60 megadaltons) with edge widths of 100 nanometers. The structures were visualized by means of transmission electron microscopy and three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

DNA nanocages swallow gold nanoparticles (AuNPs) to form AuNP@DNA cage core-shell structures

DNA offers excellent programming properties to nanomaterials syntheses. Host-guest interaction between DNA nanostructures and inorganic nanoparticles (NPs) is of particular interest because the resulting complexes would possess both programming properties intrinsic to DNA and physical properties associated with inorganic NPs, such as plasmonic and magnetic features. Here, we report a class of core-shell complexes (AuNP@DNA cages): hard gold NPs (AuNPs) are encapsulated in geometrically well-defined soft DNA nanocages. The AuNP guest can be further controllably released from the host (DNA nanocages), pointing to potential applications in surface engineering of inorganic NPs and cargo delivery of DNA nanocages.

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

Design space for complex DNA structures

Nucleic acids have emerged as effective materials for assembling complex nanoscale structures. To tailor the structures to function optimally for particular applications, a broad structural design space is desired. Despite the many discrete and extended structures demonstrated in the past few decades, the design space remains to be fully explored. In particular, the complex finite-sized structures produced to date have been typically based on a small number of structural motifs. Here, we perform a comprehensive study of the design space for complex DNA structures, using more than 30 distinct motifs derived from single-stranded tiles. These motifs self-assemble to form structures with diverse strand weaving patterns and specific geometric properties, such as curvature and twist. We performed a systematic study to control and characterize the curvature of the structures, and constructed a flat structure with a corrugated strand pattern. The work here reveals the broadness of the design space for complex DNA nanostructures.

Temperature-controlled encapsulation and release of an active enzyme in the cavity of a self-assembled DNA nanocage

We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.

Coarse-graining DNA for simulations of DNA nanotechnology

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells

RNA nanotechnology is a term that refers to the design, fabrication and use of nanoparticles that are mainly composed of RNAs via bottom-up self-assembly. The packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor has been developed into a nanodelivery platform. This protocol describes the synthesis, assembly and functionalization of pRNA nanoparticles on the basis of three 'toolkits' derived from pRNA structural features: interlocking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions and an RNA three-way junction for branch extension. siRNAs, ribozymes, aptamers, chemical ligands, fluorophores and other functionalities can also be fused to the pRNA before the assembly of the nanoparticles, so as to ensure the production of homogeneous nanoparticles and the retention of appropriate folding and function of the incorporated modules. The resulting self-assembled multivalent pRNA nanoparticles are thermodynamically and chemically stable, and they remain intact at ultralow concentrations. Gene-silencing effects are progressively enhanced with increasing numbers of siRNAs in each pRNA nanoparticle. Systemic injection of the pRNA nanoparticles into xenograft-bearing mice has revealed strong binding to tumors without accumulation in vital organs or tissues. The pRNA-based nanodelivery scaffold paves a new way for nanotechnological application of pRNA-based nanoparticles for disease detection and treatment. The time required for completing one round of this protocol is 3-4 weeks when including in vitro functional assays, or 2-3 months when including in vivo studies.

DNA-based self-assembly for functional nanomaterials

The unprecedented development of DNA nanotechnology has caused DNA self-assembly to attract close attention in many disciplines. In this research news article, the employment of DNA self-assembly in the fields of materials science and nanotechnology is described. DNA self-assembly can be used to prepare bulk-scale hydrogels and 3D macroscopic crystals with nanoscale internal structures, to induce the crystallization of nanoparticles, to template the fabrication of organic conductive nanomaterials, and to act as drug delivery vehicles for therapeutic agents. The properties and functions are fully tunable because of the designability and specificity of DNA assembly. Moreover, because of the intrinsic dynamics, DNA self-assembly can act as a program switch and can efficiently control stimuli responsiveness. We highlight the power of DNA self-assembly in the preparation and function regulation of materials, aiming to motivate future multidisciplinary and interdisciplinary research. Finally, we describe some of the challenges currently faced by DNA assembly that may affect the functional evolution of such materials, and we provide our insights into the future directions of several DNA self-assembly-based nanomaterials.

Functional DNA nanostructures for photonic and biomedical applications

DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical flexibility, and biocompatibility. They have been used to organize a variety of nanoscale elements for specific functions, resulting in unprecedented improvements in the field of nanophotonics and nanomedical research. In this review, the discussion focuses on the employment of DNA nanostructures for the precise organization of noble metal nanoparticles to build interesting plasmonic nanoarchitectures, for the fabrication of visualized sensors and for targeted drug delivery. The effects offered by DNA nanostructures are highlighted in the areas of nanoantennas, collective plasmonic behaviors, single-molecule analysis, and cancer-cell targeting or killing. Finally, the challenges in the field of DNA nanotechnology for realistic application are discussed and insights for future directions are provided.

Computing phase diagrams for a quasicrystal-forming patchy-particle system

We introduce an approach to computing the free energy of quasicrystals, which we use to calculate phase diagrams for systems of two-dimensional patchy particles with five regularly arranged patches that have previously been shown to form dodecagonal quasicrystals. We find that the quasicrystal is a thermodynamically stable phase for a wide range of conditions and remains a robust feature of the system as the potential's parameters are varied. We also demonstrate that the quasicrystal is entropically stabilized over its crystalline approximants.

The braid index of complicated DNA polyhedral links

The goal of this paper is to determine the braid index of two types of complicated DNA polyhedral links introduced by chemists and biologists in recent years. We shall study it in a more broad context and actually consider so-called Jaeger's links (more general Traldi's links) which contain, as special cases, both four types of simple polyhedral links whose braid indexes have been determined and the above two types of complicated DNA polyhedral links. Denote by and the braid index and crossing number of an oriented link , respectively. Roughly speaking, in this paper, we prove that for any link in a family including Jaeger's links and contained in Traldi's links, which is obtained by combining the MFW inequality and an Ohyama's result on upper bound of the braid index. Our result may be used to to characterize and analyze the structure and complexity of DNA polyhedra and entanglement in biopolymers.

A DNA nanostructure platform for directed assembly of synthetic vaccines

Safe and effective vaccines offer the best intervention for disease control. One strategy to maximize vaccine immunogenicity without compromising safety is to rationally design molecular complexes that mimic the natural structure of immunogenic microbes but without the disease-causing components. Here we use highly programmable DNA nanostructures as platforms to assemble a model antigen and CpG adjuvants together into nanoscale complexes with precise control of the valency and spatial arrangement of each element. Our results from immunized mice show that compared to a mixture of antigen and CpG molecules, the assembled antigen-adjuvant-DNA complexes induce strong and long-lasting antibody responses against the antigen without stimulating a reaction to the DNA nanostructure itself. This result demonstrates the potential of DNA nanostructures to serve as general platforms for the rational design and construction of a variety of vaccines.

DNA polyhedra with T-linkage

This paper reports a strategy for DNA self-assembly. Cross-over-based DNA nanomotifs are held together by T-junctions instead of commonly used sticky-end cohesion. We have demonstrated this strategy by assembling a DNA tetrahedron, an octahedron, and an icosahedron. The resulting DNA polyhedra contain out-pointing, short DNA hairpin spikes. These hairpins are well-structured relative to the polyhedra core and provide potential locations for introduction of functional chemicals such as proteins and gold nanoparticles. The T-linked DNA polyhedra have been characterized by polyacrylamide gel electrophoresis, atomic force microscopy, and dynamic light scattering.

Biological stimuli and biomolecules in the assembly and manipulation of nanoscale polymeric particles

Living systems are replete with complex, stimuli-responsive nanoscale materials and molecular self-assemblies. There is an ever increasing and intense interest within the chemical sciences to understand, mimic and interface with these biological systems utilizing synthetic and/or semi-synthetic tools. Our aim in this review is to give perspective on this emerging field of research by highlighting examples of polymeric nanoparticles and micelles that are prepared utilizing biopolymers together with synthetic polymers for the purpose of developing nanomaterials capable of interacting and responding to biologically relevant stimuli. It is expected that with the merging of evolved biological molecules with synthetic materials, will come the ability to prepare complex, functional devices. A variety of applications will become accessible including self-healing materials, self-replicating systems, biodiagnostic tools, drug targeting materials and autonomous, adaptive sensors. Most importantly, the success of this type of strategy will impact how biomolecules are stabilized and incorporated into synthetic devices and at the same time, will influence how synthetic materials are utilized within biomedical applications.

A new Euler's formula for DNA polyhedra

DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components , of crossings , and of Seifert circles are related by a simple and elegant formula: . This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler's formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus.

Nucleic acid-based nanoengineering: novel structures for biomedical applications

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability

The free solution electrophoretic mobilities and thermal stabilities of hairpins formed by two complementary 26-nucleotide oligomers have been measured by capillary electrophoresis. The oligomers are predicted to form molecular beacon-like hairpins with 5 bp stems and 16 nucleotides in the loop. One hairpin, called hairpin2 (hp2), migrates with a relatively fast free solution mobility and exhibits melting temperatures that are reasonably well predicted by the popular structure-prediction program Mfold. Its complement, called hairpin1 (hp1), migrates with a slower free solution mobility and forms a stable hairpin only in solutions containing ≥200 mM Na(+). The melting temperatures observed for hp1 are ~18 °C lower than those observed for hp2 and ~20 °C lower than those predicted by Mfold. The greater thermal stability of hp2 is due to the presence of tandem GA residues on opposite sides of the loop. If the corresponding TC residues in the hp1 loop are replaced by tandem GA residues, the melting temperatures of the modified hairpin are close to those observed for hp2. Eliminating the tandem GA residues in the hp2 loop significantly decreases the thermal stability of hp2. If the loops are replaced by a loop of 16 thymine residues, the free solution mobilities and thermal stabilities of the T-loop hairpin are equal to those observed for hp1. Hence, the loop of hp1 appears to be relatively unstructured, with few base-base stacking interactions. Interactions between tandem GA residues on opposite sides of the hp2 loop appear to compact the loop and increase hairpin stability.