The Art of Designing DNA Nanostructures with CAD Software

Structural stability of DNA origami nanostructures in organic solvents

DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25-40% DMF or DMSO and up to 70-90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.

Liposome-based hybrid drug delivery systems with DNA nanostructures and metallic nanoparticles

INTRODUCTION

This review discusses novel hybrid assemblies that are based on liposomal formulations. The focus is on the hybrid constructs that are formed through the integration of liposomes/vesicles with other nano-objects such as nucleic acid nanostructures and metallic nanoparticles. The aim is to introduce some of the recent, specific examples that bridge different technologies and thus may form a new platform for advanced drug delivery applications.

AREAS COVERED

We present selected examples of liposomal formulations combined with complex nanostructures either based on biomolecules like DNA origami or on metallic materials - metal/metal oxide/magnetic particles and metallic nanostructures, such as metal organic frameworks - together with their applications in drug delivery and beyond.

EXPERT OPINION

Merging the above-mentioned techniques could lead to development of drug delivery vehicles with the most desirable properties; multifunctionality, biocompatibility, high drug loading efficiency/accuracy/capacity, and stimuli-responsiveness. In the near future, we believe that especially the strategies combining dynamic, triggerable and programmable DNA nanostructures and liposomes could be used to create artificial liposome clusters for multiple applications such as examining protein-mediated interactions between lipid bilayers and channeling materials between liposomes for enhanced pharmacokinetic properties in drug delivery.

DNA nanostructure decoration: a how-to tutorial

DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.

Molecularly or atomically precise nanostructures for bio-applications: how far have we come?

A huge variety of nanostructures are promising for biomedical applications, but only a few have been practically applied. Among the various reasons, the limited structural preciseness is a critical one, as it increases the difficulty in product quality control, accurate dosing, and ensuring the repeatability of material performance. Constructing nanoparticles with molecule-like preciseness is becoming a new research field. In this review, we focus on the artificial nanomaterials that can currently be molecularly or atomically precise, including DNA nanostructures, some metallic nanoclusters, dendrimer nanoparticles and carbon nanostructures, describing their syntheses, bio-applications and limitations, in view of up-to-date studies. A perspective on their potential for clinical translation is also given. This review is expected to provide a particular rationale for the future design of nanomedicines.

Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists

Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.

Reconfigurable pH-Responsive DNA Origami Lattices

DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.

A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures

DNA self-assembly, and in particular DNA origami, has evolved into a reliable workhorse for organizing organic and inorganic materials with nanometer precision and with exactly controlled stoichiometry. To ensure the intended performance of a given DNA structure, it is beneficial to determine its folding temperature, which in turn yields the best possible assembly of all DNA strands. Here, we show that temperature-controlled sample holders and standard fluorescence spectrometers or dynamic light-scattering setups in a static light-scattering configuration allow for monitoring the assembly progress in real time. With this robust label-free technique, we determine the folding and melting temperatures of a set of different DNA origami structures without the need for more tedious protocols. In addition, we use the method to follow digestion of DNA structures in the presence of DNase I and find strikingly different resistances toward enzymatic degradation depending on the structural design of the DNA object.

Dynamics of DNA Origami Lattices

Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.

Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView

Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.

Gentle Patterning Approaches toward Compatibility with Bio-Organic Materials and Their Environmental Aspects

Advances in material science, bioelectronic, and implantable medicine combined with recent requests for eco-friendly materials and technologies inevitably formulate new challenges for nano- and micropatterning techniques. Overall, the importance of creating micro- and nanostructures is motivated by a large manifold of fundamental and applied properties accessible only at the nanoscale. Lithography is a crucial family of fabrication methods to create prototypes and produce devices on an industrial scale. The pure trend in the miniaturization of critical electronic semiconducting components has been recently enhanced by implementing bio-organic systems in electronics. So far, significant efforts have been made to find novel lithographic approaches and develop old ones to reach compatibility with delicate bio-organic systems and minimize the impact on the environment. Herein, such delicate materials and sophisticated patterning techniques are briefly reviewed.

Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design

The building blocks of life - nucleotides, amino acids and saccharides - give rise to a large variety of components and make up the hierarchical structures found in Nature. Driven by chirality and non-covalent interactions, helical and highly organised structures are formed and the way in which they fold correlates with specific recognition and hence function. A great amount of effort is being put into mimicking these highly specialised biosystems as biomaterials for biomedical applications, ranging from drug discovery to regenerative medicine. However, as well as lacking the complexity found in Nature, their bio-activity is sometimes low and hierarchical ordering is missing or underdeveloped. Moreover, small differences in folding in natural biomolecules (e.g., caused by mutations) can have a catastrophic effect on the function they perform. In order to develop biomaterials that are more efficient in interacting with biomolecules, such as proteins, DNA and cells, we speculate that incorporating order and handedness into biomaterial design is necessary. In this review, we first focus on order and handedness found in Nature in peptides, nucleotides and saccharides, followed by selected examples of synthetic biomimetic systems based on these components that aim to capture some aspects of these ordered features. Computational simulations are very helpful in predicting atomic orientation and molecular organisation, and can provide invaluable information on how to further improve on biomaterial designs. In the last part of the review, a critical perspective is provided along with considerations that can be implemented in next-generation biomaterial designs.