Engineering Inorganic Materials with DNA Nanostructures

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.

Protein-Assisted Large-Scale Assembly and Differential Patterning of DNA Origami Lattices

Nanofabrication has experienced a big boost with the invention of DNA origami, enabling the production and assembly of complex nanoscale structures that may be able to unlock fully new functionalities in biology and beyond. The remarkable precision with which these structures can be designed and produced is, however, not yet matched by their assembly dynamics, which can be extremely slow, particularly when attached to biological templates, such as membranes. Here, the rapid and controlled formation of DNA origami lattices on the scale of hundreds of micrometers in as little as 30 minutes is demonstrated, utilizing active patterning by the E.coli Min protein system, thereby yielding a remarkable improvement over conventional passive diffusion-based assembly methods. Various patterns, including spots, inverse spots, mazes, and meshes can be produced at different scales, tailored through the shape and density of the assembled structures. The differential positioning accomplished by Min-induced diffusiophoresis even allows the introduction of "pseudo-colors", i.e., complex core-shell patterns, by simultaneously patterning different DNA origami species. Beyond the targeted functionalization of biological surfaces, this approach may also be promising for applications in plasmonics, catalysis, and molecular sensing.

Ion beam processing of DNA origami nanostructures

DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.

Multimodal Golden DNA Superstructures (GDSs) for Highly Efficient Photothermal Immunotherapy

DNA-templated metallization has emerged as an efficient strategy for creating nanoscale-metal DNA hybrid structures with a desirable conformation and function. Despite the potential of DNA-metal hybrids, their use as combinatory therapeutic agents has rarely been examined. Herein, we present a simple approach for fabricating a multipurpose DNA superstructure that serves as an efficient photoimmunotherapy agent. Specifically, we adsorb and locally concentrate Au ions onto DNA superstructures through induced local reduction, resulting in the formation of Au nanoclusters. The mechanical and optical properties of these metallic nanoclusters can be rationally controlled by their conformations and metal ions. The resulting golden DNA superstructures (GDSs) exhibit significant photothermal effects that induce cancer cell apoptosis. When sequence-specific immunostimulatory effects of DNA are combined, GDSs provide a synergistic effect to eradicate cancer and inhibit metastasis, demonstrating potential as a combinatory therapeutic agent for tumor treatment. Altogether, the DNA superstructure-templated metal casting system offers promising materials for future biomedical applications.

Nanotechnology-based Drug Delivery for Alzheimer's and Parkinson's Diseases

The delivery of drugs to the brain is quite challenging in the treatment of the central nervous system (CNS) diseases due to the blood-brain barrier and the blood-cerebrospinal fluid barrier. However, significant developments in nanomaterials employed by nanoparticle drug-delivery systems have substantial potential to cross or bypass these barriers leading to enhanced therapeutic efficacies. Advances in nanoplatform, nanosystems based on lipids, polymers and inorganic materials have been extensively studied and applied in treating Alzheimer's and Parkinson's diseases. In this review, various types of brain drug delivery nanocarriers are classified, summarized, and their potential as drug delivery systems in Alzheimer's and Parkinson's diseases is discussed. Finally, challenges facing the clinical translation of nanoparticles from bench to bedside are highlighted.

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

Assembly and optically triggered disassembly of lipid-DNA origami fibers

The co-assembly of lipids and other compounds has recently gained increasing interest. Here, we report the formation of stimuli-responsive lipid-DNA origami fibers through the electrostatic co-assembly of cationic lipids and 6-helix bundle (6HB) DNA origami. The photosensitive lipid degrades when exposed to UV-A light, which allows a photoinduced, controlled release of the 6HBs from the fibers. The presented complexation strategy may find uses in developing responsive nanomaterials e.g. for therapeutics.

Importance of isothermal titration calorimetry for the detection of the direct binding of metal ions to mismatched base pairs in duplex DNA

Metal ion-nucleic acid interactions contribute substantially to the structure and biological activity of nucleic acids and have a wide range of potential applications in nanotechnology. In this study, we examined the interactions between metal ions and mismatched base pairs in duplex DNA to reveal the underlying molecular mechanism. UV melting analyses showed that the melting temperature (Tm) of a 21-base pair duplex DNA with each of the C-A, C-C and C-T mismatched base pairs increased upon the addition of Ag+. However, isothermal titration calorimetry (ITC) demonstrated that Ag+ only bound to the C-C mismatched base pair of the duplex DNA to form C-Ag-C bonds, without binding to the C-A and C-T mismatches. These results showed that Tm increased even when metal ions did not bind to the mismatched base pairs of the duplex DNA. Although the increase in Tm upon the addition of the metal ions is often used to detect metal ion binding to mismatched base pairs of duplex DNA, these results indicated that UV melting analyses are unable to detect the direct binding of metal ions to the mismatched base pairs. Because ITC analyses directly detect the heat derived from metal ion binding to mismatched base pairs of duplex DNA, we concluded that this may be an effective detection approach.

Cation-dependent assembly of hexagonal DNA origami lattices on SiO2 surfaces

DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.

DNA Assembly of Plasmonic Nanostructures Enables In Vivo SERS-Based MicroRNA Detection and Tumor Photoacoustic Imaging

Controllable self-assembly of the DNA-linked gold nanoparticle (AuNP) architecture for in vivo biomedical applications remains a key challenge. Here, we describe the use of the programmed DNA tetrahedral structure to control the assembly of three different types of AuNPs (∼20, 10, and 5 nm) by organizing them into defined positioning and arrangement. A DNA-assembled "core-satellite" architecture is built by DNA sequencing where satellite AuNPs (10 and 5 nm) surround a central core AuNP (20 nm). The density and arrangement of the AuNP satellites around the core AuNP were controlled by tuning the size and amount of the DNA tetrahedron functionalized on the core AuNPs, resulting in strong electromagnetic field enhancement derived from hybridized plasmonic coupling effects. By conjugating with the Raman molecule, strong surface-enhanced Raman scattering photoacoustic imaging signals could be generated, which were able to image microRNA-21 and tumor tissues in vivo. These results provided an efficient strategy to build precision plasmonic superstructures in plasmonic-based bioanalysis and imaging.

Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures

DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.

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.

Raman enhancement in bowtie-shaped aperture-particle hybrid nanostructures fabricated with DNA-assisted lithography

We report on efficient surface-enhanced Raman spectroscopy (SERS) supporting substrates, which are based on deoxyribonucleic acid (DNA)-assisted lithography (DALI) and a layered configuration of materials. In detail, we used nanoscopic DNA origami bowtie templates to form hybrid nanostructures consisting of aligned silver bowtie-shaped particles and apertures of similar shape in a silver film. We hypothesized that this particular geometry could facilitate a four-fold advantage in Raman enhancement compared to common particle-based SERS substrates, and further, we verified these hypotheses experimentally and by finite difference time domain simulations. In summary, our DALI-fabricated hybrid structures suppress the background emission, allow emission predominantly from the areas of high field enhancement, and support additional resonances associated with the nanoscopic apertures. Finally, these nanoapertures also enhance the fields associated with the resonances of the underlying bowtie particles. The versatility and parallel nature of our DNA origami-based nanofabrication scheme and all of the above-mentioned features of the hybrid structures therefore make our optically resonant substrates attractive for various SERS-based applications.

Specific binding of Hg2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA

Metal ion-nucleic acid interactions contribute significantly to nucleic acid structure and biological activity and have potential applications in nanotechnology. Hg²⁺ specifically binds to the natural T-T mismatched base pair in duplex DNA to form a T-Hg-T base pair. Metal ions may enhance DNA damage induced by DNA-damaging agents, such as oxidative agents. The interactions between metal ions and damaged DNAs, such as mismatched oxidized bases, have not been well characterized. Here, we examined the possibility of Hg²⁺ binding to an asymmetric mismatched base pair involving thymine and 5-hydroxyuracil (OHdU), an oxidized base produced by the oxidative deamination of cytosine. UV melting analyses showed that only the melting temperature of the single T-OHdU mismatched duplex DNA increased upon Hg²⁺ addition. CD spectra indicated no significant change in the higher-order structure of the single T-OHdU mismatched duplex DNA upon Hg²⁺ addition. X-ray crystallographic structure with two consecutive T-OHdU mismatched base pairs and isothermal titration calorimetric analyses with the single T-OHdU mismatched base pair showed that Hg²⁺ specifically binds to the N3 positions of both T and OHdU in T-OHdU at 1:1 molar ratio, with a 5×10⁵ M^-1 binding constant of to form the T-Hg-OHdU base pair. The Hg²⁺-bound structure and the Hg²⁺-binding affinity for T-OHdU was similar to those for T-T. This study on T-Hg-OHdU metal-mediated base pair could aid in studying the molecular mechanism of metal ion-mediated DNA damage and their potential applications in nanotechnology.

Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks

The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.

DNA Mold-Based Fabrication of Palladium Nanostructures

DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20-35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.

Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles

Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (R_CT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.

Micron-Scale Fabrication of Ultrathin Amorphous Copper Nanosheets Templated by DNA Scaffolds

Two-dimensional (2D) amorphous materials could outperform their crystalline counterparts toward various applications because they have more defects and reactive sites and thus could exhibit a unique surface chemical state and provide an advanced electron/ion transport path. Nevertheless, it is challenging to fabricate ultrathin and large-sized 2D amorphous metallic nanomaterials in a mild and controllable manner due to the strong metallic bonds between metal atoms. Here, we reported a simple yet fast (10 min) DNA nanosheet (DNS)-templated method to synthesize micron-scale amorphous copper nanosheets (CuNSs) with a thickness of 1.9 ± 0.4 nm in aqueous solution at room temperature. We demonstrated the amorphous feature of the DNS/CuNSs by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Interestingly, we found that they could transform to crystalline forms under continuous electron beam irradiation. Of note, the amorphous DNS/CuNSs exhibited much stronger photoemission (∼62-fold) and photostability than dsDNA-templated discrete Cu nanoclusters due to the elevation of both the conduction band (CB) and valence band (VB). Such ultrathin amorphous DNS/CuNSs hold great potential for practical applications in biosensing, nanodevices, and photodevices.

Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies

Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.

Harnessing DNA Nanotechnology and Chemistry for Applications in Photonics and Electronics

Many photonic and electronic devices rely on nanotechnology and nanofabrication, but DNA-based approaches have yet to make a significant commercial impact in these fields even though DNA molecules are now well-established as versatile building blocks for nanostructures. As we describe here, DNA molecules can be chemically modified with a wide variety of functional groups enabling nanocargoes to be attached at precisely determined locations. DNA nanostructures can also be used as templates for the growth of inorganic structures. Together, these factors enable the use of DNA nanotechnology for the construction of many novel devices and systems. In this topical review, we discuss four case studies of potential applications in photonics and electronics: carbon nanotube transistors, devices for quantum computing, artificial electromagnetic materials, and enzymatic fuel cells. We conclude by speculating about the barriers to the exploitation of these technologies in real-world settings.

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.

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.

Block Copolymer Micellization of DNA Origami Promotes Solubility in Organic Solvents

The DNA origami technique allows the precise synthesis of complex, biocompatible nanomaterials containing small molecules, biomolecules, and inorganic nanoparticles. The negatively charged phosphates in the backbone make DNA highly water-soluble and require salts to shield its electrostatic repulsion. DNA origamis are therefore not soluble in most organic solvents. While this is not problematic for applications in biochemistry, biophysics, or nanomedicine, other potential applications, processes, and substrates are incompatible with saline solutions, which include the synthesis of many nanomaterials, and reactions in templated synthesis, the operation of nanoelectronic devices, or semiconductor fabrication. To overcome this limitation, we coated DNA origami with amphiphilic poly(ethylene glycol) polylysine block copolymers and transferred them into various organic solvents including chloroform, dichloromethane, acetone, or 1-propanol. Our approach maintains the shape of the nanostructures and protects functional elements bound to the structure, such as fluorophores, gold nanoparticles, or proteins. The DNA origami polyplex micellization (DOPM) strategy hence enables solubilization or a phase transfer of complex structures into various organic solvents, which significantly expands the use of DNA origami for a range of potential applications and technical processes.

Optically Responsive Protein Coating of DNA Origami for Triggered Antigen Targeting

DNA nanostructures have emerged as modular building blocks in several research fields including biomedicine and nanofabrication. Their proneness to degradation in various environments has led to the development of a variety of nature-inspired protection strategies. Coating of DNA origami nanostructures with proteins can circumvent degradation and alter their properties. Here, we have used a single-chain variable antibody fragment and serum albumin to construct positively charged and stimuli-responsive protein-dendron conjugates, which were complexed with DNA origami through electrostatic interactions. Using a stepwise assembly approach, the coated nanostructures were studied for their interaction with the corresponding antigen in fluorescence-based immunoassays. The results suggest that the antibody-antigen interaction can be disturbed by the addition of the bulky serum albumin. However, this effect is fully reversible upon irradiation of the structures with an optical stimulus. This leads to a selective dissociation of the serum albumin from the nanostructure due to cleavage of a photolabile group integrated in the dendron structure, exposing the antibody fragment and enabling triggered binding to the antigen, demonstrating that serum albumin can be considered as an externally controlled "camouflaging" agent. The presented stimuli-responsive complexation approach is highly versatile regarding the choice of protein components and could, therefore, find use in DNA origami protection, targeting, and delivery as well as their spatiotemporal control.

Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography

Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.

From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

ConspectusThe concept of colloids encompasses a wide range of isotropic and anisotropic particles with diverse sizes, shapes, and functions from synthetic nanoparticles, nanorods, and nanosheets to functional biological units. They are addressed in materials science for various functions, while they are ubiquitous in the biological world for multiple functions. A large variety of synthetic colloids have been researched due to their scientific and technological importance; still they characteristically suffer from finite size distributions, imperfect shapes and interactions, and not fully engineered functions. This contrasts with biological colloids that offer precision in their size, shape, and functionality. Materials science has searched for inspiration from the biological world to allow structural control by self-assembly and hierarchy and to identify novel routes for combinations of functions in bio-inspiration.Herein, we first discuss different approaches for highly defined structural control of technically relevant synthetic colloids based on guided assemblies of biological motifs. First, we describe how polydisperse nanoparticles can be assembled within hollow protein cages to allow well-defined assemblies and hierarchical packings. Another approach relies on DNA nanotechnology-based assemblies, where engineered DNA structures allow programmed assembly. Then we will discuss synthetic colloids that have either particularly narrow size dispersity or even atomically precise structures for new assemblies and potential functions. Such colloids can have well-defined packings for membranes allowing high modulus. They can be switchable using light-responsive moieties, and they can initiate packing of larger assemblies of different geometrical shapes. The emphasis is on atomically defined nanoclusters that allow well-defined assemblies by supramolecular interactions, such as directional hydrogen bonding. Finally, we will discuss stimulus-responsive colloids for new functions, even toward complex responsive functions inspired by life. Therein, stimulus-responsive materials inspired by biological learning could allow the next generation of such materials. Classical conditioning is among the simplest biological learning concepts, requiring two stimuli and triggerable memory. Therein we use thermoresponsive hydrogels with plasmonic gold nanoparticles and a spiropyran photoacid as a model. Heating is the unconditioned stimulus leading to melting of the thermoresponsive gel, whereas light (at a specified wavelength) originally leads to reduced pH without plasmonic or structural changes because of steric gel stabilization. Under heat-induced gel melting, light results in pH-decrease and chain-like aggregation of the gold nanoparticles, allowing a new plasmonic response. Thus, simultaneous heating and light irradiation allow conditioning for a newly derived stimulus, where the logic diagram is analogous to Pavlovian conditioning. The shown assemblies demonstrate the different functionalities achievable using colloids when the sizes and the dispersity are controlled.

Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond

Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective.

Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings

The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg²⁺ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg²⁺ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.