Nanoscale Growth and Patterning of Inorganic Oxides Using DNA Nanostructure Templates

DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics

Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.

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. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.

Site-directed placement of three-dimensional DNA origami

The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.

Molecular Lithography on Silicon Wafers Guided by Porous, Extended Arrays of Small DNA Tiles

Tile-based DNA self-assembly is a cost-effective fabrication method for large-scale nanopatterns. Herein, we report a protocol to directly assemble DNA 2D arrays on silicon wafers and then use the DNA nanostructures as molds to fabricate the corresponding nanostructures on the silicon wafers by hydrogen fluoride (HF) etching. Similar HF etching has been used with robust large DNA origami structures as templates. This work demonstrates that DNA nanostructures assembled from small tiles are sufficiently stable for this process. The resulting feature size (∼8.6 nm) approaches the sizes of e-beam lithography. While the reported method is parallel and inexpensive, e-beam lithography is a serial method and is expensive. We expect that this method will be very useful for preparing fine nanopatterns in large areas.

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.

Recent development in antiviral surfaces: Impact of topography and environmental conditions

The transmission of viruses is largely dependent on contact with contaminated virus-laden communal surfaces. While frequent surface disinfection and antiviral coating techniques are put forth by researchers as a plan of action to tackle transmission in dire situations like the Covid-19 pandemic caused by SARS-CoV-2 virus, these procedures are often laborious, time-consuming, cost-intensive, and toxic. Hence, surface topography-mediated antiviral surfaces have been gaining more attention in recent times. Although bioinspired hydrophobic antibacterial nanopatterned surfaces mimicking the natural sources is a very prevalent and successful strategy, the antiviral prospect of these surfaces is yet to be explored. Few recent studies have explored the potential of nanopatterned antiviral surfaces. In this review, we highlighted surface properties that have an impact on virus attachment and persistence, particularly focusing and emphasizing on the prospect of the nanotextured surface with enhanced properties to be used as antiviral surface. In addition, recent developments in surface nanopatterning techniques depending on the nano-scaled dimensions have been discussed. The impacts of environments and surface topology on virus inactivation have also been reviewed.

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.

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.

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.

Engineering DNA-Guided Hydroxyapatite Bulk Materials with High Stiffness and Outstanding Antimicrobial Ability for Dental Inlay Applications

Programmable base pair interactions at the nanoscale make DNA an attractive scaffold for forming hydroxyapatite (HAP) nanostructures. However, engineering macroscale HAP mineralization guided by DNA molecules remains challenging. To overcome this issue, a facile strategy is developed for the fabrication of ultrastiff DNA-HAP bulk composites. The electrostatic complexation of DNA and a surfactant with a quaternary ammonium salt group enables the formation of long-range ordered scaffolds using electrospinning. The growth of 1D and 2D HAP minerals is thus realized by this DNA template at a macroscale. Remarkably, the as-prepared DNA-HAP composites exhibit an ultrahigh Young's modulus of ≈25 GPa, which is comparable to natural HAP and superior to most artificial mineralized composites. Furthermore, a new type of dental inlay with outstanding antibacterial properties is developed using the stiff DNA-HAP. The encapsulated quaternary ammonium group within the dense HAP endows the composite with long-lasting and local antibacterial activity. Therefore, this new type of super-stiff biomaterial holds great potential for oral prosthetic applications.

Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays

While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.

Engineering Inorganic Materials with DNA Nanostructures

Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.

Programmable and Site-Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica

DNA origami has been widely used as a modular platform for condensation of functional molecules to assemble optical, electronic, and biological components. However, the heterogeneous condensation with greater diversities in chemical composition templated with DNA origami is still challenging. Herein, a programmable deposition method is developed to precisely condense silver-silica nanohybrids on DNA origami templates. First, the site-specific metallization of Ag is achieved by thiol group-initiated silver reduction at the designed areas of DNA origami. Next, cysteamine is used to selectively modify the condensed Ag surface with positively charged amino groups for creating an electronically different environment for site-specific placement of silica by a modified Stöber method. Using these strategies, customized patterning of both silver and silica on tubular and rectangular DNA origami nanostructures is successfully achieved with nanoscale spatial resolution. These findings will greatly facilitate the development of DNA nanotechnology-based bottom-up nanofabrication.

Scaling Up DNA Origami Lattice Assembly

The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.

Three-dimensional nanolithography guided by DNA modular epitaxy

Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-ultraviolet lithography produce a line pitch down to around 30 nm, which might be further scaled to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50% smaller than state-of-the-art results. We use a DNA modular epitaxy approach to fabricate 3D DNA masks with prescribed structural parameters (geometry, pitch and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm. The nanolithography guided by DNA modular epitaxy achieves a smaller pitch than the projected values for advanced technology nodes in field-effect transistors, and provides a potential complement to the existing lithographic tools for advanced 3D nanomanufacturing.

Biomineralization: An Opportunity and Challenge of Nanoparticle Drug Delivery Systems for Cancer Therapy

Biomineralization is a common process in organisms to produce hard biomaterials by combining inorganic ions with biomacromolecules. Multifunctional nanoplatforms are developed based on the mechanism of biomineralization in many biomedical applications. In the past few years, biomineralization-based nanoparticle drug delivery systems for the cancer treatment have gained a lot of research attention due to the advantages including simple preparation, good biocompatibility, degradability, easy modification, versatility, and targeting. In this review, the research trends of biomineralization-based nanoparticle drug delivery systems and their applications in cancer therapy are summarized. This work aims to promote future researches on cancer therapy based on biomineralization. Rational design of nanoparticle drug delivery systems can overcome the bottleneck in the clinical transformation of nanomaterials. At the same time, biomineralization has also provided new research ideas for cancer treatment, i.e., targeted therapy, which has significantly better performance.

Area-Selective Atomic Layer Deposition of Metal Oxides on DNA Nanostructures and Its Applications

We demonstrate area-selective atomic layer deposition (ALD) of oxides on DNA nanostructures. Area-selective ALD of Al₂O₃, TiO₂, and HfO₂ was successfully achieved on both 2D and 3D DNA nanostructures deposited on a polystyrene (PS) substrate. The resulting DNA-inorganic hybrid structure was used as a hard mask to achieve deep etching of a Si wafer for antireflection applications. ALD is a widely used process in coating and thin film deposition; our work points to a way to pattern oxide materials using DNA templates and to enhance the chemical/physical stability of DNA nanostructures for applications in surface engineering.

Controlling Matter at the Molecular Scale with DNA Circuits

In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.

Precise pitch-scaling of carbon nanotube arrays within three-dimensional DNA nanotrenches

Precise fabrication of semiconducting carbon nanotubes (CNTs) into densely aligned evenly spaced arrays is required for ultrascaled technology nodes. We report the precise scaling of inter-CNT pitch using a supramolecular assembly method called spatially hindered integration of nanotube electronics. Specifically, by using DNA brick crystal-based nanotrenches to align DNA-wrapped CNTs through DNA hybridization, we constructed parallel CNT arrays with a uniform pitch as small as 10.4 nanometers, at an angular deviation <2° and an assembly yield >95%.

Site-Specific Synthesis of Silica Nanostructures on DNA Origami Templates

DNA origami has been widely investigated as a template for the organization of various functional elements, leading to potential applications in many fields such as biosensing, nanoelectronics, and nanophotonics. However, the synthesis of inorganic nonmetallic nanomaterials with predesigned patterns using DNA origami templates has seldom been explored. Here, a novel method is reported to site-specifically synthesize silica nanostructures with designed patterns on DNA origami templates. The molecular dynamic simulation confirms that the positively charged silica precursors have a stronger electrostatic affinity to protruding double-stranded DNA (dsDNA) than DNA origami surfaces. The work describes a novel strategy to fabricate silica nanostructures with nanoscale precision. Moreover, the site-specific silicification of DNA nanoarchitectures expands the scope of customized synthesis of inorganic nonmetallic nanomaterials.

Functionalized DNA nanostructures as scaffolds for guided mineralization

The field of DNA nanotechnology uses synthetic DNA strands as building blocks for designing complex shapes in one-, two- and three-dimensions. Here, we investigate whether DNA nanostructures are feasible platforms for the precise organization of polyaspartic acid (pAsp), a known mineral carrier, with a goal towards biomimetic mineralization for enamel regeneration. We describe the preparation of DNA-pAsp conjugates and their subsequent assembly into ordered nanostructures. Covalent attachment of pAsp to DNA was noted to hinder DNA nanostructure formation past a certain threshold (50% pAsp) when tested on a previously published DNA system. However, a simplified double stranded DNA system (3sDH system) was more robust and efficient in its pAsp incorporation. In addition, the 3sDH system was successful in organizing mineral inducing groups in one dimension at repeating intervals of 28.7 ± 4.0 nm, as determined by atomic force microscopy. Our results demonstrate that DNA nanostructures can be functionalized with pAsp and act as a platform to investigate guided mineralization.

DNA-Based Nanofabrication for Antifouling Applications

This paper reports antifouling properties of nanostructured SiO₂ substrates patterned by DNA lithography. We used DNA triangle nanostructures as templates to produce triangular-shaped trenches ca. 130 nm in size on SiO₂ surfaces. Using B. subtilis as a bacterial model, we found that such nanopatterned surface showed a 75% reduction in bacterial adhesion and 72% reduction in biofilm density at 35% surface coverage of the nanoscale triangular trenches. DNA-based nanofabrication can produce high-resolution designer patterns, but aligning these patterns has been one of the major technical challenges for its applications in nanoelectronics. This work demonstrates the potential of DNA-based nanofabrication in antifouling applications, where surface patterning of micro/nanostructures is required but not their precise alignment.

Solidifying framework nucleic acids with silica

Soft matter can serve as a template to guide the growth of inorganic components with well-controlled structural features. However, the limited design space of conventional organic and biomolecular templates restricts the complexity and accuracy of templated growth. In past decades, the blossoming of structural DNA nanotechnology has provided us with a large reservoir of delicate-framework nucleic acids with design precision down to a single base. Here, we describe a DNA origami silicification (DOS) approach for generating complex silica composite nanomaterials. By utilizing modified silica sol-gel chemistry, pre-hydrolyzed silica precursor clusters can be uniformly coated onto the surface of DNA frameworks; thus, user-defined DNA-silica hybrid materials with ~3-nm precision can be achieved. More importantly, this method is applicable to various 1D, 2D and 3D DNA frameworks that range from 10 to >1,000 nm. Compared to pure DNA scaffolds, a tenfold increase in the Young's modulus (E modulus) of these composites was observed, owing to their soft inner core and solid silica shell. We further demonstrate the use of solidified DNA frameworks to create 3D metal plasmonic devices. This protocol provides a platform for synthesizing inorganic materials with unprecedented complexity and tailored structural properties. The whole protocol takes ~10 d to complete.

DNA-Based Nanofabrication: Pathway to Applications in Surface Engineering

This Concept provides an overview of recent developments of DNA-based nanofabrication and discusses its potential applications in the area of surface engineering. The first part of the paper discusses the strength and limitations of existing DNA-based nanofabrication methods. The second part highlights several examples of surface engineering applications involving nano- and microscale surface textures. It finishes with a discussion of the opportunities and remaining challenges of applying DNA-based nanofabrication in surface engineering applications.

Create Nanoscale Patterns with DNA Origami

Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.

Directed Protein Adsorption Through DNA Origami Masks

The DNA origami technique has made its way into various areas of nanotechnology, materials science, biophysics, and medicine. Among the many applications of DNA origami nanostructures, their use as masks for patterning of organic and inorganic materials by molecular lithography has received great attention. Here, we describe a protocol for the self-assembly of ordered monolayers of DNA origami nanostructures on mica surfaces and the subsequent fabrication of regular protein patterns over large surface areas via directed adsorption through the DNA origami mask. While the geometry of the pattern is determined by the shape of the DNA origami nanostructures, protein coverage inside the holes of the mask can be varied from single proteins to dense monolayers by adjusting the protein concentration and cationic strength of the adsorption buffer.

DNA-Assisted Molecular Lithography

During the past decade, DNA origami has become a popular method to build custom two- (2D) and three-dimensional (3D) DNA nanostructures. These programmable structures could further serve as templates for accurate nanoscale patterning, and therefore they could find uses in various biotechnological applications. However, to transfer the spatial information of DNA origami to metal nanostructures has been limited to either direct nanoparticle-based patterning or chemical growth of metallic seed particles that are attached to the DNA objects. Here, we present an alternative way by combining DNA origami with conventional lithography techniques. With this DNA-assisted lithography (DALI) method, we can create plasmonic, entirely metallic nanostructures in a highly accurate and parallel manner on different substrates. We demonstrate our technique by patterning a transparent substrate with discrete bowtie-shaped nanoparticles, i.e., "nanoantennas" or "optical antennas," with a feature size of approximately 10 nm. Owing to the versatility of DNA origami, this method can be effortlessly generalized to other shapes and sizes.

Atomic force microscopy study of EDTA induced desorption of metal ions immobilized DNA from mica surface

Adsorption of DNA molecules onto substrate, such as mica, is well documented. However, desorption of the immobilized DNA molecules from substrate, which is also an important aspect of DNA behavior on substrate, has not been paid much attention. Here, DNA molecules were first immobilized on mica surface by using divalent metal ions as the bridge agents. Desorption of the immobilized DNA from mica surface was realized via ethylenediamine tetraacetic acid disodium salt (EDTA) treatment. EDTA is a chelating agent; it can remove the bridging metal ions between DNA and mica, which leads to the release of DNA molecules from mica substrate. The divalent metal ions assisted DNA adsorption onto mica surface and the EDTA induced DNA desorption from mica surface were followed by atomic force microscopy (AFM). Randomly dispersed DNA strands and DNA networks are two distinct adsorption morphologies of DNA on mica surface and their desorption processes from mica surface induced by EDTA are also different. Other factors that influence the EDTA-induced DNA desorption, such as type of bridging metal ion and DNA molecule length, have also been systematically studied. Moreover, EDTA treatment has no effect on the integrity of DNA molecule. The EDTA induced desorption of metal ions immobilized DNA from mica surface is simple and effective, which has potential applications in DNA separation and purification, DNA biophysics, and DNA-based nanotechnology.

Dynamics of DNA Origami Lattice Formation at Solid-Liquid Interfaces

The self-organized formation of regular patterns is not only a fascinating topic encountered in a multitude of natural and artificial systems, but also presents a versatile and powerful route toward large-scale nanostructure assembly and materials synthesis. The hierarchical, interface-assisted assembly of DNA origami nanostructures into regular, 2D lattices represents a particularly promising example, as the resulting lattices may exhibit an astonishing degree of order and can be further utilized as masks in molecular lithography. Here, we thus investigate the development of order in such 2D DNA origami lattices assembled on mica surfaces by employing in situ high-speed atomic force microscopy imaging. DNA origami lattice formation is found to resemble thin-film growth in several aspects. In particular, the Na⁺/Mg²⁺ ratio controls DNA origami adsorption, surface diffusion, and desorption, and is thus equivalent in its effects to substrate temperature which controls adatom dynamics in thin-film deposition. Consequently, we observe a pronounced dependence of lattice order on Na⁺ concentration. At low Na⁺ concentrations, lattice formation resembles random deposition and results in unordered monolayers, whereas very high Na⁺ concentrations are accompanied by rapid diffusion and especially DNA origami desorption, which prevent lattice formation. At intermediate Na⁺ concentrations, highly ordered DNA origami lattices are obtained that display an intricate symmetry, stemming from the complex shape of the employed Rothemund triangle. Nevertheless, even under such optimized conditions, the lattices display a considerable number of defects, including grain boundaries, point and line defects, and screw-like dislocations. By monitoring the dynamics of selected lattice defects, we identify mechanisms that limit the obtainable degree of lattice order. Possible routes toward further increasing lattice order by postassembly annealing are discussed.

DNA Origami Nanophotonics and Plasmonics at Interfaces

DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics-especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.

Graphene-Encapsulated DNA Nanostructure: Preservation of Topographic Features at High Temperature and Site-Specific Oxidation of Graphene

This paper reports the effect of graphene encapsulation on the thermal stability of DNA nanostructures and the thermal oxidation of graphene in the presence of DNA nanostructures. Triangular-shaped DNA nanostructures were deposited onto a Si/SiO₂ substrate and covered with single-layer graphene. The apparent height of the DNA nanostructure significantly decreased upon thermal annealing at 250 °C and higher temperatures. The topographical features of the DNA nanostructure, as measured by atomic force microscopy (AFM), disappeared after annealing at 300 °C for 5 h but reappeared after 23 h. In contrast, in the absence of a graphene coating, the topographical features of DNA nanostructure disappeared after heating at 300 °C for 45 min. After heating at 300 °C for 29 h, oxidation produced nanometer-sized holes on graphene, some of which were triangular and spatially overlapped with DNA nanostructures. These results suggest that the inorganic residues produced by the decomposition of DNA nanostructures enhance the oxidation of graphene in a site-specific manner.

Structural stability of DNA origami nanostructures under application-specific conditions

With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis. Since many of those applications rely on structurally intact, well-definedDNA origami shapes, the issue of DNA origami stability under numerous application-relevant environmental conditions has received increasing interest in the past few years. In this mini-review we discuss the structural stability, denaturation, and degradation of DNA origami nanostructures under different conditions relevant to the fields of biophysics and biochemistry, biomedicine, and materials science, and the methods to improve their stability for desired applications.

Creating metamaterial building blocks with directed photochemical metallization of silver onto DNA origami templates

DNA origami can be used to create a variety of complex and geometrically unique nanostructures that can be further modified to produce building blocks for applications such as in optical metamaterials. We describe a method for creating metal-coated nanostructures using DNA origami templates and a photochemical metallization technique. Triangular DNA origami forms were fabricated and coated with a thin metal layer by photochemical silver reduction while in solution or supported on a surface. The DNA origami template serves as a localized photosensitizer to facilitate reduction of silver ions directly from solution onto the DNA surface. The metallizing process is shown to result in a conformal metal coating, which grows in height to a self-limiting value with increasing photoreduction steps. Although this coating process results in a slight decrease in the triangle dimensions, the overall template shape is retained. Notably, this coating method exhibits characteristics of self-limiting and defect-filling growth, which results in a metal nanostructure that maps the shape of the original DNA template with a continuous and uniform metal layer and stops growing once all available DNA sites are exhausted.

Boron-Implanted Silicon Substrates for Physical Adsorption of DNA Origami

DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alternative, we developed an ion implantation process that tailors the surface potential of silicon substrates to facilitate adsorption of DNA nanostructures without the need for chemical functionalization. Industry standard 300 mm silicon wafers were processed, and we showed controlled adsorption of DNA origami onto boron-implanted silicon patterns; selective to a surrounding silicon oxide matrix. The hydrophilic substrate achieves very high surface selectivity by exploiting pH-dependent protonation of silanol-groups on silicon dioxide (SiO₂), across a range of solution pH values and magnesium chloride (MgCl₂) buffer concentrations.

Advanced Cell and Tissue Biomanufacturing

This position paper assesses state-of-the-art advanced biomanufacturing and identifies paths forward to advance this emerging field in biotechnology and biomedical engineering, including new research opportunities and translational and corporate activities. The vision for the field is to see advanced biomanufacturing emerge as a discipline in academic and industrial communities as well as a technological opportunity to spur research and industry growth. To navigate this vision, the paths to move forward and to identify major barriers were a focal point of discussions at a National Science Foundation-sponsored workshop focused on the topic. Some of the major needs include but are not limited to the integration of specific scientific and engineering disciplines and guidance from regulatory agencies, infrastructure requirements, and strategies for reliable systems integration. Some of the recommendations, major targets, and opportunities were also outlined, including some "grand challenges" to spur interest and progress in the field based on the participants at the workshop. Many of these recommendations have been expanded, materialized, and adopted by the field. For instance, the formation of an initial collaboration network in the community was established. This report provides suggestions for the opportunities and challenges to help move the field of advanced biomanufacturing forward. The field is in the early stages of effecting science and technology in biomanufacturing with a bright and important future impact evident based on the rapid scientific advances in recent years and industry progress.

Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures

The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Plasmonic nanostructures through DNA-assisted lithography

Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al2O3 and its application in imprinting lithography

We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al₂O₃. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O₃ oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films.

Metrology of DNA arrays by super-resolution microscopy

Recent results in the assembly of DNA into structures and arrays with nanoscale features and patterns have opened the possibility of using DNA for sub-10 nm lithographic patterning of semiconductor devices. Super-resolution microscopy is being actively developed for DNA-based imaging and is compatible with inline optical metrology techniques for high volume manufacturing. Here, we combine DNA tile assembly with state-dependent super-resolution microscopy to introduce crystal-PAINT as a novel approach for metrology of DNA arrays. Using this approach, we demonstrate optical imaging and characterization of DNA arrays revealing grain boundaries and the temperature dependence of array quality. For finite arrays, analysis of crystal-PAINT images provides further quantitative information of array properties. This metrology approach enables defect detection and classification and facilitates statistical analysis of self-assembled DNA nanostructures.

Deposition of DNA Nanostructures on Highly Oriented Pyrolytic Graphite

We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO₂. This process is potentially useful for a range of applications that include but are not limited to nanostructure fabrication, sensing, and electronic and surface engineering.

DNA Nanostructures-Mediated Molecular Imprinting Lithography

This paper describes the fabrication of polymer stamps using DNA nanostructure templates. This process creates stamps having diverse nanoscale features with dimensions ranging from several tens of nanometers to micrometers. DNA nanostructures including DNA nanotubes, stretched λ-DNA, two-dimensional (2D) DNA brick crystals with three-dimensional (3D) features, hexagonal DNA 2D arrays, and triangular DNA origami were used as master templates to transfer patterns to poly(methyl methacrylate) and poly(l-lactic acid) with high fidelity. The resulting polymer stamps were used as molds to transfer the pattern to acryloxy perfluoropolyether polymer. This work establishes an approach to using self-assembled DNA templates for applications in soft lithography.