Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning

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.

Three-Dimensional Molecular Transfer from DNA Nanocages to Inner Gold Nanoparticle Surfaces

It is of great interest to construct DNA-functionalized gold nanoparticles (DNA-AuNPs) with a controllable number of DNA strands and relative orientations. Herein, we describe a three-dimensional (3D) molecular transfer strategy, in which a pattern of DNA strands can be transferred from a DNA icosahedron cage (I-Cage) to the wrapped AuNP surface. The results show that DNA-AuNPs produced by this method inherit DNA pattern information encoded in the transient I-Cage template with high fidelity. Controllable numbers and positions of DNA on the surface of AuNPs can be simultaneously realized by direct "printing" of a DNA pattern from the nanoshell (I-Cage) to the nanocore (AuNP), further expanding the applications of DNA nanotechnology to nanolithography. Prospectively, the customized DNA-printed nanoparticles possess great potential for constructing programmable architectures for optoelectronic devices as well as smart biosensors for biomedical applications.

Autonomously designed free-form 2D DNA origami

Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.

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.

Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures

DNA origami is a powerful method for the creation of 3D nanoscale objects, and in the past few years, interest in wireframe origami designs has increased due to their potential for biomedical applications. In DNA wireframe designs, the construction material is double-stranded DNA, which has a persistence length of around 50 nm. In this work, we study the effect of various design choices on the stiffness versus final size of nanoscale wireframe rods, given the constraints on origami designs set by the DNA origami scaffold size. An initial theoretical analysis predicts two competing mechanisms limiting rod stiffness, whose balancing results in an optimal edge length. For small edge lengths, the bending of the rod's overall frame geometry is the dominant factor, while the flexibility of individual DNA edges has a greater contribution at larger edge lengths. We evaluate our design choices through simulations and experiments and find that the stiffness of the structures increases with the number of sides in the cross-section polygon and that there are indications of an optimal member edge length. We also ascertain the effect of nicked DNA edges on the stiffness of the wireframe rods and demonstrate that ligation of the staple breakpoint nicks reduces the observed flexibility. Our simulations also indicate that the persistence length of wireframe DNA structures significantly decreases with increasing monovalent salt concentration.

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.

DNA Origami and G-Quadruplex Hybrid Complexes Induce Size Control of Single-Walled Carbon Nanotubes via Biological Activation

DNA self-assembly has enabled the programmable fabrication of nanoarchitectures, and these nanoarchitectures combined with nanomaterials have provided several applications. Here, we develop an approach for cutting single-walled carbon nanotubes (SWNTs) of predetermined lengths, using DNA origami and G-quadruplex hybrid complexes. This approach is based on features of DNA: (1) wrapping SWNTs with DNA to improve the dispersibility of SWNTs in water; (2) using G-quadruplex DNA to confine hemin in close proximity to SWNTs and enhance the biological activation of hydrogen peroxide by hemin; and (3) forming DNA origami platforms to allow for the precise placement of G-quadruplexes, enabling size control. These integrated features of DNA allow for temporally efficient cutting of SWNTs into desired lengths, thus expanding the availability of SWNTs for applications in the fields of nanoelectronics, nanomedicine, nanomaterials, and quantum physics, as well as in fundamental studies.

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.

PMMA-Assisted Plasma Patterning of Graphene

Microelectronic fabrication of Si typically involves high-temperature or high-energy processes. For instance, wafer fabrication, transistor fabrication, and silicidation are all above 500°C. Contrary to that tradition, we believe low-energy processes constitute a better alternative to enable the industrial application of single-molecule devices based on 2D materials. The present work addresses the postsynthesis processing of graphene at unconventional low temperature, low energy, and low pressure in the poly methyl-methacrylate- (PMMA-) assisted transfer of graphene to oxide wafer, in the electron-beam lithography with PMMA, and in the plasma patterning of graphene with a PMMA ribbon mask. During the exposure to the oxygen plasma, unprotected areas of graphene are converted to graphene oxide. The exposure time required to produce the ribbon patterns on graphene is 2 minutes. We produce graphene ribbon patterns with ∼50 nm width and integrate them into solid state and liquid gated transistor devices.

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.

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg²⁺ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.

Dynamics of self-assembled cytosine nucleobases on graphene

Molecular self-assembly of cytosine (C _n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C _n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C _n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C _n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

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.

DNA-based construction at the nanoscale: emerging trends and applications

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

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.

Single-stranded DNA and RNA origami

Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.

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.

Sub-10 nm patterning with DNA nanostructures: a short perspective

DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ∼10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either 'top-down' or 'bottom-up' approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. This perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography. Emphasis is put on the challenges and prospects of DNA nanolithography as the next generation nanomanufacturing technique.

Nanoscale patterning of self-assembled monolayer (SAM)-functionalised substrates with single molecule contact printing

Defined arrangements of individual molecules are covalenty connected ("printed") onto SAM-functionalised gold substrates with nanometer resolution. Substrates were initially pre-functionlised by coating with 3,3'-dithiodipropionic acid (DTPA) to form a self-assembled monolayer (SAM), which was characterised by atomic force microscopy (AFM), contact angle goniometry, cyclic voltammetry and surface plasmon resonance (SPR) spectroscopy. Pre-defined "ink" patterns displayed on DNA origami-based single-use carriers ("stamp") were covalently conjugated to the SAM using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC) and N-hydroxy-succinimide (NHS). These anchor points were used to create nanometer-precise single-molecule arrays, here with complementary DNA and streptavidin. Sequential steps of the printing process were evaluated by AFM and SPR spectroscopy. It was shown that 30% of the detected arrangements closely match the expected length distribution of designed patterns, whereas another 40% exhibit error within the range of only 1 streptavidin molecule. SPR results indicate that imposing a defined separation between molecular anchor points within the pattern through this printing process enhances the efficiency for association of specific binding partners for systems with high sterical hindrance. This study expands upon earlier findings where geometrical information was conserved by the application of DNA nanostructures, by establishing a generalisable strategy which is universally applicable to nearly any type of prefunctionalised substrate such as metals, plastics, silicates, ITO or 2D materials.

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.

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices.

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.

Direct Nanofabrication Using DNA Nanostructure

Recent advances in DNA nanotechnology make it possible to fabricate arbitrarily shaped 1D, 2D, and 3D DNA nanostructures through controlled folding and/or hierarchical assembly of up to several thousands of unique sequenced DNA strands. Both individual DNA nanostructures and their assembly can be made with almost arbitrarily shaped patterns at a theoretical resolution down to 2 nm. Furthermore, the deposition of DNA nanostructures on a substrate can be made with precise control of their location and orientation, making them ideal templates for bottom-up nanofabrication. However, many fabrication processes require harsh conditions, such as corrosive chemicals and high temperatures. It still remains a challenge to overcome the limited stability of DNA nanostructures during the fabrication process.This chapter focuses on the proof-of-principle study to directly convert the structural information of DNA nanostructure to various kinds of materials by nanofabrication.

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

Metallic Nanostructures Based on DNA Nanoshapes

Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects.

Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes

The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two-dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Label-free electrochemical detection of DNA methyltransferase activity via a DNA tetrahedron-structured probe

Label-free electrochemical detection of DNA methyltransferase activityviaDNA tetrahedron-structured probe.

Fabrication of a nano-scale pattern with various functional materials using electrohydrodynamic lithography and functionalization

Direct patterning with inorganic based materials has been developed using electrohydrodynamic lithography. Various sizes and morphologies of inorganic patterns were successfully replicated.

Interaction of nucleobases with silicon doped and defective silicon doped graphene and optical properties

The interaction of nucleobases (NBs) with the surface of silicon doped graphene (SiGr) and defective silicon doped graphene (dSiGr) has been studied using electronic structure methods.

Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates

We describe a method to pattern arbitrary-shaped silane self-assembled monolayers (SAMs) with nm scale resolution using DNA nanostructures as templates. The DNA nanostructures assembled on a silicon substrate act as a soft-mask to negatively pattern SAMs. Mixed SAMs can be prepared by back filling the negative tone patterns with a different silane.

A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors

Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

Nanomanufacturing of 2D Transition Metal Dichalcogenide Materials Using Self-Assembled DNA Nanotubes

2D transition metal dichalcogenides (TMDCs) are nanomanufactured using a generalized strategy with self-assembled DNA nanotubes. DNA nanotubes of various lengths serve as lithographic etch masks for the dry etching of TMDCs. The nanostructured TMDCs are studied by atomic force microscopy, photoluminescence, and Raman spectroscopy. This parallel approach can be used to manufacture 2D TMDC nanostructures of arbitrary geometries with molecular-scale precision.

Custom-shaped metal nanostructures based on DNA origami silhouettes

The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.

Enzymatic Polymerization on DNA Modified Gold Nanowire for Label-Free Detection of Pathogen DNA

This paper presents a label-free biosensor for the detection of single-stranded pathogen DNA through the target-enhanced gelation between gold nanowires (AuNW) and the primer DNAs branched on AuNW. The target DNA enables circularization of the linear DNA template, and the primer DNA is elongated continuously via rolling circle amplification. As a result, in the presence of the target DNA, a macroscopic hydrogel was fabricated by the entanglement of the elongated DNA with AuNWs as a scaffold fiber for effective gelation. In contrast, very small separate particles were generated in the absence of the target DNA. This label-free biosensor might be a promising tool for the detection of pathogen DNAs without any devices for further analysis. Moreover, the biosensor based on the weaving of AuNW and DNAs suggests a novel direction for the applications of AuNWs in biological engineering.

Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems

We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.

Engineering artificial machines from designable DNA materials for biomedical applications

Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.

Electronically addressable nanomechanical switching of i-motif DNA origami assembled on basal plane HOPG

Here, a pH-induced nanomechanical switching of i-motif structures incorporated into DNA origami bound onto cysteamine-modified basal plane HOPG was electronically addressed, demonstrating for the first time the electrochemical read-out of the nanomechanics of DNA origami.

Capillary force assisted fabrication of DNA templated silver wires

Re-arrangement of DNA molecules along micro-scratches assisted by capillary force.