Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates

Fabrication of DNA-Templated Pt Nanostructures by Area-Selective Atomic Layer Deposition

We report the fabrication of DNA-templated Pt nanostructures by area-selective atomic layer deposition. A DNA-templated self-assembled monolayer was used to mediate the area-selective deposition of Pt. Using this approach, we demonstrated the fabrication of both single- and two-component nanostructure patterns, including Pt, TiO₂/Pt, and Al₂O₃/Pt. These nanoscale patterns were used as hard masks for plasma deep etching of Si to fabricate anti-reflection surfaces. This work demonstrated a gas-phase, DNA-templated fabrication of metal nanostructures, which complements earlier work of solution-based DNA metallization. The nanostructures obtained here are useful for applications in nanoelectronics, nanophotonics, and surface engineering.

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.

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.

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.

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.

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.

Vapor-Phase Nanopatterning of Aminosilanes with Electron Beam Lithography: Understanding and Minimizing Background Functionalization

Electron beam lithography (EBL) is a highly precise, serial method for patterning surfaces. Positive tone EBL resists enable patterned exposure of the underlying surface, which can be subsequently functionalized for the application of interest. In the case of widely used native oxide-capped silicon surfaces, coupling an activated silane with electron beam lithography would enable nanoscale chemical patterning of the exposed regions. Aminoalkoxysilanes are extremely useful due to their reactive amino functionality but have seen little attention for nanopatterning silicon surfaces with an EBL resist due to background contamination. In this work, we investigated three commercial positive tone EBL resists, PMMA (950k and 495k) and ZEP520A (57k), as templates for vapor-phase patterning of two commonly used aminoalkoxysilanes, 3-aminopropyltrimethoxysilane (APTMS) and 3-aminopropyldiisopropylethoxysilane (APDIPES). The PMMA resists were susceptible to significant background reaction within unpatterned areas, a problem that was particularly acute with APTMS. On the other hand, with both APTMS and APDIPES exposure, unpatterned regions of silicon covered by the ZEP520A resist emerged pristine, as shown both with SEM images of the surfaces of the underlying silicon and through the lack of electrostatically driven binding of negatively charged gold nanoparticles. The ZEP520A resist allowed for the highly selective deposition of these alkoxyaminosilanes in the exposed areas, leaving the unpatterned areas clean, a claim also supported by contact angle measurements with four probe liquids and X-ray photoelectron spectroscopy (XPS). We investigated the mechanistic reasons for the stark contrast between the PMMA resists and ZEP520A, and it was found that the efficacy of resist removal appeared to be the critical factor in reducing the background functionalization. Differences in the molecular weight of the PMMA resists and the resulting influence on APTMS diffusion through the resist films are unlikely to have a significant impact. Area-selective nanopatterning of 15 nm gold nanoparticles using the ZEP520A resist was demonstrated, with no observable background conjugation noted in the unexposed areas on the silicon surface by SEM.

Constructing a Multiplexed DNA Pattern by Combining Precise Magnetic Manipulation and DNA-Driven Assembly

There is an urgent demand to construct multiplexed biomolecular patterns to obtain more biological information from a single experiment. However, with only limited reports focusing on defective top-down approaches, challenges remain to develop a bottom-up strategy for multiplexed patterning. To this end, a novel strategy has been proposed to fabricate multiplexed DNA patterns via macroscopic assembly through combined precise magnetic manipulation and DNA hybridization-driven self-assembly. Therefore, a multiplexed DNA pattern composed of glass fibers loaded with multiple specific strands of DNA was constructed, and its potential application in simultaneous detection of multiplex target DNA was demonstrated. Moreover, the fabricated multiplexed DNA pattern shows an erasable behavior because the hybridized DNA can be disassembled by strand displacement.

Enhanced bioactivity and osteoinductivity of carboxymethyl chitosan/nanohydroxyapatite/graphene oxide nanocomposites

Tissue engineering approaches combine a bioscaffold with stem cells to provide biological substitutes that can repair bone defects and eventually improve tissue functions. The prospective bioscaffold should have good osteoinductivity. Surface chemical and roughness modifications are regarded as valuable strategies for developing bioscaffolds because of their positive effects on enhancing osteogenic differentiation. However, the synergistic combination of the two strategies is currently poorly studied. In this work, a nanoengineered scaffold with surface chemistry (oxygen-containing groups) and roughness (R_q = 74.1 nm) modifications was fabricated by doping nanohydroxyapatite (nHA), chemically crosslinked graphene oxide (GO) and carboxymethyl chitosan (CMC). The biocompatibility and osteoinductivity of the nanoengineered CMC/nHA/GO scaffold was evaluated in vitro and in vivo, and the osteogenic differentiation mechanism of the nanoengineered scaffold was preliminarily investigated. Our data demonstrated that the enhanced osteoinductivity of CMC/nHA/GO may profit from the surface chemistry and roughness, which benefit the β1 integrin interactions with the extracellular matrix and activate the FAK–ERK signaling pathway to upregulate the expression of osteogenic special proteins. This study indicates that the nanocomposite scaffold with surface chemistry and roughness modifications could serve as a novel and promising bone substitute for tissue engineering.

The CMC/nHA/GO scaffold with the surface chemistry and roughness dual effects and the release of phosphate and calcium ions synergistically assist the mineralization and facilitate the bone regeneration.

Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride

The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na⁺ and Mg²⁺ concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm⁺ to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes.

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.

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.

Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks

DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.