DNA-Based Fabrication for Nanoelectronics

Self-Replicating DNA-Based Nanoassemblies

The properties of DNA that make it an effective genetic material also allow it to be ideal for programmed self-assembly. Such DNA-programmed assembly has been utilized to construct responsive DNA origami and wireframe nanoassemblies, yet replicating these hybrid nanomaterials remains challenging. Here we report a strategy for replicating DNA wireframe nanoassemblies using the isothermal ligase chain reaction lesion-induced DNA amplification (LIDA). We designed a triangle wireframe structure that can be formed in one step by ring-closing of its linear analog. Introducing a small amount of the wireframe triangle to an excess of the linear analog and complementary fragments, one of which contains a destabilizing abasic lesion, leads to rapid, sigmoidal self-replication of the wireframe triangle via cross-catalysis. Using the same cross-catalytic strategy we also demonstrate rapid self-replication of a hybrid wireframe triangle containing synthetic vertices as well as the self-replication of circular DNA. This work reveals the suitability of isothermal ligase chain reactions such as LIDA to self-replicate complex DNA architectures, opening the door to incorporating self-replication, a hallmark of life, into biomimetic DNA nanotechnology.

Peptide-based self-assembled monolayers (SAMs): what peptides can do for SAMs and vice versa

Self-assembled monolayers (SAMs) represent highly ordered molecular materials with versatile biochemical features and multidisciplinary applications. Research on SAMs has made much progress since the early begginings of Au substrates and alkanethiols, and numerous examples of peptide-displaying SAMs can be found in the literature. Peptides, presenting increasing structural complexity, stimuli-responsiveness, and biological relevance, represent versatile functional components in SAMs-based platforms. This review examines the major findings and progress made on the use of peptide building blocks displayed as part of SAMs with specific functions, such as selective cell adhesion, migration and differentiation, biomolecular binding, advanced biosensing, molecular electronics, antimicrobial, osteointegrative and antifouling surfaces, among others. Peptide selection and design, functionalisation strategies, as well as structural and functional characteristics from selected examples are discussed. Additionally, advanced fabrication methods for dynamic peptide spatiotemporal presentation are presented, as well as a number of characterisation techniques. All together, these features and approaches enable the preparation and use of increasingly complex peptide-based SAMs to mimic and study biological processes, and provide convergent platforms for high throughput screening discovery and validation of promising therapeutics and technologies.

Organometallic modification confers oligonucleotides new functionalities

To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.

Selective Formation of Pd-DNA Hybrids Using Tailored Palladium-Mediated Base Pairs: Towards Heteroleptic Pd-DNA Systems

The formation of highly organized metal-DNA structures has significant implications in bioinorganic chemistry, molecular biology and material science due to their unique properties and potential applications. In this study, we report on the conversion of single-stranded polydeoxycytidine (dC15 ) into a Pd-DNA supramolecular structure using the [Pd(Aqa)] complex (Aqa=8-amino-4-hydroxyquinoline-2-carboxylic acid) through a self-assembly process. The resulting Pd-DNA assembly closely resembles a natural double helix, with continuous [Pd(Aqa)(C)] (C=cytosine) units serving as palladium-mediated base pairs, forming interbase hydrogen bonds and intrastrand stacking interactions. Notably, the design of the [Pd(Aqa)] complex favours the interaction with cytosine, distinguishing it from our previously reported [Pd(Cheld)] complex (Cheld=chelidamic acid). This finding opens possibilities for creating heteroleptic Pd-DNA hybrids where different complexes specifically bind to nucleobases. We confirmed the Pd-DNA supramolecular structural assembly and selective binding of the complexes using NMR spectroscopy, circular dichroism, mass spectrometry, isothermal titration calorimetry, and DFT calculations.

Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization

Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.

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.

Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars

The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.

Molecular elements: novel approaches for molecular building

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Towards atom manufacturing with framework nucleic acids

Atom manufacturing has become a blooming frontier direction in the field of material and chemical science in recent years, focusing on the fabrication of functional materials and devices with individual atoms or with atomic precision. Framework nucleic acids (FNAs) refer to nanoscale nucleic acid framework structures with novel properties distinct from those of conventional nucleic acids. Due to their ability to be precisely positioned and assembled at the nanometer or even atomic scale, FNAs are ideal materials for atom manufacturing. They hold great promise for the bottom-up construction of electronic devices by precisely arranging and integrating building blocks with atomic or near-atomic precision. In this review, we summarize the progress of atom manufacturing based on FNAs. We begin by introducing the atomic-precision construction of FNAs and the intrinsic electrical properties of DNA molecules. Then, we describe various approaches for the fabrication of FNAs templated materials and devices, which are classified as conducting, insulating, or semiconducting based on their electrical properties. We highlight the role of FNAs in the fabrication of functional electronic devices with atomic precision, as well as the challenges and opportunities for atom manufacturing with FNAs.

Electrical modulation properties of DNA drug molecules

DNA drug molecules are not only widely used in gene therapy, but also play an important role in controlling the electrical properties of molecular electronics. Covalent binding, groove binding and intercalation are all important forms of drug-DNA interaction. But its applications are limited due to a lack of understanding of the electron transport mechanisms after different drug-DNA interaction modes. Here, we used a combination of density functional theory calculations and nonequilibrium Green's function formulation with decoherence to study the effect of drug molecules on the charge transport property of DNA under three different binding modes. Conductance of DNA is found to decrease from 2.35E-5 G0 to 1.95E-6 G0 upon doxorubicin intercalation due to modifications of the density of states in the near-highest occupied molecular orbital region, δG = 1105.13%. Additionally, the conductance of DNA after cis-[Pt(NH3)2(py)Cl]+ covalent binding increases from 1.02E-6 G0 to 5.25E-5 G0, δG = 5047.06%. However, in the case of pentamidine groove binding, because there is no direct change in DNA molecular structure during drug binding, the conductance changes before and after drug binding is much smaller than in the two above cases, δG = 90.43%. Our theoretical calculations suggest that the conductance of DNA can be regulated by different drug molecules or switching the interaction modes between small molecules and DNA. This regulation opens new possibilities for their potential applications in controllable modulation of the electron transport property of DNA.

Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures

Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson-Crick base pairing.

Concepts and principles of self-n-doping in perylene diimide chromophores for applications in biochemistry, energy harvesting, energy storage, and catalysis

Self-doping is an essential method of increasing carrier concentrations in organic electronics that eliminates the need to tailor host-dopant miscibility, a necessary step when employing molecular dopants. Self-n-doping can be accomplished using amines or ammonium counterions as an electron source, which are being incorporated into an ever-increasingly diverse range of organic materials spanning many applications. Self-n-doped materials have demonstrated exemplary and, in many cases, benchmark performances in a variety of applications. However, an in-depth review of the method is lacking. Perylene diimide (PDI) chromophores are an important mainstay in the semiconductor literature with well-known structure-function characteristics and are also one of the most widely utilized scaffolds for self-n-doping. In this review, we describe the unique properties of self-n-doped PDIs, delineate structure-function relationships, and discuss self-n-doped PDI performance in a range of applications. In particular, the impact of amine/ammonium incorporation into the PDI scaffold on doping efficiency is reviewed with regard to attachment mode, tether distance, counterion selection, and steric encumbrance. Self-n-doped PDIs are a unique set of PDI structural derivatives whose properties are amenable to a broad range of applications such as biochemistry, solar energy conversion, thermoelectric modules, batteries, and photocatalysis. Finally, we discuss challenges and the future outlook of self-n-doping principles.

DNA-Mediated Assembly of Carbon Nanomaterials

Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.

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.

DNA Optoelectronics: Versatile Systems for On-Demand Functional Electrochemical Applications

Herein, we propose innovative deoxyribonucleic acid (DNA)-based gels and their applications in diverse optoelectronics. We prepared the optoelectronic DNA-based gels (^OpDNA Gel) through molecular complexation, that is, groove binding and ionic interactions of DNA and 1,1'-diheptyl-4,4'-bipyridinium (DHV). This process is feasible even with sequence-nonspecific DNA extracted from nature (e.g., salmon testes), resulting in the expansion of the application scope of DNA-based gels. ^OpDNA Gel possessed good mechanical characteristics (e.g., high compressibility, thermoplasticity, and outstanding viscoelastic properties) that have not been observed in typical DNA hydrogels. Moreover, the electrochromic (EC) characteristics of DHV were not lost when combined with ^OpDNA Gel. By taking advantage of the facile moldability, voltage-tunable EC behavior, and biocompatibility/biodegradability of ^OpDNA Gel, we successfully demonstrated its applicability in a variety of functional electrochemical systems, including on-demand information coding systems, user-customized EC displays, and microorganism monitoring systems. The ^OpDNA Gel is a promising platform for the application of DNA-based biomaterials in electrochemical optoelectronics.

Novel pathway for the sonochemical synthesis of silver nanoparticles with near-spherical shape and high stability in aqueous media

The present study shows the development of a novel sonochemical synthesis pathway of sub-15 nm silver nanoparticles (AgNPs) with quasi-spherical shape and high stability in aqueous suspension. Different analytical techniques such as on-line UV-Vis spectroscopy, Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM) were complementarily used to characterize the evolution of the properties of AgNPs synthesized with this new route. Furthermore, different centrifugation conditions were studied to establish a practical, simple and straightforward purification method. Particle size was determined by TEM employing two different deposition methods, showing that purified AgNPs have a size of 8.1 nm ± 2.4 nm with a narrow dispersion of the size distribution (95% coverage interval from 3.4 to 13 nm). Critical information of the shape and crystalline structure of these sub-15 nm AgNPs, provided by shape descriptors (circularity and roundness) using TEM and high resolution (HR)-TEM measurements, confirmed the generation of AgNPs with quasi-spherical shapes with certain twin-fault particles promoted by the high energy of the ultrasonic treatment. Elemental analysis by TEM-EDS confirmed the high purity of the sub-15 nm AgNPs, consisting solely of Ag. At the optical level, these AgNPs showed a bandgap energy of (2.795 ± 0.002) eV. Finally, the evaluation of the effects of ultraviolet radiation (UVC: 254 nm and UVA: 365 nm) and storage temperature on the spectral stability revealed high stability of the optical properties and subsequently dimensional properties of sub-15 nm AgNPs in the short-term (600 min) and long-term (24 weeks).

Programmed Assembly of DNA Templates by Silver Nanowires

DNA origami templates are known to exhibit many advantages to integrate functional components at desirable locations for nanoelectronic applications. In order to immobilize conducting or semiconducting species in a bottom-up approach, the programmed assembly of DNA templates is of utmost necessity. This report demonstrates the silver nanowires enabled bridging of two linear DNA origami (DO) nanostructures by utilizing the host-guest interaction of biotin-STV and sequence-specific silver metallization of poly(dG-dC) DNA nanowires (in 10 % yield) using (dA)₁₀ coated AgNPs (15 nm). The enzymatic synthesis of 750 bp, 1500 bp and 3000 bp bis-biotinylated poly(dG-dC), facile synthesis of 1 : 1 biotin-STV and silver-nanowire bridged DNA templates were characterized by gel electrophoresis, atomic force microscope imaging techniques. The strategy utilized here provides a method that can precisely connect heterogeneous templates towards bottom-up fabrication of practical nanoelectronics.

Sequence Does Not Matter: The Biomedical Applications of DNA-Based Coatings and Cores

Biomedical applications of DNA are diverse but are usually associated with specific recognition of target nucleotide sequences or proteins and with gene delivery for therapeutic or biotechnological purposes. However, other aspects of DNA functionalities, like its nontoxicity, biodegradability, polyelectrolyte nature, stability, thermo-responsivity and charge transfer ability that are rather independent of its sequence, have recently become highly appreciated in material science and biomedicine. Whereas the latest achievements in structural DNA nanotechnology associated with DNA sequence recognition and Watson–Crick base pairing between complementary nucleotides are regularly reviewed, the recent uses of DNA as a raw material in biomedicine have not been summarized. This review paper describes the main biomedical applications of DNA that do not involve any synthesis or extraction of oligo- or polynucleotides with specified sequences. These sequence-independent applications currently include some types of drug delivery systems, biocompatible coatings, fire retardant and antimicrobial coatings and biosensors. The reinforcement of DNA properties by DNA complexation with nanoparticles is also described as a field of further research.

Integrated Tapping Mode Kelvin Probe Force Microscopy with Photoinduced Force Microscopy for Correlative Chemical and Surface Potential Mapping

Kelvin probe force microscopy (KPFM) is a popular technique for mapping the surface potential at the nanoscale through measurement of the Coulombic force between an atomic force microscopy (AFM) tip and sample. The lateral resolution of conventional KPFM variants is limited to between ≈35 and 100 nm in ambient conditions due to the long-range nature of the Coulombic force. In this article, a novel way of generating the Coulombic force in tapping mode KPFM without the need for an external AC driving voltage is presented. A field-effect transistor (FET) is used to directly switch the electrical connectivity of the tip and sample on and off periodically. The resulting Coulomb force induced by Fermi level alignment of the tip and sample results in a detectable change of the cantilever oscillation at the FET-switching frequency. The resulting FET-switched KPFM delivers a spatial resolution of ≈25 nm and inherits the high operational speed of the AFM tapping mode. Moreover, the FET-switched KPFM is integrated with photoinduced force microscopy (PiFM), enabling simultaneous acquisitions of high spatial resolution chemical distributions and surface potential maps. The integrated FET-switched KPFM with PiFM is expected to facilitate characterizations of nanoscale electrical properties of photoactive materials, semiconductors, and ferroelectric materials.

Chiral 3D DNA origami structures for ordered heterologous arrays

The DNA origami technique allows the facile design and production of three-dimensional shapes from single template strands of DNA. These can act as functional devices with multiple potential applications but are constrained by practical limitations on size. Multi-functionality could be achieved by connecting together distinct DNA origami modules in an ordered manner. Arraying of non-identical, three-dimensional DNA origamis in an ordered manner is challenging due for example, to a lack of compatible rotational symmetries. Here we show that we can design and build ordered DNA structures using non-identical 3D building blocks by using DNA origami snub-cubes in left-handed and right-handed forms. These can be modified such that one form only binds to the opposite-handed form allowing regular arrays wherein building blocks demonstrate alternating chirality.