Multiple-unit interlocking enhances the single-stranded tiles assembly of DNA nanostructures

Single-stranded tiles (DNA brick) assembly has provided a simple and modular tool for constructing nanostructures with the potential for numerous applications. However, in this strategy, the short-strand building blocks are susceptible to environmental fluctuations and bring about rapid dissociation during assembly, resulting in instability and prolonged annealing. Thus, developing new strategies which can enhance the stability and accelerate the assembly process of DNA bricks is important. In this study, we applied the kinetically interlocking multiple-unit (KIMU) strategy to tune the process of DNA brick assembly by adopting long DNA strands as building blocks, ranging from tens of to 1000 nucleotides. We constructed a series of DNA structures with improved stability over DNA bricks. Furthermore, the annealing process could be accelerated by increasing the number of units. Our study demonstrated that DNA assembly based on the KIMU strategy using multiple-unit DNA strands could be a promising method for constructing relatively stable DNA nanostructures.

Removing Conjugated Polymers from Aligned Carbon Nanotube Arrays

Aligned carbon nanotube (A-CNT) with high semiconducting purity and high-density have been considered as one of the most promising active channels for field-effect transistors (FETs), but conjugated polymer dispersant residues on the surface of A-CNT have become the main obstacle for its further development in electronics applications. In this work, a series of removable conjugated polymers (CPs) are designed and synthesized to achieve favorable purification and alignment for CNT arrays with a high density of ≈360 CNTs/µm. Furthermore, a removal process of CPs on the CNT array film is developed. Raman spectra show that the CNTs in array film are almost not damaged after the removal process, and the G/D ratio is as high as 35. The field-effect transistors (FETs) are fabricated with a saturation current density up to 600 µA µm-1 and a current on-off ratio of ≈105, even with a relatively long channel length of ≈3 µm.

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

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.

A functional RNA-origami as direct thrombin inhibitor with fast-acting and specific single-molecule reversal agents in vivo model

Injectable anticoagulants are widely used in medical procedures to prevent unwanted blood clotting. However, many lack safe, effective reversal agents. Here, we present new data on a previously described RNA origami-based, direct thrombin inhibitor (HEX01). We describe a new, fast-acting, specific, single-molecule reversal agent (antidote) and present in vivo data for the first time, including efficacy, reversibility, preliminary safety, and initial biodistribution studies. HEX01 contains multiple thrombin-binding aptamers appended on an RNA origami. It exhibits excellent anticoagulation activity in vitro and in vivo. The new single-molecule, DNA antidote (HEX02) reverses anticoagulation activity of HEX01 in human plasma within 30 s in vitro and functions effectively in a murine liver laceration model. Biodistribution studies of HEX01 in whole mice using ex vivo imaging show accumulation mainly in the liver over 24 h and with 10-fold lower concentrations in the kidneys. Additionally, we show that the HEX01/HEX02 system is non-cytotoxic to epithelial cell lines and non-hemolytic in vitro. Furthermore, we found no serum cytokine response to HEX01/HEX02 in a murine model. HEX01 and HEX02 represent a safe and effective coagulation control system with a fast-acting, specific reversal agent showing promise for potential drug development.

Rapid Silicification of a DNA Origami with Shape Fidelity

High-fidelity patterning of DNA origami nanostructures on various interfaces holds great potential for nanoelectronics and nanophotonics. However, distortion of a DNA origami often occurs due to the strong interface interactions, e.g., on two-dimensional (2D) materials. In this study, we discovered that the adsorption of silica precursors in rapid silicification can prevent the distortion caused by graphene and generates a high shape-fidelity DNA origami-silica composite on a graphene interface. We found that an incubation time of 1 min and silicification time of 16 h resulted in the formation of DNA origami-silica composites with the highest shape fidelity of 99%. By comparing the distortion of the DNA origami on the graphene interface with and without silicification, we observed that rapid silicification effectively preserved the integrity of the DNA origami. Statistical analysis of scanning electron microscopy data indicates that compared to bare DNA origami, the DNA origami-silica composite has an increased shape fidelity by more than two folds. Furthermore, molecular dynamics simulations revealed that rapid silicification effectively suppresses the distortion of the DNA origami through the interhelical insertion of silica precursors. Our strategy provides a simple yet effective solution to maintain the shape-fidelity DNA origami on interfaces that have strong interaction with DNA molecules, expanding the applicable interfaces for patterning 2D DNA origamis.

Ionic Strength-Mediated "DNA Corona Defects" for Efficient Arrangement of Single-Walled Carbon Nanotubes

Single-stranded DNA oligonucleotides wrapping on the surface of single-walled carbon nanotubes (SWCNTs), described as DNA corona, are often used as a dispersing agent for SWCNTs. The uneven distribution of DNA corona along SWCNTs is related to the photoelectric properties and the surface activity of SWCNTs. An ionic strength-mediated "DNA corona defects" (DCDs) strategy is proposed to acquire an exposed surface of SWCNTs (accessible surface) as large as possible while maintaining good dispersibility via modulating the conformation of DNA corona. By adjusting the solution ionic strength, the DNA corona phase transitioned from an even-distributed and loose conformation to a locally compact conformation. The resulting enlarged exposed surface of SWCNTs is called DCDs, which provide active sites for molecular adsorption. This strategy is applied for the arrangement of SWCNTs on DNA origami. SWCNTs with ≈11 nm DCD, providing enough space for the adsorption of "capture ssDNA" (≈7 nm width required for 24-nt) extended from DNA origami structures are fabricated. The DCD strategy has potential applications in SWCNT-based optoelectronic devices.

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Self-Aligning Nanojunctions for Integrated Single-Molecule Circuits

Robust, high-yield integration of nanoscale components such as graphene nanoribbons, nanoparticles, or single-molecules with conventional electronic circuits has proven to be challenging. This difficulty arises because the contacts to these nanoscale devices must be precisely fabricated with angstrom-level resolution to make reliable connections, and at manufacturing scales this cannot be achieved with even the highest-resolution lithographic tools. Here we introduce an approach that circumvents this issue by precisely creating nanometer-scale gaps between metallic carbon electrodes by using a self-aligning, solution-phase process, which allows facile integration with conventional electronic systems with yields approaching 50%. The electrode separation is controlled by covalently binding metallic single-walled carbon nanotube (mCNT) electrodes to individual DNA duplexes to create mCNT-DNA-mCNT nanojunctions, where the gap is precisely matched to the DNA length. These junctions are then integrated with top-down lithographic techniques to create single-molecule circuits that have electronic properties dominated by the DNA in the junction, have reproducible conductance values with low dispersion, and are stable and robust enough to be utilized as active, high-specificity electronic biosensors for dynamic single-molecule detection of specific oligonucleotides, such as those related to the SARS-CoV-2 genome. This scalable approach for high-yield integration of nanometer-scale devices will enable opportunities for manufacturing of hybrid electronic systems for a wide range of applications.

Programming and monitoring surface-confined DNA computing

DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.

Single-Crystal Silicon Nanotubes, Hollow Nanocones, and Branched Nanotube Networks

We report a general approach for the synthesis of single-crystal silicon nanotubes, involving epitaxial deposition of silicon shells on germanium nanowire templates followed by removal of the germanium template by selective wet etching. By exploiting advances in the synthesis of germanium nanowires, we were able to rationally tune the nanotube internal diameters (5-80 nm), wall thicknesses (3-12 nm), and taper angles (0-9°) and additionally demonstrated branched silicon nanotube networks. Field effect transistors fabricated from p-type nanotubes exhibited a strong gate effect, and fluid transport experiments demonstrated that small molecules could be electrophoretically driven through the nanotubes. These results demonstrate the suitability of silicon nanotubes for the design of nanoelectrofluidic devices.

Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly

Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.

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.

Direct Writing of Aligned Carbon Nanotubes across a Trench

Aligned and suspended carbon nanotubes can outperform randomly oriented networks in electronic biosensing and thin-film electronics. However, carbon nanotubes tend to bundle and form random networks. Here, we show that carbon nanotubes spontaneously align in an ammonium deoxycholate surfactant gel even under low shear forces, allowing direct writing and printing of nanotubes into electrically conducting wires and aligned thin layers across trenches. To demonstrate its application potential, we directly printed arrays of disposable electrical biosensors, which show femtomolar sensitivity in the detection of DNA and SARS-CoV-2 RNA.

Biotemplated precise assembly approach toward ultra-scaled high-performance electronics

Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 μA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.

Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds

Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.

DNA Origami Tessellations

Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami nanostructures are excellent building blocks for constructing tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, we present a general method for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. Interhelical distance (D) was identified as a critical design parameter determining tile conformation and tessellation outcome. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability, enabling the formation of single-crystalline lattices ranging from tens to hundreds of square micrometers. The general applicability of the design method was demonstrated by 9 tile geometries, 15 unique tile designs, and 12 tessellation patterns covering Platonic, Laves, and Archimedean tilings. Particularly, we took two strategies to increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and coassembling tiles of different geometries. Both yielded various tiling patterns that rivaled Platonic tilings in size and quality, indicating the robustness of the optimized tessellation system. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Surface engineering of colloidal nanoparticles

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.

Engineering Geobacter pili to produce metal:organic filaments

The organized self-assembly of conductive biological structures holds promise for creating new bioelectronic devices. In particular, Geobacter sulfurreducens type IVa pili have proven to be a versatile material for fabricating protein nanowire-based devices. To scale the production of conductive pili, we designed a strain of Shewanella oneidensis that heterologously expressed abundant, conductive Geobacter pili when grown aerobically in liquid culture. S. oneidensis expressing a cysteine-modified pilin, designed to enhance the capability to bind to gold, generated conductive pili that self-assembled into biohybrid filaments in the presence of gold nanoparticles. Elemental composition analysis confirmed the filament-metal interactions within the structures, which were several orders of magnitude larger than previously described metal:organic filaments. The results demonstrate that the S. oneidensis chassis significantly advances the possibilities for facile conductive protein nanowire design and fabrication.

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.

Harnessing DNA Nanotechnology and Chemistry for Applications in Photonics and Electronics

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

DNA Origami: Recent Progress and Applications

This chapter explores the basic concept of DNA origami and its various types. By showing the progress made in structural DNA nanotechnology during the last 15 years, the chapter draws attention to the capability of DNA origami to construct complex structures in both 2D and 3D level. As well as looking at a few examples of dynamic DNA nanostructures, the chapter also explores the possible applications of DNA origami in different fields, such as biological computing, nanorobotics, and DNA walkers.

Controlled Preparation of Single-Walled Carbon Nanotubes as Materials for Electronics

Single-walled carbon nanotubes (SWCNTs) are of particular interest as channel materials for field-effect transistors due to their unique structure and excellent properties. The controlled preparation of SWCNTs that meet the requirement of semiconducting and chiral purity, high density, and good alignment for high-performance electronics has become a key challenge in this field. In this Outlook, we outline the efforts in the preparation of SWCNTs for electronics from three main aspects, structure-controlled growth, selective sorting, and solution assembly, and discuss the remaining challenges and opportunities. We expect that this Outlook can provide some ideas for addressing the existing challenges and inspire the development of SWCNT-based high-performance electronics.

Carbon nanotube transistors: Making electronics from molecules

Semiconducting carbon nanotubes are robust molecules with nanometer-scale diameters that can be used in field-effect transistors, from larger thin-film implementation to devices that work in conjunction with silicon electronics, and can potentially be used as a platform for high-performance digital electronics as well as radio-frequency and sensing applications. Recent progress in the materials, devices, and technologies related to carbon nanotube transistors is briefly reviewed. Emphasis is placed on the most broadly impactful advancements that have evolved from single-nanotube devices to implementations with aligned nanotubes and even nanotube thin films. There are obstacles that remain to be addressed, including material synthesis and processing control, device structure design and transport considerations, and further integration demonstrations with improved reproducibility and reliability; however, the integration of more than 10,000 devices in single functional chips has already been realized.

Compositional Analysis of ssDNA-Coated Single-Wall Carbon Nanotubes through UV Absorption Spectroscopy

Aqueous suspensions of single-wall carbon nanotubes (SWCNTs) coated by ssDNA are analyzed using UV absorption and total carbon measurements. The results give absolute average concentrations of both components in samples without free ssDNA. From those values, the average mid-UV SWCNT absorptivity is deduced for three different batches of relatively small diameter nanotubes: two HiPco and one CoMoCAT. The absorptivity values enable the use of simple spectrophotometry to measure absolute concentrations of similar SWCNT samples in aqueous SDS. The results also quantify the mass ratio of ssDNA to SWCNT, defining the average number of nanotube carbon atoms suspended by one ssDNA strand of T₁₅GT₁₅ or T₃₀G. Comparing this experimental parameter with results from replica exchange molecular dynamics simulations of one ssDNA strand freely adsorbed on a (6,5) segment shows close agreement between the computed number of SWCNT atoms covered per strand and the measured number of SWCNT atoms suspended per strand.

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

Parallel Field-Effect Nanosensors Detect Trace Biomarkers Rapidly at Physiological High-Ionic-Strength Conditions

Sensitivity and speed of detection are contradicting demands that profoundly impact the electrical sensing of molecular biomarkers. Although single-molecule sensitivity can now be achieved with single-nanotube field-effect transistors, these tiny sensors, with a diameter less than 1 nm, may take hours to days to capture the molecular target at trace concentrations. Here, we show that this sensitivity-speed challenge can be addressed using covalently functionalized double-wall CNTs that form many individualized, parallel pathways between two electrodes. Each carrier that travels across the electrodes is forced to take one of these pathways that are fully gated chemically by the target-probe binding events. This sensor design allows us to electrically detect Lyme disease oligonucleotide biomarkers directly at the physiological high-salt concentrations, simultaneously achieving both ultrahigh sensitivity (as low as 1 fM) and detection speed (<15 s). This unexpectedly simple strategy may open opportunities for sensor designs to broadly achieve instant detection of trace biomarkers and real-time probing of biomolecular functions directly at their physiological states.

Selected-Area Fabrication of a Single-Walled Carbon Nanotube Schottky Junction with Tunable Gate Rectification

Single-walled carbon nanotube (SWNT)-based devices are expected to play an important role in the next generation of electronic integrated circuits. As an important structural unit for SWNT-based electronics, the Schottky junction has a series of functions such as rectification, photoelectric detection, switching, etc. Here, we demonstrate a well-controlled localized radical reaction method to prepare an intramolecular SWNT Schottky junction with a closed edge. This junction exhibits strong gate-dependent rectifying behavior and a high rectification ratio of 962. Furthermore, the semiconducting part on the junction side could be effectively tuned from p-type doping to n-type doping, resulting in reversible rectifying behavior. Our work paves a new avenue for the design and synthesis of an SWNT Schottky junction, which is very important to future applications for carbon-based nanoelectronic devices.

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson–Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Insight and Recent Advances into the Role of Topography on the Cell Differentiation and Proliferation on Biopolymeric Surfaces

It is well known that surface topography plays an important role in cell behavior, including adhesion, migration, orientation, elongation, proliferation and differentiation. Studying these cell functions is essential in order to better understand and control specific characteristics of the cells and thus to enhance their potential in various biomedical applications. This review proposes to investigate the extent to which various surface relief patterns, imprinted in biopolymer films or in polymeric films coated with biopolymers, by utilizing specific lithographic techniques, influence cell behavior and development. We aim to understand how characteristics such as shape, dimension or chemical functionality of surface relief patterns alter the orientation and elongation of cells, and thus, finally make their mark on the cell proliferation and differentiation. We infer that such an insight is a prerequisite for pushing forward the comprehension of the methodologies and technologies used in tissue engineering applications and products, including skin or bone implants and wound or fracture healing.

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.

Two-Stage Assembly of Nanoparticle Superlattices with Multiscale Organization

Self-assembly processes, while promising for enabling the fabrication of complexly organized nanomaterials from nanoparticles, are often limited in creating structures with multiscale order. These limitations are due to difficulties in practically realizing the assembly processes required to achieve such complex organizations. For a long time, a hierarchical assembly attracted interest as a potentially powerful approach. However, due to the experimental limitations, intermediate-level structures are often heterogeneous in composition and structure, which significantly impacts the formation of large-scale organizations. Here, we introduce a two-stage assembly strategy: DNA origami frames scaffold a coordination of nanoparticles into designed 3D nanoclusters, and then these clusters are assembled into ordered lattices whose types are determined by the clusters' valence. Through modulating the nanocluster architectures and intercluster bindings, we demonstrate the successful formation of complexly organized nanoparticle crystals. The presented two-stage assembly method provides a powerful fabrication strategy for creating nanoparticle superlattices with prescribed unit cells.

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.

Guanine-Specific Chemical Reaction Reveals ssDNA Interactions on Carbon Nanotube Surfaces

Understanding the conformations of physisorbed single-stranded DNA (ssDNA) oligos on single-wall carbon nanotube (SWCNT) surfaces is important for advancing basic nanoscience and for developing applications in biomedicine and quantum information processing. Here we report evidence that the ssDNA strands are partly desorbed from the nanotube surface under common conditions. SWCNT suspensions were prepared in eight ssDNA oligos, each containing 1 guanine and 30 thymine bases but differing in the position of the guanine within the strand. Singlet oxygen exposure then covalently functionalized the guanine to the SWCNT surface, red-shifting the nanotube fluorescence by an amount reflecting the guanine spatial density at the surface. Spectral shifts were greatest for central guanine positions and smallest for end positions. In conjunction with steered molecular dynamics simulations, the results suggest that steric interference between neighboring ssDNA strands on an individual nanotube causes significant dislocation or desorption of the strand ends while central regions remain better wrapped around the nanotube. This effect decreases with decreasing concentrations of free ssDNA.

Engineering bacterial surface interactions using DNA as a programmable material

The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.

Soft-lock drawing of super-aligned carbon nanotube bundles for nanometre electrical contacts

The assembly of single-walled carbon nanotubes (CNTs) into high-density horizontal arrays is strongly desired for practical applications, but challenges remain despite myriads of research efforts. Herein, we developed a non-destructive soft-lock drawing method to achieve ultraclean single-walled CNT arrays with a very high degree of alignment (angle standard deviation of ~0.03°). These arrays contained a large portion of nanometre-sized CNT bundles, yielding a high packing density (~400 µm^-1) and high current carrying capacity (∼1.8 × 10⁸ A cm^-2). This alignment strategy can be generally extended to diverse substrates or sources of raw single-walled CNTs. Significantly, the assembled CNT bundles were used as nanometre electrical contacts of high-density monolayer molybdenum disulfide (MoS₂) transistors, exhibiting high current density (~38 µA µm^-1), low contact resistance (~1.6 kΩ µm), excellent device-to-device uniformity and highly reduced device areas (0.06 µm² per device), demonstrating their potential for future electronic devices and advanced integration technologies.

Carbon Nanotube Devices for Quantum Technology

Carbon nanotubes, quintessentially one-dimensional quantum objects, possess a variety of electrical, optical, and mechanical properties that are suited for developing devices that operate on quantum mechanical principles. The states of one-dimensional electrons, excitons, and phonons in carbon nanotubes with exceptionally large quantization energies are promising for high-operating-temperature quantum devices. Here, we discuss recent progress in the development of carbon-nanotube-based devices for quantum technology, i.e., quantum mechanical strategies for revolutionizing computation, sensing, and communication. We cover fundamental properties of carbon nanotubes, their growth and purification methods, and methodologies for assembling them into architectures of ordered nanotubes that manifest macroscopic quantum properties. Most importantly, recent developments and proposals for quantum information processing devices based on individual and assembled nanotubes are reviewed.

Nanobase.org: a repository for DNA and RNA nanostructures

We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.

Characterizing and Harnessing the Mechanical Properties of Short Single-Stranded DNA in Structured Assemblies

Precise engineering of DNA structures is of growing interest to solve challenging problems in biomolecular applications and beyond. The introduction of single-stranded DNA (ssDNA) into the DNA structure can play a pivotal role in providing high controllability of critical structural features. Herein, we present a computational model of ssDNA with structural applications to harness its characteristics. The nonlinear properties of nucleotide gaps are systematically characterized to construct a structural model of the ssDNA across length scales with the incorporation of a finite element framework. The proposed method shows the programmability of structural bending, twisting, and persistence length by implementing the ssDNA in various DNA structures with experimental validation. Our results have significant implications for DNA nanotechnology in expanding the boundary of design and analysis of structural shape and stiffness.

DNA Origami-Encoded Integration of Heterostructures

Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. The structural DNA nanotechnology provides a universal platform for precision assembly of materials; nevertheless, heterogeneous integration of dissimilar materials with DNA nanostructures has yet to be explored. Here we report a DNA origami-encoded strategy for integrating silica-metal heterostructures. Theoretical and experimental studies reveal distinctive mechanisms for the binding and aggregation of silica and metal clusters on protruding double-stranded DNA (dsDNA) strands that are prescribed on the DNA origami template. In particular, the binding energy differences of silica/metal clusters and DNA molecules underlies the accessibilities of dissimilar material areas on DNA origami. We find that, by programming the densities and lengths of protruding dsDNA strands on DNA origami, silica and metal materials can be independently deposited at their predefined areas with a high vertical precision of 2 nm. We demonstrate the integration of silica-gold and silica-silver heterostructures with high site addressability. This DNA nanotechnology-based strategy is thus applicable for integrating various types of dissimilar materials, which opens new routes for bottom-up electronics.

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.

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds

A quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

Building a Bridge for Carbon Nanotubes from Nanoscale Structure to Macroscopic Application

Through 30 years of research, researchers have gained a deep understanding of the synthesis, characteristics, and applications of carbon nanotubes (CNTs). However, up to now, there are still few industries using CNT as the leading material. The difficulty of CNTs to be applied in industry is the gap between the properties of CNT-based aggregates and those of a single carbon nanotube. Therefore, how to maintain the intrinsic properties of CNTs when they are assembled into aggregates is of great significance. Herein, we summarize and analyze the research status of CNT materials applied in different fields from proven techniques to potential industries, including energy storage, electronics, mechanical and other applications. For each application, the intrinsic properties of CNTs and the real performances of their aggregates are compared to figure out the key problems in CNT synthesis. Finally, we give an outlook for building a bridge for CNTs from nanoscale structure to macroscopic application, giving inspiration to researchers making efforts toward the real application of carbon nanotubes.

Beyond Color: The New Carbon Ink

For thousands of years, carbon ink has been used as a black color pigment for writing and painting purposes. However, recent discoveries of nanocarbon materials, including fullerenes, carbon nanotubes, graphene, and their various derivative forms, together with the advances in large-scale synthesis, are enabling a whole new generation of carbon inks that can serve as an intrinsically programmable materials platform for developing advanced functionalities far beyond color. The marriage between these multifunctional nanocarbon inks with modern printing technologies is facilitating and even transforming many applications, including flexible electronics, wearable and implantable sensors, actuators, and autonomous robotics. This review examines recent progress in the reborn field of carbon inks, highlighting their programmability and multifunctionality for applications in flexible electronics and stimuli-responsive devices. Current challenges and opportunities will also be discussed from a materials science perspective towards the advancement of carbon ink for new applications beyond color.

Aligned 2D carbon nanotube liquid crystals for wafer-scale electronics

Semiconducting carbon nanotubes promise faster performance and lower power consumption than Si in field-effect transistors (FETs) if they can be aligned in dense arrays. Here, we demonstrate that nanotubes collected at a liquid/liquid interface self-organize to form two-dimensional (2D) nematic liquid crystals that globally align with flow. The 2D liquid crystals are transferred onto substrates in a continuous process generating dense arrays of nanotubes aligned within ±6°, ideal for electronics. Nanotube ordering improves with increasing concentration and decreasing temperature due to the underlying liquid crystal phenomena. The excellent alignment and uniformity of the transferred assemblies enable FETs with exceptional on-state current density averaging 520 μA μm⁻¹at only −0.6 V, and variation of only 19%. FETs with ion gel top gates demonstrate subthreshold swing as low as 60 mV decade⁻¹. Deposition across a 10-cm substrate is achieved, evidencing the promise of 2D nanotube liquid crystals for commercial semiconductor electronics.

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices

The ability to detect proteins through gating conductance by their unique surface electrostatic signature holds great potential for improving biosensing sensitivity and precision. Two challenges are: (1) defining the electrostatic surface of the incoming ligand protein presented to the conductive surface; (2) bridging the Debye gap to generate a measurable response. Herein, we report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets. Using a β-lactamase binding protein (BLIP2) as the capture protein attached to carbon nanotube field effect transistors in different defined orientations. Device conductance had influence on binding TEM-1, an important β-lactamase involved in antimicrobial resistance (AMR). Conductance increased or decreased depending on TEM-1 presenting either negative or positive local charge patches, demonstrating that local electrostatic properties, as opposed to protein net charge, act as the key driving force for electrostatic gating. This, in turn can, improve our ability to tune the gating of electrical biosensors toward optimized detection, including for AMR as outlined herein.