Synthesis and Stretching of Rolling Circle Amplification Products in a Flow‐Through System

Enzymatic isothermal rolling circle amplification (RCA) produces long concatemeric single‐stranded DNA (ssDNA) molecules if a small circular ssDNA molecule is applied as the template. A method is presented here in which the RCA reaction is carried out in a flow‐through system, starting from isolated surface‐tethered DNA primers. This approach combines gentle fluidic handling of the single‐stranded RCA products, such as staining or stretching via a receding meniscus, with the option of simultaneous (fluorescence) microscopic observation. It is shown that the stretched and surface‐attached RCA products are accessible for hybridization of complementary oligonucleotides, which demonstrates their addressability by complementary base pairing. The long RCA products should be well suited to bridge the gap between biomolecular nanoscale building‐blocks and structures at the micro‐ and macroscale, especially at the single‐molecule level presented here.     

Tunable Confinement for Bridging Single‐Cell Manipulation and Single‐Molecule DNA Linearization

DNA linearization by nanoconfinement has offered a new avenue toward large‐scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single‐cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic‐length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub‐millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single‐cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp‐long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single‐cell, single‐genome analysis.     

Design and Analysis of Localized DNA Hybridization Chain Reactions

Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed‐up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track. The localized DNA hybridization reaction of the proposed system is triggered by a DNA strand which initiates the subsequent self‐assembly. Fluorescence kinetics indicates that the half‐time completion of a localized DNA hybridization chain reaction is six times faster than the same reaction in the absence of the substrate. The proposed system provides one of the first known quantification of the speed‐up of DNA hybridization reactions due to the locality effect.     

Light-induced in situ patterning of DNA-tagged biomolecules and nanoparticles

We present an in situ method for the selective manipulation of DNA-tagged nano-objects such as vesicles or gold colloids in aqueous solution, at neutral pH. The method makes use of the photosensitizer concept found in photodynamic therapy. Here, single-stranded DNA is immobilized onto a surface via the biotin/streptavidin linkage. If the streptavidin is fluorescently labeled, reactive species will be created during laser-induced photobleaching of the label. These reactive species can then completely or partly suppress the DNA hybridization and cause the removal of the streptavidin. The technique thereby enables a dynamic on–off control over surface density of immobilized DNA-tagged nano-objects. Furthermore, combining this in situ manipulation of DNA with prepatterning of single-stranded DNA in the micro and later in the nano range provides a means for the dynamic patterning required for applications in biosensing and nanotechnology.     

Isothermal Hybridization Kinetics of DNA Assembly of Two‐Dimensional DNA Origami

The Watson–Crick base‐pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA‐based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room‐temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple‐scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.     

Surface Modification of Solid‐State Nanopores for Sticky‐Free Translocation of Single‐Stranded DNA

Nanopore technology is one of the most promising approaches for fast and low‐cost DNA sequencing application. Single‐stranded DNA detection is primary objective in such device, while solid‐state nanopores remain less explored than their biological counterparts due to bio‐molecule clogging issue caused by surface interaction between DNA and nanopore wall. By surface coating a layer of polyethylene glycol (PEG), solid‐state nanopore can achieve long lifetime for single‐stranded DNA sticky‐free translocation at pH 11.5. Associated with elimination of non‐specific binding of molecule, PEG coated nanopore presents new surface characteristic as less hydrophility, lower 1/f noise, and passivated surface charge responsiveness on pH. Meanwhile, conductance blockage of single‐stranded DNA is found to be deeper than double‐stranded DNA, which can be well described by a string of blobs model for a quasi‐equilibrium state polymer in constraint space.     

Intramolecularly Protein‐Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity

DNA micro‐ and nanogels—small‐sized hydrogels made of a crosslinked DNA backbone—constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub‐micrometer‐sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base‐pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein‐crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry‐shaped and pearl‐necklace‐like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin–protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization).     

Two‐Dimensional Self‐Organization of an Ordered Au Silicide Nanowire Network on a Si(110)‐16 × 2 Surface

A well‐ordered two‐dimensional (2D) network consisting of two crossed Au silicide nanowire (NW) arrays is self‐organized on a Si(110)‐16 × 2 surface by the direct‐current heating of ≈1.5 monolayers of Au on the surface at 1100 K. Such a highly regular crossbar nanomesh exhibits both a perfect long‐range spatial order and a high integration density over a mesoscopic area, and these two self‐ordering crossed arrays of parallel‐aligned NWs have distinctly different sizes and conductivities. NWs are fabricated with widths and pitches as small as ≈2 and ≈5 nm, respectively. The difference in the conductivities of two crossed‐NW arrays opens up the possibility for their utilization in nanodevices of crossbar architecture. Scanning tunneling microscopy/spectroscopy studies show that the 2D self‐organization of this perfect Au silicide nanomesh can be achieved through two different directional electromigrations of Au silicide NWs along different orientations of two nonorthogonal 16 × 2 domains, which are driven by the electrical field of direct‐current heating. Prospects for this Au silicide nanomesh are also discussed.     

New Developments in Transmission Electron Microscopy for Nanotechnology

High‐resolution transmission electron microscopy (HRTEM) is one of the most powerful tools used for characterizing nanomaterials, and it is indispensable for nanotechnology. This paper reviews some of the most recent developments in electron microscopy techniques for characterizing nanomaterials. The review covers the following areas: in‐situ microscopy for studying dynamic shape transformation of nanocrystals; in‐situ nanoscale property measurements on the mechanical, electrical and field emission properties of nanotubes/nanowires; environmental microscopy for direct observation of surface reactions; aberration‐free angstrom‐resolution imaging of light elements (such as oxygen and lithium); high‐angle annular‐dark‐field scanning transmission electron microscopy (STEM); imaging of atom clusters with atomic resolution chemical information; electron holography of magnetic materials; and high‐spatial resolution electron energy‐loss spectroscopy (EELS) for nanoscale electronic and chemical analysis. It is demonstrated that the picometer‐scale science provided by HRTEM is the foundation of nanometer‐scale technology.     

Probing Adsorption Behaviors of BSA onto Chiral Surfaces of Nanoparticles

Chiral properties of nanoscale materials are of importance as they dominate interactions with proteins in physiological environments; however, they have rarely been investigated. In this study, a systematic investigation is conducted for the adsorption behaviors of bovine serum albumin (BSA) onto the chiral surfaces of gold nanoparticles (AuNPs), involving multiple techniques and molecular dynamic (MD) simulation. The adsorption of BSA onto both L‐ and D‐chiral surfaces of AuNPs shows discernible differences involving thermodynamics, adsorption orientation, exposed charges, and affinity. As a powerful supplement, MD simulation provides a molecular‐level understanding of protein adsorption onto nanochiral surfaces. Salt bridge interaction is proposed as a major driving force at protein–nanochiral interface interaction. The spatial distribution features of functional groups (? COO^?, ? NH₃⁺, and ? CH₃) of chiral molecules on the nanosurface play a key role in the formation and location of salt bridges, which determine the BSA adsorption orientation and binding strength to chiral surfaces. Sequentially, BSA corona coated on nanochiral surfaces affects their uptake by cells. The results enhance the understanding of protein corona, which are important for biological effects of nanochirality in living organisms.     

Sharpening the Thermal Release of DNA from Nanoparticles: Towards a Sequential Release Strategy

Unlike the sharp melting behavior of DNA‐linked nanoparticle aggregates, the melting of DNA strands from individual gold nanoparticles is broad despite the high surface density of bound DNA. Here, it is demonstrated how sharpened melting can be achieved in colloidal nanoparticle systems using branched DNA–doubler structures hybridized with complementary DNA‐doublers bound to the gold nanoparticle. Moreover, sharpened transitions are observed when DNA‐doublers are hybridized with linear DNA‐modified gold nanoparticles. This result suggests that the DNA density on nanoparticles is intrinsically great enough to form cooperative structures with the DNA‐doublers. Finally, by introducing abasic destabilizing groups, the melting temperature of these DNA‐doublers decreases without decreasing the sharpness. Consequently, by varying the temperature, two DNA‐doublers with different stabilities dissociate sequentially from the gold nanoparticle surface, without overlapping and within a narrow temperature window. Owing to the excellent thermal selectivities exhibited by this system, the implementation of DNA‐doublers in sequential photothermal therapies and with other nanomedicine delivery agents that rely on DNA dissociation as the mechanism of selective release is anticipated.     

Tunable Fluorescence from Dye‐Modified DNA‐Assembled Plasmonic Nanocube Arrays

Colloidal crystal engineering with DNA on template‐confined surfaces is used to prepare arrays of nanocube‐based plasmonic antennas and deliberately place dyes with sub‐nm precision into their hotspots, on the DNA bonds that confine the cubes to the underlying gold substrate. This combined top‐down and bottom‐up approach provides independent control over both the plasmonic gap and photonic lattice modes of the surface‐confined particle assemblies and allows for the tuning of the interactions between the excited dyes and plasmonically active antennas. Furthermore, the gap mode of the antennas can be modified in situ by utilizing the solvent‐dependent structure of the DNA bonds. This is studied by placing two dyes, with different emission wavelengths, under the nanocubes and recording their solvent‐dependent emission. It is shown that dye emission not only depends upon the in‐plane structure of the antennas but also the size of the gap, which is regulated with solvent. Importantly, this approach allows for the systematic understanding of the relationship between nanoscale architecture and plasmonically coupled dye emission, and points toward the use of colloidal crystal engineering with DNA to create stimuli responsive architectures, which can find use in chemical sensing and tunable light sources.     

Modulation of Biointeractions by Electrically Switchable Oligopeptide Surfaces: Structural Requirements and Mechanism

Understanding the dynamic behavior of switchable surfaces is of paramount importance for the development of controllable and tailor‐made surface materials. Herein, electrically switchable mixed self‐assembled monolayers based on oligopeptides have been investigated in order to elucidate their conformational mechanism and structural requirements for the regulation of biomolecular interactions between proteins and ligands appended to the end of surface tethered oligopeptides. The interaction of the neutravidin protein to a surface appended biotin ligand was chosen as a model system. All the considerable experimental data, taken together with detailed computational work, support a switching mechanism in which biomolecular interactions are controlled by conformational changes between fully extended (“ON” state) and collapsed (“OFF” state) oligopeptide conformer structures. In the fully extended conformation, the biotin appended to the oligopeptide is largely free from steric factors allowing it to efficiently bind to the neutravidin from solution. While under a collapsed conformation, the ligand presented at the surface is partially embedded in the second component of the mixed SAM, and thus sterically shielded and inaccessible for neutravidin binding. Steric hindrances aroused from the neighboring surface‐confined oligopeptide chains exert a great influence over the conformational behaviour of the oligopeptides, and as a consequence, over the switching efficiency. Our results also highlight the role of oligopeptide length in controlling binding switching efficiency. This study lays the foundation for designing and constructing dynamic surface materials with novel biological functions and capabilities, enabling their utilization in a wide variety of biological and medical applications.     

Shape‐Shifting 3D Protein Microstructures with Programmable Directionality via Quantitative Nanoscale Stiffness Modulation

The ability to shape‐shift in response to a stimulus increases an organism's survivability in nature. Similarly, man‐made dynamic and responsive “smart” microtechnology is crucial for the advancement of human technology. Here, 10–30 μm shape‐changing 3D BSA protein hydrogel microstructures are fabricated with dynamic, quantitative, directional, and angle‐resolved bending via two‐photon photolithography. The controlled directional responsiveness is achieved by spatially controlling the cross‐linking density of BSA at a nanometer lengthscale. Atomic force microscopy measurements of Young's moduli of structures indicate that increasing the laser writing distance at the z‐axis from 100–500 nm decreases the modulus of the structure. Hence, through nanoscale modulation of the laser writing z‐layer distance at the nanoscale, control over the cross‐linking density is possible, allowing for the swelling extent of the microstructures to be quantified and controlled with high precision. This method of segmented moduli is applied within a single microstructure for the design of shape‐shifting microstructures that exhibit stimulus‐induced chirality, as well as for the fabrication of a free‐standing 3D microtrap which is able to open and close in response to a pH change.     

Oligothiophene Assemblies Defined by DNA Interaction: From Single Chains to Disordered Clusters

The organization of conjugated polyelectrolytes (CPEs) interacting with biomolecules sets conditions for the biodetection of biological processes and identity, through the use of optical emission from the CPE. Herein, a well‐defined CPE and its binding to DNA is studied. By using dynamic light scattering and circular dichroism spectroscopy, it is shown that the CPE forms a multimolecule ensemble in aqueous solution that is more than doubled in size when interacting with a small DNA chain, while single chains are evident in ethanol. The related changes in the fluorescence spectra upon polymer aggregation are assigned to oscillator strength redistribution between vibronic transitions in weakly coupled H‐aggregates. An enhanced single‐molecule spectroscopy technique that allows full control of excitation and emission light polarization is applied to combed and decorated λDNA chains. It is found that the organization of combed CPE–λDNA complexes (when dry on the surface) allows considerable variation of CPE distances and direction relative to the DNA chain. By analysis of the polarization data energy transfer between the polymer chains in individual complexes is confirmed and their sizes estimated.     

Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami

DNA origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on DNA origami. We find that the kinetics of hybridization to single-stranded extensions on DNA origami is similar to isolated substrate-immobilized DNA with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to DNA nanostructures for PAINT (points accumulation for imaging in nanoscale topography) imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures.     

High‐Durable AgNi Nanomesh Film for a Transparent Conducting Electrode

Uniform metal nanomesh structures are promising candidates that may replace of indium‐tin oxide (ITO) in transparent conducting electrodes (TCEs). However, the durability of the uniform metal mesh has not yet been studied. For this reason, a comparative analysis of the durability of TCEs based on pure Ag and AgNi nanomesh, which are fabricated by using simple transfer printing, is performed. The AgNi nanomesh shows high long‐term stability to oxidation, heat, and chemicals compared with that of pure Ag nanomesh. This is because of nickel in the AgNi nanomesh. Furthermore, the AgNi nanomesh shows strong adhesion to a transparent substrate and good stability after repeated bending.     

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single‐Base Pairing

Self‐assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl₂, spontaneous reduction of the interparticle distance is observed with TEM and cryo‐electron microscopy. By contrast, when the terminal‐mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA‐functionalized nanoparticle assemblies.     

Vibrational Spectroscopy of Water with High Spatial Resolution

The ability to examine the vibrational spectra of liquids with nanometer spatial resolution will greatly expand the potential to study liquids and liquid interfaces. In fact, the fundamental properties of water, including complexities in its phase diagram, electrochemistry, and bonding due to nanoscale confinement are current research topics. For any liquid, direct investigation of ordered liquid structures, interfacial double layers, and adsorbed species at liquid–solid interfaces are of interest. Here, a novel way of characterizing the vibrational properties of liquid water with high spatial resolution using transmission electron microscopy is reported. By encapsulating water between two sheets of boron nitride, the ability to capture vibrational spectra to quantify the structure of the liquid, its interaction with the liquid‐cell surfaces, and the ability to identify isotopes including H₂O and D₂O using electron energy‐loss spectroscopy is demonstrated. The electron microscope used here, equipped with a high‐energy‐resolution monochromator, is able to record vibrational spectra of liquids and molecules and is sensitive to surface and bulk morphological properties both at the nano‐ and micrometer scales. These results represent an important milestone for liquid and isotope‐labeled materials characterization with high spatial resolution, combining nanoscale imaging with vibrational spectroscopy.     

Directed Assembly of Gold Nanorods by Terminal‐Base Pairing of Surface‐Grafted DNA

Directed assemblies of anisotropic metal nanoparticles exhibit attractive physical and chemical properties. However, an effective methodology to prepare differently directed assemblies from the same anisotropic nanoparticles is not yet available. Gold nanorods (AuNRs) region‐selectively modified with different DNA strands can form side‐by‐side (SBS) and end‐to‐end (ETE) assemblies in a non‐crosslinking manner. When the complementary DNA is hybridized to the surface‐bound DNA, stacking interaction between the blunt ends takes place in the designated regions. Such AuNRs assemble into highly ordered structures, assisted by capillary forces emerging on the substrate surface. Moreover, insertion of a mercury(II)‐mediated thymine–thymine base pair into the periphery of the DNA layer allows selective formation of the SBS or ETE assemblies from the strictly identical AuNRs with or without mercury(II).