Time-Dependent DNA Origami Denaturation by Guanidinium Chloride,Guanidinium Sulfate,and Guanidinium Thiocyanate

Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm₂SO₄), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm₂SO₄ at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm₂SO₄ with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.     

Effect of Ionic Strength on the Thermal Stability of DNA Origami Nanostructures

The stability of DNA origami nanostructures in aqueous media is closely tied to the presence of cations that screen electrostatic inter-helix repulsion. Here, the thermal melting behavior of different DNA origami nanostructures is investigated in dependence on Mg²⁺ concentration and compared to calculated ensemble melting temperatures of the staple strands used in DNA origami folding. Strong deviations of the measured DNA origami melting temperatures from the calculated ones are observed, in particular at high ionic strength where the melting temperature saturates and becomes independent of ionic strength. The degree of deviation between the measured and calculated melting temperatures further depends on the superstructure and in particular the mechanical properties of the DNA origami nanostructures. This indicates that thermal stability of a given DNA origami design at high ionic strength is governed predominantly not by electrostatic inter-helix repulsion but mostly by mechanical strain.     

How We Make DNA Origami

DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know‐how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know‐how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage‐free preparation of DNA origami. These methods are agarose‐gel purification, filtration through molecular cut‐off membranes, PEG precipitation, size‐exclusion chromatography, and ultracentrifugation‐based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.     

In-Situ Configuration Studies on Segmented DNA Origami Nanotubes

One-dimensional nanotubes are of considerable interest in materials and biochemical sciences. A particular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs, templating of other materials into linear arrays and the construction of artificial membrane channels. However, little is known about the structures of assembled DNA nanotubes in solution. Here we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informative in the context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomic force microscopy (AFM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). In particular, the SAXS data revealed important structural information on these DNA nanotubes, such as the in-solution diameters (≈25 nm), which could be obtained only with difficulty by use of other methods. Our results establish SAXS as a reliable structural analysis method for long DNA nanotubes and could assist in the rational design of these structures.     

Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate

DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.     

Real-Time Observation of Superstructure-Dependent DNA Origami Digestion by DNase I Using High-Speed Atomic Force Microscopy

DNA nanostructures have emerged as intriguing tools for numerous biomedical applications. However, in many of those applications and most notably in drug delivery, their stability and function may be compromised by the biological media. A particularly important issue for medical applications is their interaction with proteins such as endonucleases, which may degrade the well-defined nanoscale shapes. Herein, fundamental insights into this interaction are provided by monitoring DNase I digestion of four structurally distinct DNA origami nanostructures (DONs) in real time and at a single-structure level by using high-speed atomic force microscopy. The effect of the solid–liquid interface on DON digestion is also assessed by comparison with experiments in bulk solution. It is shown that DON digestion is strongly dependent on its superstructure and flexibility and on the local topology of the individual structure.     

DNA Origami as Scaffolds for Self-Assembly of Lipids and Proteins

Since first being reported in 2006, the DNA origami approach has attracted increasing attention due to programmable shapes, structural stability, biocompatibility, and fantastic addressability. Herein, we provide an account of recent developments of DNA origami as scaffolds for templating the selfassembly of distinct biocomponents, essentially proteins and lipids, into a diverse spectrum of integrated supramolecular architectures. First, the historical development of the DNA origami concept is briefly reviewed. Next, various applications of DNA origami constructs in controllable directed assembly of soluble proteins are discussed. The manipulation and self-assembly of lipid membranes and membrane proteins by using DNA origami as scaffolds are also addressed. Furthermore, recent progress in applying DNA origami in cryoelectron microscopy analysis is discussed. These advances collectively emphasize that the DNA origami approach is a highly versatile, fast evolving tool that may be integrated with lipids and proteins in a way that meets future challenges in molecular biology and nanomedicine.     

DNA Morphology: Global Alteration of DNA Topological States Induced by Chemotherapeutic Agents and Its Implication in Cancer

The dynamic topological states of chromosomal DNA regulate many cellular fundamental processes universally in all three domains of life, that is, bacteria, archaea, and eukaryotes. DNA-binding proteins maintain the regional and global supercoiling of the chromosome and thereby regulate the chromatin architecture that ultimately influences the gene expression network and other DNA-centric molecular events in various microenvironments and growth phases. DNA-binding small molecules are pivotal weapons for treating a wide range of cancers. Recent advances in single-molecule biophysical tools have uncovered the fact that many DNA-binding ligands not only alter the regional DNA supercoiling but also modulate the overall morphology of DNA. Here we provide insight into recent advances in atomic force microscopy (AFM) acquired DNA structural change induced by therapeutically important mono- and bis-intercalating anticancer agents as well as DNA-adduct-forming anticancer drugs. We also emphasize the growing evidence of the mechanistic relevance of changes in DNA topology in the anticancer cellular responses of DNA-targeting chemotherapeutic agents.     

Nanorings to Probe Mechanical Stress of Single-Stranded DNA Mediated by the DNA Duplex

The interplay between the mechanical properties of double-stranded and single-stranded DNA is a phenomenon that contributes to various genetic processes in which both types of DNA structures coexist. Highly stiff DNA duplexes can stretch single-stranded DNA (ssDNA) segments between the duplexes in a topologically constrained domain. To evaluate such an effect, we designed short DNA nanorings in which a DNA duplex with 160 bp is connected by a 30 nt single-stranded DNA segment. The stretching effect of the duplex in such a DNA construct can lead to the elongation of ssDNA, and this effect can be measured directly using atomic force microscopy (AFM) imaging. In AFM images of the nanorings, the ssDNA regions were identified, and the end-to-end distance of ssDNA was measured. The data revealed a stretching of the ssDNA segment with a median end-to-end distance which was 16% higher compared with the control. These data are in line with theoretical estimates of the stretching of ssDNA by the rigid DNA duplex holding the ssDNA segment within the nanoring construct. Time-lapse AFM data revealed substantial dynamics of the DNA rings, allowing for the formation of transient crossed nanoring formations with end-to-end distances as much as 30% larger than those of the longer-lived morphologies. The generated nanorings are an attractive model system for investigation of the effects of mechanical stretching of ssDNA on its biochemical properties, including interaction with proteins.     

Tip-Induced Charging of Free Standing Semiconductor Nanowires and Carbon Nanotubes

We investigate the distribution of charges injected into one-dimensional nanostructures like semiconductor nanowires and carbon nanotubes. The charges are injected by an atomic force microscope tip and monitored by means of electrostatic force microscopy. We demonstrate that the charges distribute rapidly along the axes of both types of nanostructures. The charges deposited on nanowires are shown to migrate to the substrate on a shorter time scale than those deposited on nanotubes, while the holes migrate even slower than the electrons. This behaviour is attributed to the amount and type of available trap states in the respective nanostructure.     

Formation of a DNA/N‐dodecylated chitosan complex and salt‐induced gene delivery

An N‐dodecylated chitosan (CS‐12) was synthesized from dodecyl bromide and chitosan and was assembled with DNA to form a polyelectrolyte complex (DNA/CS‐12 PEC). UV was used to examine the thermal stability of DNA embedded in PEC. The results indicate that the incorporation of dodecylated chitosan can enhance the thermal stability of DNA. The analysis of AFM image shows that PEC develops a globule‐like structure composed of 40–115 DNA molecules. Dissociation of PEC was investigated by the addition of low molecular weight electrolytes. The added small molecular salts dissociate the PEC, inducing DNA to release. The ability of Mg²⁺ to dissociate PEC is greater compared to that of Na⁺ and K⁺. From AFM images, it can be visualized that DNA remains intact and undamaged due to the protection from DNase offered by alkylated chitosan. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 82: 3391–3395, 2001     

硅纳米线研究进展概述

硅纳米线由于量子限制效应,表现出与体材料不同的物理性质。文章概述了国内外对硅纳米线结构、形貌、成分和力学、电学等物理特性的表征研究的最新进展,揭示了硅纳米线尺寸、表面结构和粒子这三者与性能之间的关系。最后介绍硅纳米线表征研究成果在纳米器件上的应用,并对硅纳米线制备技术和表征技术在未来的发展做了展望。     

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.     

Immobilization of metal nanoparticles on polyurethane membranes: synthesis and electrical properties

Ag and Cu nanoparticles were immobilized into crosslinked polyurethane (PU) membranes by taking advantage of the swelling characteristics of the membranes. The formation, shape and size of the nanoparticles inside the post‐swollen PU membranes were observed by transmission electron microscopy and atomic force microscopy. X‐ray diffraction indicated the presence of the pure Ag and Cu embedded in the amorphous PU matrix. Because of their compatibility, the nanoparticles improved the thermal stability and increased the glass transition temperature of PU. The membranes exhibited interesting conducting behavior with increasing temperature. The metal immobilization increased the ionic conductivity which further increased with temperature, with an activation energy of 0.15 eV indicating a thermally activated conduction mechanism. The optical and electrical properties of these starch‐based membranes can be utilized in the development of novel sensors for biomedical applications. Copyright © 2012 Society of Chemical Industry     

Reconfigurable DNA Nanoswitches for Graphical Readout of Molecular Signals

This study reports a DNA nanoswitch that can be used for visual display of outputs resulting from hybridization events of specific molecular inputs. Conformational changes of the DNA nanoswitch triggered by input DNA strands yield different “pixels” that collectively produce a graphical output on an agarose gel. This system has potential in molecular computation and biosensing approaches in which individual binding results can be translated into macromolecular visual readouts.     

Characterization of metal-polymer interaction forces by AFM for insert molding applications

There is a growing interest in the overmolding of electronics with thermoplastics and the embedding of electronics in 3D printed parts. However long term device reliability requires good adhesion between the metallic surfaces of the electronic components and the overmolding polymer. In order to provide a guide to material selection, interaction forces between tin, a common electronics metallization and six commodity thermoplastics were studied. The force measurements were undertaken using atomic force microscopy (AFM) with probes functionalized with tin particles. The particles were attached to the probes by a novel method using a focused ion beam (FIB) instrument. Highly consistent cantilever deflections at pull-off were obtained, allowing the thermoplastics to be robustly ranked by strength of interaction with tin as: PC > PMMA > PBT > ABS > PS > PA 6. From consideration of possible contributions to the pull-off forces measured, it was concluded the data and the developed AFM tip functionalization technique are likely to be useful in materials selection for electronics overmolding with thermoplastics. The FIB functionalization technique may be useful in the wider context of investigations of other metal-polymer interaction forces, for example with alloys, where other methods of functionalization may be difficult to apply.     

Correlation of exfoliation performance with interlayer cations of montmorillonite in the preparation of two-dimensional nanosheets

Montmorillonite (MMT) can be exfoliated into nanosheets used in a wide range of applications as two-dimensional (2D) material. The exfoliated MMT nanosheets with high diameter–thickness ratio appear to show superior properties in preparation of nanocomposites and other functional materials. In this work, the correlation of exfoliation performance with interlayer cations of MMT in the preparation of 2D nanosheets was investigated. The thickness and lateral diameter of MMT nanosheets were quantitatively measured by atomic force microscopy (AFM) technique. AFM results showed the exfoliated K-MMT had larger lateral diameter and thinner thickness than the exfoliated Ca-MMT under the same exfoliation conditions. Molecular simulation was applied to investigate the interlayer-binding energy (IBE), population analysis and density of states. K-MMT structures tend to have higher in-plane chemical bond intensity than Ca-MMT because of the impact of antibonding. The IBE of K-MMT was higher than that of Ca-MMT after the sorption of water molecules into the neighboring monolayers, indicating that thinner naonosheets tend to be easier obtained from Ca-MMT than K-MMT in liquid exfoliation. These findings might be helpful for the preparation and application of 2D MMTNS through controlling interlayer cation species and the exfoliation properties of MMT.     

Processing and morphology of molecularly imprinted nylon thin films

The characterization of thin, selectively imprinted films of nylon‐6 was performed. Amino acids were used as template molecules. Spin‐cast films were prepared with sizes ranging from 2 μm to 300 nm, depending on the nylon and template concentration in the casting solution. The morphological characteristics of the film surface were examined by atomic force microscopy, and the structure within the films was observed by freeze‐fracture scanning electron microscopy. The film activity was clearly coordinated with the appearance of nanometer‐sized pores both on the surface and within the film. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 2919–2926, 2006     

Visual characterization and quantitative measurement of artemisinin-induced DNA breakage

DNA conformational change and breakage induced by artemisinin, a traditional Chinese herbal medicine, have been visually characterized and quantitatively measured by the multiple tools of electrochemistry, UV-vis absorption spectroscopy, atomic force microscopy (AFM), and DNA electrophoresis. Electrochemical and spectroscopic results confirm that artemisinin can intercalate into DNA double helix, which causes DNA conformational changes. AFM imaging vividly demonstrates uneven DNA strand breaking induced by QHS interaction. To assess these DNA breakages, quantitative analysis of the extent of DNA breakage has been performed by analyzing AFM images. Basing on the statistical analysis, the occurrence of DNA breaks is found to depend on the concentration of artemisinin. DNA electrophoresis further validates that the intact DNA molecules are unwound due to the breakages occur at the single strands. A reliable scheme is proposed to explain the process of artemisinin-induced DNA cleavage. These results can provide further information for better understanding the anticancer activity of artemisinin.     

Effect of the molecular architecture of graft copolymers on the phase morphology and tensile properties of PS/EVA blends

Graft copolymers of poly(ethylene‐co‐vinyl acetate) (EVA) grafted with polystyrene (PS) with different molecular weight and different EVA/PS ratio were prepared by coupling reaction between acyl chloride functionalized PS (PS‐COCl) and hydrolyzed EVA. PS‐COCl with controlled molecular weight was prepared by anionic polymerization of styrene, followed by end capping with phosgene. The effect of the molecular architecture of the graft copolymer on the compatibilization of PS/EVA blends was investigated. Substantial improvement in the elongation at break and ductility was observed using the graft copolymer with PS segments with molecular weight as high as 66,000 g/mol and with a PS proportion equal or higher than EVA. The effect of the compatibilization on the morphology was also investigated by scanning electron microscopy and atomic force microscopy. The blend that presented the highest value of elongation at break also displayed dispersed phase constituted by inclusions of the PS phase inside the EVA particle forming a cocontinuous structure, as observed by AFM. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008