Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy

We introduce herein the use of atomic-force electrochemical microscopy (AFM-SECM) to simultaneously probe locally the conformation and motional dynamics of nanometer-sized single-stranded (ss) and double-stranded (ds) DNA oligonucleotides end-tethered to electrode surfaces. The ss-DNA system studied here consists of a low-density monolayer of (dT)20 oligonucleotides, 5'-thiol end-tethered onto a flat gold surface via a C6 alkyl linker and bearing at their free 3'-end a redox ferrocene label. It is shown that, as a result of the flexibility of the relatively long C6 linker, hinge motion, rather than elastic deformation of the DNA chain, is the major component of the dynamics of both the (dT)20 strand and its post-hybridized (dT-dA)20 duplex. DNA chain elasticity is nevertheless sufficiently contributing to the overall dynamics to result in approximately 4 times slower dynamics for (dT-dA)20 than for (dT)20. Taking advantage of this dissimilar dynamical behavior of ss- and ds-DNA, it is demonstrated that hybridization can be easily locally detected at the scale of approximately 200 molecules by AFM-SECM.     

锂电池电极过程的原位电化学原子力显微镜研究进展

随着人类对能源的使用与存储需求不断增加,高能量密度和高安全性能的二次锂电池体系正在被不断地开发与完善.深入理解充放电过程中锂电池内部电极/电解质界面的电化学过程以及微观反应机理,有利于指导电池材料的优化设计.原位电化学原子力显微镜将原子力显微镜的高分辨表界面分析优势与电化学反应装置相结合,能够在电池运行条件下实现对电极/电解质界面的原位可视化研究,并进一步从纳米尺度上揭示界面结构的演化规律与动力学过程.本文总结了原位电化学原子力显微镜在锂电池电极过程中的最新研究进展,主要包括基于转化型反应的正极过程、固体电解质中间相的动态演化以及固态电池界面演化与失效分析.     

In situ atomic force microscopy of zeolite A dissolution

In the present study, the {100} surface of zeolite A was exposed to a range of solutions and the response was monitored in real-time by means of atomic force microscopy (AFM). The zeolite dissolves by a well-defined layer process that is characterised by uncorrelated dissolution of units that are structurally unconnected and terrace retreat when building units are inter-connected. This process was observed to be coupled with the formation of nano-squares that are stabilized at the zeolite surface for a period before complete dissolution. Theoretical work suggests that three terminating structures are central to understanding the dissolution mechanism. Stripping the surface of the secondary building unit, the single 4-ring, is predicted to be a rate-determining step in dissolution, but this process occurs by removing monomeric rather than oligomeric units.     

On-line electrochemical preconcentration of manganese for graphite furnace atomic absorption spectrometry using a flow-through electrochemical cell

A flow system incorporating a 2-electrode electrochemical microcell with a working electrode made from crushed reticulated vitreous carbon and a graphite furnace AAS instrument was used for the preconcentration and determination of trace amounts of Mn. The sample, rinsing and elution solutions were pneumatically transported through the system. Mn²⁺ ions can be quantitatively deposited both anodically and cathodically at a voltage of +1.5 to + 3 V and –2.5 to –4V, respectively applied to the cell. Samples of 0.1 to 1 ml volume were analyzed within 5–10 min. The limits of detection and determination were 8.7 and 29 pg, respectively. The reproducibility was 1.5 to 5%. The electrochemical behaviour of Mn in the flow system was studied by using a 3-electrode flow-through cell coupled on-line to a flame AAS instrument.On leave from Department of Analytical Chemistry, Slovak Technical University, CS-812 37 Bratislava, Czechoslovakia     

Recent progress in the application of in situ atomic force microscopy for rechargeable batteries

High energy density batteries are urgently required for sustainable life. The intrinsic understanding of the reaction mechanism at the interfaces is essential for the progress. In this short overview, recent advances in rechargeable batteries by in situ atomic force microscopy are summarized, providing nanoscale information on the solid product evolution and metal plating/stripping inside working batteries. Besides, the multifunctional imaging of the morphology along with mechanical and electrical properties can be achieved to assist further interfacial design. Extensive applications of in situ atomic force microscopy are encouraged to explore the electrochemical mechanism and advanced engineering.     

In situ annealing and thickening of single crystals of C294H590 observed by atomic force microscopy

The annealing behavior of twice-folded crystals of the long-chain alkane C294H590 is examined in situ, in real time, by atomic force microscopy (AFM). AFM is capable of following processes in real time provided that the time scale is sufficiently long for several images to be collected during the process. In this paper, we focus on the temperature dependence and the thickened morphology. We are able to investigate where the thickening starts and how this depends on temperature and how melting is influenced by morphology. By following the motion of holes within the crystal, a lower limit for the rate of diffusion of crystalline polyethylene is estimated. We also focus on the substrate effect on the crystal morphology and thickening, using mica, glass, and graphite.     

In‐situ characterization of the early stage of pipeline steel corrosion in bicarbonate solutions by electrochemical atomic force microscopy

An electrochemical atomic force microscope was used to characterize the early stage of corrosion of an X100 pipeline steel in bicarbonate solutions with varied concentrations by synchronous measurements of electrochemical potential of the steel and its topographic evolution with time. Upon immersion of the steel in 0.01 M NaHCO₃ solution, both electrochemical potential and topographic profile are associated with the dissolution of air‐formed oxides present on the steel surface. The potential drops and the surface roughness increases rapidly. When corrosion of the steel occurs, the potential further drops and the surface roughness of the steel increases gradually. As the steel corrosion achieves a steady state, the generation of corrosion products reaches a dynamic equilibrium state. The surface roughness maintain an approximately stable value. In solutions containing increased bicarbonate concentrations, such as 0.1 M and 0.5 M NaHCO₃, the steel can be passivated. The formed passive film can eliminate some surface features and improves the surface roughness. The topographic profile of the steel surface in 0.5 M NaHCO₃ solution is smoother than that in 0.1 M solution. The surface features within 20 nm become eliminated after 4500 s of immersion in 0.1 M NaHCO₃ solution, while larger features within 50 nm in size are eliminated in 0.5 M NaHCO₃ solution in the same time period. Copyright © 2016 John Wiley & Sons, Ltd.     

An in situ atomic force microscopy study of uric acid crystal growth

Kidney stones are heterogeneous polycrystalline aggregates that can consist of several different building blocks. A significant number of human stones contain uric acid crystals as a crystalline component, though the molecular-level growth of this important biomaterial has not been previously well-characterized. In the present study, in situ atomic force microscopy (AFM) is used to investigate the real-time growth on the (100) surface of uric acid (UA) single crystals as a function of fundamental solution parameters. Layer-by-layer growth on UA (100) was found to be initiated at screw dislocation sites and to proceed via highly anisotropic rates which depend on the crystallographic direction. The smallest b-steps exhibited minimum heights corresponding to two molecular layers, while fast-moving c-steps more commonly showed monolayer heights. Growth kinetics measured under a range of flow rates, supersaturation levels, and pH values reveal linear trends in the growth kinetics, with faster growth attained in solutions with higher supersaturation and/or pH. The calculated kinetic parameters for UA growth derived from these experiments are in good agreement with the values reported for other crystal systems.     

Advances in electrochemical detection for probing protein aggregation

Electrochemistry provides an array of methods to investigate protein aggregation and determine biomarkers of neurodenenerative diseases. Biosensors detecting monomeric or oligomeric biomarkers of Alzheimer's disease and Parkinson's disease evolved toward femtomolar, multiplexed detection in blood and biological fluids for less invasive diagnosis. The biosensors also serve as complementary tools in studies investigating putative biomarkers for the assessment of patient's cognitive decline. The study of protein aggregation via the direct electrochemical oxidation focused recently on enhanced sensitivity and on establishing correlations between protein structure and aggregation propensity. Departing from classic approaches, nanopore resistive pulse sensing and single-particle collision electrochemistry enable studying aggregates in solution. Growing applications converge toward accurate evaluation of aggregate populations and method adoption beyond proof of principle.     

Robust electrochemical system for screening single nucleotide polymorphisms

A highly sensitive and selective electrochemical DNA signaling scheme, which identifies the point mutation existing in target DNA sequence, is developed based on the combination of label-free hairpin probe (HP)/DNA endonuclease with zirconia (ZrO(2)) nanoparticle film, representing a promising screening platform for the accurate diagnosis of infections and genetic diseases as well as for environmental and forensic applications.     

Direct imaging and probing of the p-n junction in a planar polymer light-emitting electrochemical cell

A vast array of semiconductor applications relies on the ability to dope the materials by the controlled introduction of impurities in order to achieve desired charge carrier concentration and conduction type. In this way, various functional metal/semiconductor or semiconductor/semiconductor junctions can be constructed for device applications. Conjugated polymers are organic semiconductors that can be electrochemically doped to form a dynamic p-n junction. The electronic structure and even the existence of such a polymer p-n junction had been the subject of intense scrutiny and debate. In this work, the formation of the world's largest frozen polymer p-n junction and its light-emission are visualized. With a pair of micromanipulated probes, we mapped the potential distribution of the p-n junction under bias across the entire interelectrode gap of over 10 mm. Site-selective current-voltage measurements reveal that the polymer junction is a graded p-n junction, with a much more conductive p region than n region.     

Photoswitching behavior of a novel single molecular tip for noncontact atomic force microscopy designed for chemical identification

A tripod molecule with an azobenzene arm was designed as a single molecular tip for noncontact atomic force microscopy (NC-AFM). The azobenzene moiety showed photoisomerization that enabled measurements of the same position of the sample by different tip apexes with different interactions. Photoswitching behavior of the molecule synthesized and adsorbed on Au surfaces was examined and reversible switching between the trans- and cis forms was successfully confirmed by NC-AFM measurements.     

Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

Methods for in situ spectroscopic probing of the synthesis of a zeolite

Unraveling the crystallization mechanism of zeolites remains an increasingly important challenge in chemistry. During the last decade, in situ spectroscopic methods have provided an unprecedented level of detail of the underlying molecular mechanisms and their kinetics. Magnetic resonance, vibrational and X-ray absorption techniques have emerged as principal tools for the in situ observation of crystallization. In this tutorial review, we discuss how these in situ methods have contributed to our understanding of the complex and diverse molecular processes that govern zeolite crystallization.     

Preconcentration of palladium in a flow-through electrochemical cell for determination by graphite furnace atomic absorption spectrometry

An electrochemical preconcentration at a controlled potential on the electrode in a flow-through mode followed by graphite furnace atomic absorption spectrometric (GFAAS) detection is proposed for determination of trace amounts of palladium. After electrolysis the polarization of the electrodes was changed and deposited metal was dissolved electrochemically in the presence of an appropriate stripping reagent. Conditions for the electrodeposition, such as pH of the solutions, a deposition potential, dissolution potential and a composition of stripping solution were optimised. The graphite electrode (GE) and glassy carbon electrode (GCE) were tested for the palladium reduction process. The detection limit of 0.05 ng ml⁻¹ Pd (1 pg) was obtained after palladium preconcentration on the GCE and dissolution with 0.2 mol l⁻¹ thiourea in 0.1 mol l⁻¹ HCl followed by GFAAS detection. The method was applied for the determination of palladium in spiked tap water and road dust samples.     

Ex situ atomic force microscopy analysis of beta-amyloid self-assembly and deposition on a synthetic template

The beta-amyloid (Abeta) deposition, which is the conversion of soluble Abeta peptides to insoluble plaques on a surface, is an essential pathological process in Alzheimer's disease (AD). The identification and characterization of possible environmental factors that may influence amyloid deposition in vivo are important to unveil the underlying etiology of AD. According to the amyloid cascade hypothesis, diffuse plaques are initial and visual deposits in the early event of AD, leading to amyloid plaques. To study amyloid deposition and growth in vitro, we prepared a synthetic template by immobilizing Abeta seeds on an N-hydroxysuccinimide ester-activated solid surface. According to our analysis with an ex situ atomic force microscope, the formation of amyloid plaque-like aggregates was mediated by the interaction between Abeta in a solution and on a synthetic template, suggesting that Abeta oligomers function well as seeds for amyloid deposition. It was observed that insoluble amyloid aggregates formed on the template surface serve as a sink of soluble Abeta in a solution as well as mediate the formation of intermediates in the pathway of amyloid fibrillization in a solution. Relative seeding efficiencies of fresh monomers, oligomers, and fully grown fibrils were analyzed by measuring the deposited plaque volume and its height distribution through atomic force microscopy. The result revealed that oligomeric forms of Abeta act more efficiently as seeds than monomers or fibrils do. Fluorescence spectroscopy with thioflavin T confirmed that amyloid aggregate formation proceeds in a concentration-dependent manner. Analysis with Fourier transform infrared spectroscopy indicated a progressive transition of soluble Abeta42 monomer to amyloid fibrils having antiparallel beta-sheet structure on the template. Furthermore, studies on the interaction between Abeta40 and 42, two major variants of Abeta derived from the amyloid precursor protein, showed that amyloid aggregate formation on the surface was accelerated further by the homogeneous association of soluble Abeta42 onto Abeta42 seeds than by other combinations. A slightly acidic condition was found to be unfavorable for amyloid formation. This study gives insight into understanding the effects of environmental factors on amyloid formation via the use of a synthetic template system.     

In situ Raman imaging of astaxanthin in a single microalgal cell

Raman imaging is shown to be a highly selective and sensitive method of studying in situ and in vivo astaxanthin distribution, concentration and molecular structure in the cyst form of the unicellular microalgae Haematococcus pluvialis.     

Simple test system for single molecule recognition force microscopy

We have established an easy-to-use test system for detecting receptor-ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin-biotin, probably the best characterized receptor-ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6 nm poly(ethylene glycol) (PEG) chain and a functional succinimide group at the other end, was newly synthesized and covalently coupled to amine-functionalized AFM tips. In particular, PEG₈₀₀ diamine was glutarylated, the mono-adduct NH₂-PEG-COOH was isolated by ion exchange chromatography and reacted with biotin succinimidylester to give biotin-PEG-COOH which was then activated as N-hydroxysuccinimide (NHS) ester to give the biotin-PEG-NHS conjugate which was coupled to the aminofunctionalized AFM tip. The motional freedom provided by PEG allows for free rotation of the biotin molecule on the AFM sensor and for specific binding to avidin which had been adsorbed to mica surfaces via electrostatic interactions. Specific avidin-biotin recognition events were discriminated from nonspecific tip-mica adhesion by their typical unbinding force (∼40 pN at 1.4 nN/s loading rate), unbinding length (<13 nm), the characteristic nonlinear force-distance relation of the PEG linker, and by specific block with excess of free d-biotin. The convenience of the test system allowed to evaluate, and compare, different methods and conditions of tip aminofunctionalization with respect to specific binding and nonspecific adhesion. It is concluded that this system is well suited as calibration or start-up kit for single molecule recognition force microscopy.     

Substrate-facilitated assembly of elastin-like peptides: studies by variable-temperature in situ atomic force microscopy

Extended duration in situ variable-temperature atomic force microscopy performed on a series of coacervating hydrophobic peptides based on human elastin revealed a novel multistage surface assembly process. Formation of epitaxially arranged peptide rods was preceded by rapid expansion of a two-dimensional film on the nucleating substrate, a process facilitated by specific hydrophobic peptide-substrate and intrapeptide interactions.     

A new technique for membrane characterisation: direct measurement of the force of adhesion of a single particle using an atomic force microscope

An Atomic Force Microscope (AFM) has been used to quantify directly the adhesive force between a colloid probe and two polymeric ultrafiltration membranes of similar MWCO (4000 Da) but different materials (ES 404 and XP 117, PCI Membrane Systems (UK)). The colloid probe was made from a polystyrene sphere (diameter 11 μm) glued to a V shaped AFM cantilever. Measurements were made in 10⁻² M NaCl solution at pH 8. It was found that the adhesive force at the ES 404 membrane was more than five times greater than that at the XP 117 membrane. As it allows direct quantification of particle/membrane interactions, this technique should be invaluable in the development of new membrane materials and in the elucidation of process behaviour.