Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA

Factors affecting the functionalization of mica with aminosilanes, in particular, aminopropyltriethoxysilane (APTES-mica), formed from the vapor phase have been systematically studied. The relative humidity (RH) during vapor deposition has been varied, and postdeposition treatment through baking has been used, as well as the comparison of mono and trifunctionality, to investigate how optimal surfaces for AFM imaging of DNA are formed. It is found that the stability of the APTES layers is a consequence of lateral polymerization and not covalent attachment to the mica substrate. At low RH (<25%), DNA adopts an open, well-resolved conformation, whereas at >25% RH, DNA surface-induced condensation occurs. Contact mode AFM scratching experiments show that two main structures of the silane layer exist at different humidity: a monolayer exists at RH < 25%, and a bilayer structure exists at RH > 25%. Finally, structural changes that these two layer types undergo after baking at 150 degrees C were investigated by AFM and X-ray photoelectron spectroscopy (XPS), and these now prevented DNA from binding to the APTES-mica, except in the presence of Mg(II) ions.     

Interaction of human plasma fibrinogen with commercially pure titanium as studied with atomic force microscopy and X-ray photoelectron spectroscopy

The surface of a biomaterial interacts with the body fluid upon implantation in the human body. The biocompatibility of a material is strongly influenced by the adsorption of proteins onto the surface. Titanium is frequently used as a biomaterial for implants in orthopedics and cardiovascular devices. Understanding the biocompatibility is very important to improve implants. The surface chemistry of an implant material and its influence on the interaction with body fluid is crucial in that perspective. The main goal of this study was to investigate the conformation of human plasma fibrinogen (HPF) adsorbed on commercially pure titanium (CP Ti) on a molecular level by means of ex situ atomic force microscopy (AFM). With X-ray photoelectron spectroscopy combined with argon ion beam depth profiling, it was shown that the oxide layer present at the surface was mainly composed of TiO2, with a small percentage of Ti2O3. Ex situ AFM imaging showed the conformation of HPF on CP Ti. Single molecules and aggregates of fibrinogen were observed. The trinodular structure of single HPF molecules (two spherical D domains at the distal ends of the extended molecule and the central spherical E domain) adsorbed onto CP Ti was visualized. Aggregate formation through the connection of the D domains of the HPF molecules was observed on CP Ti. The alphaC domains of HPF were not visible on CP Ti. The ex situ AFM images indicated conformational changes of HPF upon adsorption onto CP Ti. The conformation of the adsorbed HPF molecules was different on mica and titanium. The difference in wettability between both substrates caused a larger spread of the protein on the CP Ti surface and thus resulted in a larger perturbation to the native structure of HPF as compared to mica.     

Atomic force microscopy study of beta-substituted-T7 oligothiophene films on mica: mechanical properties and humidity-dependent phases

The structural and mechanical properties of Langmuir-Blodgett monolayer and multilayer films of 3",4"-didecyl-5,2'; 5',2"; 5",2'; 5',2"; 5",2''; 5'',2"-heptathiophene-4'-acetic acid on mica have been studied by atomic force microscopy (AFM) as a function of humidity, temperature, and applied force. The molecules orient with the carboxylic acid group pointing toward the mica surface and expose the alkyl side chains to the air interface. As the load applied by the AFM tip increases, the film is compressed easily from an initial height of 2 to 1.2 nm. After compression the films can support much higher loads without loss of height. The state of aggregation of the molecules was found to be sensitive to the environmental humidity, which induced reversible changes. Annealing the samples with monolayer or multilayer films resulted in irreversible changes when the temperature exceeded approximately 100 degrees C.     

Anionic polyelectrolyte adsorption on mica mediated by multivalent cations: a solution to DNA imaging by atomic force microscopy under high ionic strengths

Adsorption of DNA molecules on mica, a highly negatively charged surface, mediated by divalent or trivalent cations is considered. By analyzing atomic force microscope (AFM) images of DNA molecules adsorbed on mica, phase diagrams of DNA molecules interacting with a mica surface are established in terms of concentrations of monovalent salt (NaCl) and divalent (MgCl2) or multivalent (spermidine, cobalt hexamine) salts. These diagrams show two transitions between nonadsorption and adsorption. The first one arises when the concentration of multivalent counterions is larger than a limit value, which is not sensitive to the monovalent salt concentration. The second transition is due to the binding competition between monovalent and multivalent counterions. In addition, we develop a model of polyelectrolyte adsorption on like-charged surfaces with multivalent counterions. This model shows that the correlations of the multivalent counterions at the interface between DNA and mica play a critical role. Furthermore, it appears that DNA adsorption takes place when the energy gain in counterion correlations overcomes an energy barrier. This barrier is induced by the entropy loss in confining DNA in a thin adsorbed layer, the entropy loss in the interpenetration of the clouds of mica and DNA counterions, and the electrostatic repulsion between DNA and mica. The analysis of the experimental results provides an estimation of this energy barrier. We then discuss some important issues, including DNA adsorption under physiological conditions.     

Conformational change in an isolated single synthetic polymer chain on a mica surface observed by atomic force microscopy

The random coil conformation of an isolated conventional synthetic polymer chain was clearly imaged by atomic force microscopy (AFM). The sample used was a poly(styrene)-block-poly(methyl methacrylate) diblock copolymer. A very dilute solution of the copolymer with benzene was spread on a water surface. The structure thus formed on water was subsequently transferred and deposited onto mica at various surface pressures and observed under AFM. The AFM images obtained with films deposited at a low surface pressure (<0.1 mN/m) showed a single polystyrene (PS) block chain aggregated into a single PS particle with a single poly(methyl methacrylate) (PMMA) block chain emanating from the particle. Immediately after the deposition, the single PMMA block chain aggregated to form a condensed monolayer around the polystyrene particles. However, after exposing the deposited film to highly humid air for 1 day, the PMMA chains spread out so that the single PMMA block chain could be identified as a random coil on the substrate. The thin water layer formed on the mica substrate in humid air may enable the PMMA block chain to be mobilized on the substrate, leading to the conformational rearrangement from the condensed monolayer conformation to an expanded and elongated coil. The elongation of the PMMA chain was highly sensitive to the humidity; the maximum elongation was obtained at 79% relative humidity. The elongation was a slow process and took about 20 h.     

Nanoscale Wetting of Single Viruses

The epidemic spread of many viral infections is mediated by the environmental conditions and influenced by the ambient humidity. Single virus particles have been mainly visualized by atomic force microscopy (AFM) in liquid conditions, where the effect of the relative humidity on virus topography and surface cannot be systematically assessed. In this work, we employed multi-frequency AFM, simultaneously with standard topography imaging, to study the nanoscale wetting of individual Tobacco Mosaic virions (TMV) from ambient relative humidity to water condensation (RH > 100%). We recorded amplitude and phase vs. distance curves (APD curves) on top of single virions at various RH and converted them into force vs. distance curves. The high sensitivity of multifrequency AFM to visualize condensed water and sub-micrometer droplets, filling gaps between individual TMV particles at RH > 100%, is demonstrated. Dynamic force spectroscopy allows detecting a thin water layer of thickness ~1 nm, adsorbed on the outer surface of single TMV particles at RH < 60%.     

Ru(TAP)3]2+-photosensitized DNA cleavage studied by atomic force microscopy and gel electrophoresis: a comparative study

Topological modifications of plasmid DNA adsorbed on a variety of surfaces were investigated by using atomic force microscopy (AFM). On mica modified with 3-aminopropyltriethoxysilane (APS) or poly-L-lysine, the interaction between the plasmid DNA and the surface "freezes" the plasmid DNA conformation deposited from solution, and the AFM images resemble the projection of the three-dimensional conformation of the plasmid DNA in solution. Modified mica with low concentrations of Mg(2+) leads to a decrease in the interaction strength between plasmid DNA and the substrate, and the AFM images reflect the relaxed or equilibrium conformation of the adsorbed plasmid DNA. Under these optimized deposition conditions, topological modifications of plasmid DNA were produced under irradiation in the presence of [Ru(TAP)(3)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene), which is a non-intercalating complex, and were followed as a function of illumination time. The observed structural changes correlate well with the conversion of the supercoiled covalently closed circular form (ccc form) into the open circular form (oc form), induced by a single-strand photocleavage. The AFM results obtained after fine-tuning of the plasmid DNA-substrate interaction compare well with those observed from gel electrophoresis, indicating that under the appropriate deposition conditions, AFM is a reliable technique to investigate irradiation-induced topological changes in plasmid DNA.     

Nanostructure formation in polymer thin films influenced by humidity

The influence of relative humidity (RH) during the film preparation on the surface morphology and on the material distribution of the resulting technical polymer blend films consisting of poly (methyl methacrylate) (PMMA) and poly (vinyl butyral) (PVB) is investigated by atomic force microscopy. Both pure polymers and polymer blends with different compositions of PVB/PMMA dissolved in tetrahydrofuran (THF) were used. Polymer films prepared under dry conditions (RH < 20%) are compared with those that have the same polymer composition but were prepared under increased humidity conditions (RH > 80%). The films consisting of the pure polymers showed a nonporous surface morphology for low‐humidity preparation conditions, whereas high‐humidity preparation conditions lead to porous PVB and PMMA films, respectively. These pores are explained as the result of a breath figure formation. In the case of the polymer blend films containing both polymers, porous or phase‐separated surface structures were observed even at low‐humidity conditions. A superposition of the effects of phase separation and breath figure formation is observed in the case of polymer blend films prepared under high‐humidity conditions. Atomic force microscopy (AFM) images taken before and after the treatment with ethanol as a selective solvent for PVB indicate that PMMA is deposited on top of a PVB layer in the case of the low‐humidity preparation process whereas for high‐humidity conditions the silicon substrate is covered with a PMMA film. Copyright © 2006 John Wiley & Sons, Ltd.     

Humidity-dependent surface tension measurements of individual inorganic and organic submicrometre liquid particles

Surface tension, an important property of liquids, is easily measured for bulk samples. However, for droplets smaller than one micron in size, there are currently no reported measurements. In this study, atomic force microscopy (AFM) and force spectroscopy have been utilized to measure surface tension of individual submicron sized droplets at ambient pressure and controlled relative humidity (RH). Since the surface tension of atmospheric aerosols is a key factor in understanding aerosol climate effects, three atmospherically relevant systems (NaCl, malonic and glutaric acids) were studied. Single particle AFM measurements were successfully implemented in measuring the surface tension of deliquesced particles on the order of 200 to 500 nm in diameter. Deliquesced particles continuously uptake water at high RH, which changes the concentration and surface tension of the droplets. Therefore, surface tension as a function of RH was measured. AFM based surface tension measurements are close to predicted values based on bulk measurements and activities of these three chemical systems. Non-ideal behaviour in concentrated organic acid droplets is thought to be important and the reason for differences observed between bulk solution predictions and AFM data. Consequently, these measurements are crucial in order to improve atmospheric climate models as direct measurements hitherto have been previously inaccessible due to instrument limitations.     

Time-resolved chloroquine-induced relaxation of supercoiled plasmid DNA

Herein, we report on the in vitro change of DNA conformation of plasmids bound to a 3-aminopropyl-modified mica surface and monitoring the events by atomic force microscopy (AFM) imaging under near physiological conditions. In our study, we used an intercalating drug, chloroquine, which is known to decrease the twist of the double helix and thus altered the conformation of the whole DNA. During our experiments, a chloroquine solution was added while imaging a few highly condensed plasmid nanoparticles in solution. AFM images recorded after the drug addition clearly show a time-resolved relaxation of these bionanoparticles into a mixture of loose DNA strands.     

Initial stages of water adsorption on NaCl (100) studied by scanning polarization force microscopy

Scanning polarization force microscopy was used to study the topography, polarizability, and contact potential of cleaved NaCl(100) as a function of the relative humidity (RH) between < 5% and 40%. In this humidity range there are reversible changes in surface potential and polarizability, while large scale modifications in step topography and irreversible ion redistribution occur above 40% RH. In dry conditions the surface contact potential was more negative near atomic steps than over flat terraces. As humidity was increased, changes were observed in the local polarizability of the steps due to ionic solvation, and the contact potential of the terraces became more negative. At 40% RH surface-potential differences between steps and terraces could no longer be detected. These results are interpreted in terms of preferential anion solvation, initially localized near steps, and later spreading over the entire surface.     

Investigation of surface changes on mica induced by atomic force microscopy imaging under liquids

Surface changes on muscovite mica induced by tip-surface interactions in atomic force microscopy (AFM) experiments under liquids are described. Investigations have been performed with AFM operated both in contact mode (CM-AFM) and in tapping mode (TM-AFM). Additionally, force-distance measurements have been carried out. In contrast to CM-AFM pronounced surface changes can be observed in TM-AFM experiments. However, TM-AFM images of areas previously scanned in contact mode show that imaging in contact mode changes the surface, too. An evaluation of force-distance measurements reveals that these changes depend on the adhesive interaction between tip and sample, which in turn strongly depends on the surrounding medium. The artefact can be avoided by changing the pH-value of the medium or by working with mixtures of ethanol and water. This greatly enhances the applicability of TM-AFM for in-situ investigation of surface processes on mica, which is a frequently used substrate for many technological and biological applications.     

Fabrication of a Biocompatible Mica/Gold Surface for Tip-Enhanced Raman Spectroscopy

Tip-enhanced Raman spectroscopy (TERS) is a promising technique for structural studies of biological systems and biomolecules, owing to its ability to provide a chemical fingerprint with sub-diffraction-limit spatial resolution. This application of TERS has thus far been limited, due to difficulties in generating high field enhancements while maintaining biocompatibility. The high sensitivity achievable through TERS arises from the excitation of a localized surface plasmon resonance in a noble metal atomic force microscope (AFM) tip, which in combination with a metallic surface can produce huge enhancements in the local optical field. However, metals have poor biocompatibility, potentially introducing difficulties in characterizing native structure and conformation in biomolecules, whereas biocompatible surfaces have weak optical field enhancements. Herein, a novel, biocompatible, highly enhancing surface is designed and fabricated based on few-monolayer mica flakes, mechanically exfoliated on a metal surface. These surfaces allow the formation of coupled plasmon enhancements for TERS imaging, while maintaining the biocompatibility and atomic flatness of the mica surface for high resolution AFM. The capability of these substrates for TERS is confirmed numerically and experimentally. We demonstrate up to five orders of magnitude improvement in TERS signals over conventional mica surfaces, expanding the sensitivity of TERS to a wide range of non-resonant biomolecules with weak Raman cross-sections. The increase in sensitivity obtained through this approach also enables the collection of nanoscale spectra with short integration times, improving hyperspectral mapping for these applications. These mica/metal surfaces therefore have the potential to revolutionize spectromicroscopy of complex, heterogeneous biological systems such as DNA and protein complexes.     

Conformation and distribution of groups on the surface of amphiphilic polyether-co-polyester dendrimers: effect of molecular architecture

Amphiphilic polyester-co-polyether (PEPE) dendrimers synthesized from poly(ethylene glycol) (PEG) were examined to understand the influence of alterations in the architecture of dendrimers on their conformation at interfaces and distribution of various groups on their surface. Effect of changes in the number of branching points, type of terminal functional groups and generation of dendrimer was primarily evaluated. Dendrimers were deposited on mica by spin coating at 0.1 mg/mL. Tapping mode atomic force microscopy (AFM) was employed for the visualization of dendrimer topographies while, X-ray photoelectron spectroscopy (XPS), AFM phase and force imaging were used as the tools for characterization of their surfaces. Individual dendrimer molecules could be imaged by AFM, which showed that they are round or oval in topography. Dendrimers were also flattened on mica but the extent of flattening differed with the chemical structure; for instance, third generation dendrimers were more flattened than second generation dendrimers whereas, dendrimers with higher number of branches had greater height above the mica surface. Hydrophilic and hydrophobic groups present towards the aerial interface existed in distinct zones rather than being distributed randomly, except in dendrimer with higher number of branches. The percentage of various hydrophobic groups on the surface of dendrimer was enhanced by increase in the number of branches but, was lowered by the presence of hydroxyl groups as the pendant terminal groups. Furthermore, the core of dendrimers was not always located towards the centre, its position was found to be altered by the number of branching points, type of terminal functional groups and the generation of dendrimer.     

Atomic force microscopy studies on DNA structural changes induced by vincristine sulfate and aspirin.

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.     

Visualization of a protein-protein interaction at a single-molecule level by atomic force microscopy

Atomic force microscopy is unmatched in terms of high-resolution imaging under ambient conditions. Over the years, substantial progress has been made using this technique to improve our understanding of biological systems on the nanometer scale, such as visualization of single biomolecules. For monitoring also the interaction between biomolecules, in situ high-speed imaging is making enormous progress. Here, we describe an alternative ex situ imaging method where identical molecules are recorded before and after reaction with a binding partner. Relocation of the identical molecules on the mica surface was thereby achieved by using a nanoscale scratch as marker. The method was successfully applied to study the complex formation between von Willebrand factor (VWF) and factor VIII (FVIII), two essential haemostatic components of human blood. FVIII binding was discernible by an appearance of globular domains appended to the N-terminal large globular domains of VWF. The specificity of the approach could be demonstrated by incubating VWF with FVIII in the presence of a high salt buffer which inhibits the interaction between these two proteins. The results obtained indicate that proteins can maintain their reactivity for subsequent interactions with other molecules when gently immobilized on a solid substrate and subjected to intermittent drying steps. The technique described opens up a new analytical perspective for studying protein-protein interactions as it circumvents some of the obstacles encountered by in situ imaging and other ex situ techniques.

The AFM observation of linear chain and crystalline conformations of ultrahigh molecular weight polyethylene molecules on mica and graphite

Atomic force microscopy (AFM) has been applied to visualize expanded linear chain and compact crystalline conformations of ultrahigh molecular weight polyethylene (PE) molecules deposited on mica and graphite from diluted solutions at elevated temperatures. Isolated PE chains are visualized on mica with the apparent negative AFM height and the contour length much shorter than the molecular length. The chain conformations have both the kinked random‐coil sites and the sites of the unexpectedly large two‐dimensional expansion. The crystalline conformations on mica are small single‐molecule rod‐like nanocrystallites and the isolated block‐type “edge‐on” nanolamellae comprising several PE molecules. Noticeable fluctuations of the fold length in the range of approximately 10–20 nm around the averaged value of about 15 nm are observed for nanocrystallites and on tips of some nanolamellae. The explanation of the experimentally observed features of chain surface conformations on mica is proposed. It implies the immobilization of PE molecules in the nm‐thickness salt layer formed on mica surface at ambient conditions after PE deposition and the presence along the chain of multiple expanded chain folds. Only isolated lamellae and lamellar domains of a monolayer height are observed on graphite samples. The substrate/polymer epitaxial incommensurability important for the observation of the PE linear chain surface conformations is discussed from the comparison of the results obtained for mica and graphite, the coil‐to‐crystal intramolecular transformation is assumed to be inhibited on mica surface. The slow disintegration of the original gel structure of PE stock‐solution used for the high‐temperature depositions was found to result in the characteristic large‐scale morphological heterogeneity of the samples. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 766–777, 2010     

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

We demonstrate the single‐molecule imaging of the catalytic reaction of a Zn²⁺‐dependent DNAzyme in a DNA origami nanostructure. The single‐molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high‐speed atomic force microscopy (AFM). This nanostructure‐based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single‐molecule level.     

液体环境单分子免疫球蛋白G的原子力显微镜高分辨成像

原子力显微镜技术( AFM)具有纳米级高分辨成像能力,是研究生物大分子结构和功能的重要工具之一。制备合适的样品是获取高分辨成像的关键要素。本研究结合DNA折纸技术,将抗原分子修饰在DNA折纸上,通过分子识别作用,抗体分子与抗原分子特异性结合,形成由DNA折纸和抗原抗体复合物构成的纳米结构。利用DNA折纸在云母表面上的吸附特点,使得抗体分子选择性地吸附在衬底表面上,由此获得了液体环境中的单个地高辛抗体免疫球蛋白G( IgG)分子的“Y”超微结构形貌。本方法简单、方便,为AFM在单分子水平上检测和表征生物分子结构和功能提供帮助。     

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.