Thermal properties and influence of orientation on crystalline morphologies in stereoblock polypropylene and related elastomers

Atomic force microscopy (AFM), small angle X‐ray scattering (SAXS), temperature modulated differential scanning calorimetry (TMDSC), variable heating rate DSC, an independent rapid heating rate method for melting points, and cyclic mechanical testing were used to study semicrystalline thermoplastic elastomeric polypropylenes (ELPPs) and related semicrystalline polyolefins including ethylene copolymers. Low crystallinity (ca., 9 and 15%) ELPP samples were studied by AFM in the nonoriented and melt‐oriented states. AFM images taken as a function of time after quenching of a melt‐drawn and highly nucleated film resolved details of secondary crystallization involving lateral growth on the ordered row‐nucleated structures. For nonoriented films, isothermal melt crystallization at high temperatures (110 °C) led to similar features for the two ELPPs. The dominant crystalline morphology studied by AFM consisted of small (several nm in width) granular crystallites organized into immature but large spherulites spanning tens of microns. A striking cross‐hatch morphology was detected in regions of the surface in 110 °C crystallized samples, which is contrasted with melt‐drawn films where row nucleated structures dominated the morphology in the film under no external stress. AFM was also used to monitor the morphological changes that occurred as the films were stretched at 25 °C. Break‐down of lamellae was observed, resulting in oriented narrow fibrils. Cyclic stress‐strain curves showed the expected result where lower crystallinity ELPPs had higher recoverable levels of set after both 100 and 500% elongation. TMDSC was used to resolve the broad melting and recrystallization regions in these low to medium crystallinity ELPP systems, and to contrast the results with ethylene copolymers. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Effect of protein solution components in the adsorption of Herbaspirillum seropedicae GlnB protein on mica

The adsorption of proteins and its buffer solution on mica surfaces was investigated by atomic force microscopy (AFM). Different salt concentration of the Herbaspirillum seropedicae GlnB protein (GlnB-Hs) solution deposited on mica was investigated. This protein is a globular, soluble homotrimer (36 kDa), member of PII-like proteins family involved in signal transducing in prokaryote. Supramolecular structures were formed when this protein was deposited onto bare mica surface. The topographic AFM images of the GlnB-Hs films showed that at high salt concentration the supramolecular structures are spherical-like, instead of the typical doughnut-like shape for low salt concentration. AFM images of NaCl and Tris from the buffer solution showed structures with the same pattern as those observed for high salt protein solution, misleading the image interpretation. XPS experiments showed that GlnB protein film covers the mica surface without chemical reaction.     

Investigating the morphology and mechanical properties of blastomeres with atomic force microscopy

Atomic force microscopy (AFM) was used to directly investigate the morphology and mechanical properties of blastomeres during the embryo development. With AFM imaging, the surface topography of blastomeres from two‐cell, four‐cell, and eight‐cell stages was visualized, and the AFM images clearly revealed the blastomere's morphological changes during the different embryo developmental stages. The section measurements of the AFM topography images of the blastomeres showed that the axis of the embryos nearly kept constant during the two‐cell, four‐cell, and eight‐cell stages. With AFM indenting, the mechanical properties of living blastomeres from several embryos were measured quantitatively under physiological conditions. The results of mechanical properties measurements indicated that the Young's modulus of the two blastomeres from two‐cell embryo was different from each other, and the four blastomeres from the four‐cell embryo also had variable Young's modulus. Besides, the blastomeres from two‐cell embryos were significantly harder than blastomeres from four‐cell embryos. These results can improve our understanding of the embryo development from the view of cell mechanics. Copyright © 2013 John Wiley & Sons, Ltd.     

Three-dimensional morphological characterization of optic nerve fibers by atomic force microscopy and by scanning electron microscopy.

A comparative study of scanning electron microscopy (SEM) and atomic force microscopy (AFM) imaging of the healthy human optic nerve was carried out to determine the similarities and the differences. In this study we compared the fine optic nerve structures as observed by SEM and AFM. The fibers of the right optic nerve of a 61-year-old man show different arrangements in transverse sections taken from the same individual 5 mm central to the optic canal and 5 mm peripheral to the optic chiasma; this difference can be recognized by light microscopy (LM), SEM, and AFM. AFM revealed such typical optic nerve fibers (taken from a point 5 mm central to the optic canal) with annular and longitudinal orientations, which were not visible by SEM in this form. By contrast, LM and SEM visualized other structures, such as pia mater and optic nerve fibers loosely arranged in bundles, none of which was visualized by AFM. The images, however, taken 5 mm peripheral from the optic chiasma show shapeless nerve fibers having a wavy course. Our results reveal that more detailed information on optic nerve morphology is obtained by exploiting the advantages of both SEM and AFM. These are the first SEM and AFM images of healthy human optic nerve fibers, containing clear representations of the three dimensions of the optic nerve.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

Subcellular features revealed on unfixed rat brain sections by phase imaging

For sectioned biologic tissues, atomic force microscopy (AFM) topographic images alone hardly provide adequate information leading to revealing biological structures. We demonstrate that phase imaging in amplitude-modulation AFM is a powerful tool in mapping structures present on the surface of unfixed rat brains sections. The contrast in phase images is originated from the difference in mechanical properties between biological structures. Visualization of the native state of biological structures by way of their mechanical properties provides a complementary technique to more traditional imaging techniques such as optical and electron microscopy.     

Amphiphilic and hydrophobic surface patterns generated from hyperbranched fluoropolymer/linear polymer networks: Minimally adhesive coatings via the crosslinking of hyperbranched fluoropolymers

Hyperbranched fluoropolymers (HBFPs), based on benzyl ether linkages and having a large number of pentafluorophenyl chain ends, were crosslinked by a reaction with diamino-terminated poly(ethylene glycol) (PEG) or diamino-terminated poly(dimethyl siloxane) (PDMS) to form hyperbranched–linear copolymer networks of different compositions, structures, and properties. The crosslinking reactions involved the nucleophilic aromatic substitution of the pentafluorophenyl para-fluorines of HBFP by the amine functionalities of the respective telechelic linear segments. The contact angles, differential scanning calorimetry, thermogravimetric analysis, tensile measurements, and atomic force microscopy (AFM) were used to characterize the resulting network film samples. The surface wettability of the crosslinked materials was affected by the nature and amount of the linear polymer crosslinking agent employed. Amphiphilic polymer networks were formed by the incorporation of diamino-terminated PEG as a crosslinker, whereas diamino-terminated PDMS produced polymer networks of a hydrophobic character. The mechanical properties improved upon crosslinking, as measured by tensile testing. The mechanical integrity of the films was also found to improve upon crosslinking, as measured by AFM machining protocols. The AFM images revealed topographical morphologies that appeared to be the result of phase segregation of HBFP from PEG or PDMS; the dimensions of the phase-segregated domains were dependent on the stoichiometry of HBFP to the linear polymer and the thickness of the coating. As the content of PEG increased, fouling by human fibrinogen, used as a model protein, decreased. Further studies are in progress to determine the effects of the surface composition, morphology, and topography on the biofouling characteristics. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3531–3540, 2003     

Structural study of DNA condensation induced by novel phosphorylcholine-based copolymers for gene delivery and relevance to DNA protection

Poly[2-(dimethylamino)ethyl methacrylate-b-2-methacryloyloxyethyl phosphorylcholine] (DMA-MPC) is currently under investigation as a new vector candidate for gene therapy. The DMA block has been previously demonstrated to condense DNA effectively. The MPC block contains a phosphorylcholine (PC) headgroup, which can be found naturally in the outside of the cell membrane. This PC-based polymer is extremely hydrophilic and acts as a biocompatible steric stabilizer. In this study, we assess in detail the morphologies of DNA complexes obtained using the diblock copolymer series DMA(x)MPC30 (where the mean degree of polymerization of the MPC block was fixed at 30 and the DMA block length was systematically varied) using transmission electron microscopy (TEM) and liquid atomic force microscopy (AFM). Both techniques indicate more compact complex morphologies (more efficient condensation) as the length of the cationic DMA block increases. However, the detailed morphologies of the DMA(x)MPC30-DNA complexes observed by TEM in vacuo and by AFM in aqueous medium are different. This phenomena is believed to be related to the highly hydrophilic nature of the MPC block. TEM studies revealed that the morphology of the complexes changes from loosely condensed structures to highly condensed rods, toroids, and oval-shaped particles as the DMA moiety increases. In contrast, morphological changes from plectonemic loops to flower-like and rectangular block-like structures, with an increase in highly condensed central regions, are observed by in situ AFM studies. The relative population of each structure is clearly dependent on the polymer molecular composition. Enzymatic degradation assays revealed that only the DMA homopolymer provided effective DNA protection against DNase I degradation, while other highly condensed copolymer complexes, as judged from TEM and gel electrophoresis, only partially protected the DNA. However, AFM images indicated that the same highly condensed complexes have less condensed regions, which we believe to be the initiation sites for enzymatic attack. This indicates that the open structures observed by AFM of the DNA complexation by the DMA(x)MPC30 copolymer series are closer to in vivo morphology when compared to TEM.     

Quantitative study of filled rubber microstructure by optical and atomic force microscopy

A comprehensive approach is proposed for studying the microstructure of filled rubbers by optical and atomic force microscopy (AFM). The optical results are found to be dependent on the illumination angle. Algorithms based on the mathematical morphology are developed for the processing of optical images (removing scratches, identifying agglomerates). AFM-images are treated by a segmentation method which separates a continuous surface into segments that match filler. Parameters of secondary filler structures and the size of an area of homogeneous filler dispersion are obtained from the analysis of the segmented images. Seven carbon black filled rubbers with different mixing times are investigated. The combination of AFM with optical imaging techniques makes it possible to perform a quantitative structural analysis at scales from tens of nanometers to tens of microns, and to establish the relationship between the mixing time and the filler microstructure over the whole range of filler peculiarities.     

Synthesis and characterization of a poly(GMA)‐graft‐poly(Z‐L‐lysine) graft copolymer with a rod‐like structure

This study applied the macromonomers and glycidyl methacrylate (GMA) to synthesize a series of the graft copolymers, poly(GMA)‐graft‐poly(Z‐L ‐lysine), and investigated the conformation of the graft copolymer. The graft copolymers were synthesized with different GMA monomer ratios (28 to 89%) and different degrees of polymerization (DP) (8 to 15) of the poly(Z‐L ‐lysine) side chain to analyze secondary structure relationships. Atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), and both wide angle and small angle X‐ray scattering spectroscopy (WAXS, SAXS) were used to investigate the relationship between the microstructure and conformation of the graft copolymers and the different monomer ratios and side chain DP. In AFM images, n8‐G89 (the graft copolymer containing 89% GMA units and the macromonomer DP is 8) showed tiny and uniform rod‐like structures, and n14‐G43 (the graft copolymer containing 43% GMA units and the macromonomer DP is 14) showed uniform rod‐like structures. FTIR spectra of the graft copolymers showed that the variations of α‐helix and β‐sheet secondary structures in the graft copolymers relate to the monomer ratios of the graft copolymers. However, the X‐ray scattering patterns indicated that the graft copolymer conformations were mainly dependent on the poly(Z‐L ‐lysine) side chain length, and these results were completely in accordance with the AFM images. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4655–4669, 2009     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.     

Surface‐Charge Differentiation of Streptavidin and Avidin by Atomic Force Microscopy–Force Spectroscopy

Chemical information can be obtained by using atomic force microscopy (AFM) and force spectroscopy (FS) with atomic or molecular resolution, even in liquid media. The aim of this paper is to demonstrate that single molecules of avidin and streptavidin anchored to a biotinylated bilayer can be differentiated by using AFM, even though AFM topographical images of the two proteins are remarkably alike. At physiological pH, the basic glycoprotein avidin is positively charged, whereas streptavidin is a neutral protein. This charge difference can be determined with AFM, which can probe electrostatic double‐layer forces by using FS. The force curves, owing to the electrostatic interaction, show major differences when measured on top of each protein as well as on the lipid substrate. FS data show that the two proteins are negatively charged. Nevertheless, avidin and streptavidin can be clearly distinguished, thus demonstrating the sensitivity of AFM to detect small changes in the charge state of macromolecules.     

High-performance transformation of protein structure representation from internal to Cartesian coordinates

We present a highly parallel algorithm to convert internal coordinates of a polymeric molecule into Cartesian coordinates. Traditionally, converting the structures of polymers (e.g., proteins) from internal to Cartesian coordinates has been performed serially, due to an inherent linear dependency along the polymer chain. We show this dependency can be removed using a tree-based concatenation of coordinate transforms between segments, and then parallelized efficiently on graphics processing units (GPUs). The conversion algorithm is applicable to protein engineering and fitting protein structures to experimental data, and we observe an order of magnitude speedup using parallel processing on a GPU compared to serial execution on a CPU.     

Preparation and characterization of individual peptide-wrapped single-walled carbon nanotubes

Two challenges for effectively exploiting the remarkable properties of single-walled carbon nanotubes (SWNTs) are the isolation of intact individual nanotubes from the raw material and the assembly of these isolated SWNTs into useful structures. In this study, we present atomic force microscopy (AFM) evidence that we can isolate individual peptide-wrapped SWNTs, possibly connected end-to-end into long fibrillar structures, using an amphiphilic alpha-helical peptide, termed nano-1. Transmission electron microscopy (TEM) and well-resolved absorption spectral features further corroborate nano-1's ability to debundle SWNTs in aqueous solution. Peptide-assisted assembly of SWNT structures, specifically in the form of Y-, X-, and intraloop junctions, was observed in the AFM and TEM images.     

Direct observation of single molecule conformational change of tight-turn paperclip DNA triplex in solution

DNA triplex modulates gene expression by forming stable conformation in physiological condition. However, it is not feasible to observe this unique molecular structure of large molecule with 54 oligodeoxynucleotides directly by conventional nuclear magnetic approach. In this study, we observed directly single molecular images of paperclip DNA triplexes formation in a buffer solution of pH 6.0 by atomic force microscopy (AFM). Meanwhile, a diffuse “tail” of unwound DNA was observed in pH 8.0 solution. This designable approach in visualizing the overall structures and shapes of oligo-DNAs at the single molecular level, by AFM, is applicable to other biopolymers as well.     

Molecular dynamics simulation on HP1 protein binding by histone H3 tail methylation and phosphorylation

Trimethylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging, and heterochromatin formation. Phosphorylation of histone H3 has been linked with mitotic chromatin condensation. During mitosis in vivo, H3 lysine 9 methylation and serine 10 phosphorylation can occur concomitantly on the same histone tail, whereas the influence of phosphorylation to trimethylation H3 tail recruiting HP1 remains controversial. In this work, molecular dynamics simulation of HP1 complexed with both trimethylated and phosphorylated H3 tail were performed and compared with the results from the previous methylated H3‐HP1 trajectory. It is clear from the 10‐ns dynamics simulation that two adjacent posttranslational modifications directly increase the flexibility of the H3 tail and weaken HP1 binding to chromatin. A combinatorial readout of two adjacent posttranslational modifications—a stable methylation and a dynamic phosphorylation mark—establish a regulatory mechanism of protein–protein interactions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Multitechnique characterization of thin films of immiscible polymer systems: PS–b‐PMMA diblock copolymers and PS–PMMA symmetric blends

Immiscible polymer systems are known to form various kinds of phase‐separated structures capable of producing self‐assembled patterns at the surface. In this study, different surface characterization methods were utilized to study the surface morphology and composition produced after annealing thin polymer films. Two different SIMS techniques—static time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) and dynamic nano‐SIMS—were used, complemented by x‐ray photoelectron spectrometry (XPS) and atomic force microscopy (AFM). Thin films (spin‐coated onto silicon wafers) of polystyrene (PS)–poly(methyl methacrylate) (PMMA) symmetric blends and diblock copolymers of similar molecular weight were investigated. Surface enrichment by PS was found on all as‐cast samples. The samples were annealed at 160 °C for different time periods, after which the blend and the copolymer films exhibited opposite behaviour as seen by ToF‐SIMS and XPS. The annealed blend surface presented an increase in the PMMA concentration whereas that of copolymers showed a decrease in PMMA concentration compared with the as‐cast sample. For blends, the nano‐SIMS as well as AFM images revealed the formation of phase‐separated domains at the surface. The composition information obtained from ToF‐SIMS and XPS, as well as the surface mapping by nano‐SIMS and AFM, allowed us to conclude that PS formed phase separated droplet‐like domains on a thin PMMA matrix on annealing. The three‐dimensional nano‐SIMS images showed that the PS droplets were supported inside a rim of PMMA and that these droplets continued from the surface like columnar rods into the film until the substrate interface. In the case of annealed copolymer samples, the AFM images revealed topographical features resembling droplet‐like domains on the surface but there was no phase difference between the domains and the matrix. In the case of copolymers, owing to the covalent bonding between the blocks, complete phase separation was not possible. The three‐dimensional nano‐SIMS images showed domain structures in the form of striations inside the film, which were not continuous until the substrate interface. Information from the different techniques was required to gain an accurate view of the surface composition and topographical changes that have occurred under the annealing conditions. Copyright © 2005 John Wiley & Sons, Ltd.     

Direct Observation of the Reversible Two‐State Unfolding and Refolding of an α/β Protein by Single‐Molecule Atomic Force Microscopy

Directly observing protein folding in real time using atomic force microscopy (AFM) is challenging. Here the use of AFM to directly monitor the folding of an α/β protein, NuG2, by using low‐drift AFM cantilevers is demonstrated. At slow pulling speeds (<50 nm s^?1), the refolding of NuG2 can be clearly observed. Lowering the pulling speed reduces the difference between the unfolding and refolding forces, bringing the non‐equilibrium unfolding–refolding reactions towards equilibrium. At very low pulling speeds (ca. 2 nm s^?1), unfolding and refolding were observed to occur in near equilibrium. Based on the Crooks fluctuation theorem, we then measured the equilibrium free energy change between folded and unfolded states of NuG2. The improved long‐term stability of AFM achieved using gold‐free cantilevers allows folding–unfolding reactions of α/β proteins to be directly monitored near equilibrium, opening the avenue towards probing the folding reactions of other mechanically important α/β and all‐β elastomeric proteins.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.