Scanning Force Microscopy as Applied to Conformational Studies in Macromolecular Research

In Situ Real-Time Atomic Force Microscopy Observation of the Surface Mobility on Each Domain of a Polystyrene-b-poly(methyl methacrylate) Film at High Temperatures

The surface chain movements within the microdomains of a polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) and corresponding homopolymer films were observed via in situ real-time atomic force microscopy (AFM) at high temperatures and analyzed quantitatively using particle image velocimetry (PIV). At low temperatures, mobility within the PS microdomains resembled that within the PS homopolymer film, but movements in the PMMA microdomains were notably accelerated compared to the PMMA homopolymer. Conversely, at high temperatures, mobility within both PS and PMMA microdomains was considerably suppressed compared to their respective homopolymer films, likely owing to the fixed linkage of the block chains at the microdomain interface. This combination of real-time AFM observation and PIV analysis is an effective method for quantitatively evaluating surface chain mobility in real space.

In Situ Real-Time Atomic Force Microscopy Observations of Chain Mobility at Polymer/Water Interfaces of Poly(methyl methacrylate), Poly(2-hydroxyethyl methacrylate), and Poly(2-methoxyethyl methacrylate) Films in Water

Polymer materials are widely used in water or in contact with an aqueous environment. However, evaluating the chain mobility, a crucial parameter, at a polymer-water interface is challenging. In this study, we, for the first time, observed poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(2-methoxyethyl methacrylate) (PMEMA) film surfaces in water via in situ real-time atomic force microscopy (AFM) in tapping mode and quantified the chain mobility. The average displacement between adjacent images (nm/8.75 min) was evaluated using particle image velocimetry. The displacement of PMMA, which has a high bulk glass-transition temperature (Tg) (108 °C) and exhibits limited water absorption, was low both in air (0.54 nm/8.75 min) and water (0.86), while PHEMA, which has a high bulk Tg (99 °C) and exhibits high water absorption, exhibited low mobility in air (0.40) but two orders of magnitude higher mobility in water (60). PMEMA, which has a low bulk Tg (14 °C) and exhibits limited water absorption, already started to move in air (4.5), and its mobility moderately increased in water (20). These behaviors were reasonable, considering the bulk Tg and water absorption characteristics of the polymers. Further, the chain mobility in water was compared with that of dried samples at high temperatures in air. The mobility of PMMA, PHEMA, and PMEMA in water corresponded to that of the dried samples observed in air below the surface Tg (97 °C) for PMMA, at ∼125 °C for PHEMA, and at ∼35 °C for PMEMA. In situ real-time AFM analysis of polymer materials in water is an effective method for evaluating the chain mobility at the polymer/water interface.

Single-molecule AFM study of hyaluronic acid softening in electrolyte solutions

Investigation of hyaluronic acid (HA) morphology and mechanical properties at a single-molecule level is important for the development of HA based biomaterials. We have developed the atomic force microscopy (AFM) based approach for quantitative characterization of conformation of HA molecules. HA molecules adsorbed on a modified graphitic surface form oriented linear segments. Conformation of HA molecules can be considered as two-dimensional quasi-projection of a three-dimensional conformation locally straightened by a substrate. The persistence length and Young's modulus of biomolecules estimated using wormlike chain model decrease from 15.7 to 9.9 nm, and from ∼21 to ∼13 GPa, respectively, when KCl concentration increases from 0 to 100 mM. The dependence of the persistence length on ionic strength supports the Odijk-Skolnick-Fixman model of polyelectrolyte stiffening in electrolyte solution. The obtained results represent a new insight into the conformation and mechanical characteristics of HA molecules and complement the characterization of this biopolymer by bulk methods.

Chain Movements at the Topmost Surface of Poly(methyl methacrylate) and Polystyrene Films Directly Evaluated by In Situ High-Temperature Atomic Force Microscopy

The surfaces of polymeric materials are thermodynamically unstable, and the glass-transition temperature (Tg) is significantly lower than that in the bulk material. However, the mobility of the chains at the top of the surface has never been directly evaluated. In this study, the movements of the topmost chains of poly(methyl methacrylate) (PMMA) and polystyrene (PS) bulk films were observed in situ at high temperatures with atomic force microscopy in tapping mode. PMMA and PS chains started moving at ∼97 and ∼50 °C, respectively, which were slightly and significantly below the values of their bulk Tg (PMMA, 108 °C; PS, 104 °C), respectively. The activation energies of the apparent diffusion constants of PMMA and PS, derived by particle image velocimetry analysis, were 193 and 151 kJ mol-1, respectively, and reasonable for the glass transition. Movements of isolated PMMA chains deposited on a PMMA film by the Langmuir-Blodgett technique were also observed and confirmed to be essentially the same as those on the PMMA film surface.

Molecular Combing of Various Poly(n-Alkyl Acrylate) Chains on Mica by the Dipping Method

If polymer chains could be deposited on a substrate as a fully extended chain, a procedure known as "molecular combing," the chain structure could be characterized by atomic force microscopy in more detail than has been possible with the measurements available today. We show here, for the first time, that flexible polymers can be molecularly combed to fully extended chains by the dipping method. We studied the molecular combing of a series of poly(n-alkyl acrylate)s on mica from a chloroform solution by the dipping method and found that poly(n-alkyl acrylate)s with an alkyl group longer than n-octyl can be molecularly combed into straight chains under optimized conditions. With increasing alkyl lengths, the number of chains deposited decreases by four orders of magnitude, and chains become molecularly combed under a wider range of conditions. The length of the molecularly combed chains is ∼80% for poly(n-octyl acrylate) but ∼100% of the all-trans conformation for poly(n-alkyl acrylate)s with an alkyl length longer than n-nonyl.

In situ AFM Observation of the Movements of Isolated Isotactic Poly(methyl methacrylate) Chains in a Precursor Film of an Oligo(methyl methacrylate) Droplet Spreading on Mica

Atomic force microscopy (AFM) is a powerful tool to observe polymer chains at the molecular level. In this study, we show that the movements of isolated linear polymer chains in a precursor film of a droplet of an oligomer spreading on a substrate could be visualized in situ at the molecular level by AFM for the first time. The system was an isotactic poly(methyl methacrylate) (it-PMMA) solubilized in an oligo(MMA) matrix (it-PMMA/oligo(MMA) = 1/10,000 w/w) spreading on mica under high humidity. Because of the limited resolution of the AFM instrument, condensed linear polymer chains could not be visualized, but a small amount of it-PMMA chains that were solubilized as isolated chains in the oligo(MMA) matrix could be visualized in the precursor film, the contrast of which came from a large difference in glass transition temperature (T_g) of it-PMMA and oligo(MMA). The it-PMMA chains in the precursor film spread in the radial direction of the droplet with vigorously changing chain conformations. The spreading rate of it-PMMA chains under 72% relative humidity was ∼1/30 of the spreading rate of the oligo(MMA) matrix, which was estimated based on the decrease in the volume of the macroscopic droplet. The spreading of the it-PMMA chains and droplet strongly depended on humidity and was suppressed with the decrease in humidity, most likely because of the increase in friction with the substrate. The difference in the spreading rate of it-PMMA and oligo(MMA) further increased under low humidity. The dynamic molecular information of a precursor film by AFM should help to elucidate the wetting dynamics on a substrate.

Preparation of a Si(111) Atomically Flat Substrate via Wet Etching and Evaluation as an AFM Substrate for Observations of Isolated Chains, Crystals, and Crystallization of Isotactic Poly(methyl methacrylate) at the Molecular Level

To observe a polymer chain deposited on a substrate by atomic force microscopy (AFM) at the molecular level, the substrate should be atomically flat and stable under laboratory conditions and adsorb polymer chains firmly. Therefore, substrates used under laboratory conditions are practically limited to mica, highly ordered pyrolytic graphite, and atomically stepped sapphire, and polymers observed by AFM at the molecular level are also limited. A silicon wafer is frequently used as a substrate for AFM observation for somewhat macroscopic observations, but the surface of the silicon wafer is too rough to observe polymer chains deposited on it at the molecular level. In this study, we prepared an atomically stepped Si(111) substrate via wet etching in NH₄F and evaluated it as an AFM substrate. The Si(111) substrate was stable as an AFM substrate, and isolated poly(methyl methacrylate) (it-PMMA) chains and a crystalline monolayer deposited on the substrate were observed by AFM at the molecular level. An it-PMMA amorphous monolayer deposited on mica crystallized under high humidity, but that on the Si(111) substrate did not because of the difference in the surface nature and the crystal structure of the substrates. The Si(111) substrate was hydrophobic, and the it-PMMA monolayers could be deposited as a multilayer, which could not be formed on hydrophilic mica. The crystallization behavior of an it-PMMA amorphous multilayer and an amorphous/crystalline mixed multilayer on the Si(111) substrate was also evaluated.

Molecular Combing of a Flexible Polymer Chain by Simple Spin-Casting

If polymer chains could be fixed on a substrate as a fully elongated chain, a procedure known as "molecular combing", the chain structure could be analyzed more precisely than has been possible with the characterization techniques available today. Although the molecular combing of a rigid biomolecule, DNA, has been attained for the mapping of genetic information, that of flexible chains has never been achieved as yet. We show here that poly(n-nonyl acrylate) (PNA) can be molecularly combed on mica by a simple spin-casting method, and that the chain lengths were in good agreement with that of the all-trans conformation. One of the key factors for successful molecular combing was found to be the weak adsorption of PNA on mica, indicating that flexible polymers may be molecularly combed by adjusting their affinity to the substrate. The molecular combing of polymer chains may open a new way not only to characterize the chain structures more precisely but also to fabricate new nanomaterials based on polymers.

Time-Lapse Single-Biomolecule Atomic Force Microscopy Investigation on Modified Graphite in Solution

Atomic force microscopy (AFM) of biomolecular processes at the single-molecule level can provide unique information for understanding molecular function. In AFM studies of biomolecular processes in solution, mica surfaces are predominantly used as substrates. However, owing to its high surface charge, mica may induce high local ionic strength in the vicinity of its surface, which may shift the equilibrium of studied biomolecular processes such as biopolymer adsorption or protein-DNA interaction. In the search for alternative substrates, we have investigated the behavior of adsorbed biomolecules, such as plasmid DNA and E. coli RNA polymerase σ⁷⁰ subunit holoenzyme (RNAP), on highly oriented pyrolytic graphite (HOPG) surfaces modified with stearylamine and oligoglycine-hydrocarbon derivative (GM) monolayers using AFM in solution. We have demonstrated ionic-strength-dependent DNA mobility on GM HOPG and nativelike dimensions of RNAP molecules adsorbed on modified HOPG surfaces. We propose an approach to the real-time AFM investigation of transcription on stearylamine monolayers on graphite. We conclude that modified graphite allows us to study biomolecules and biomolecular processes on its surface at controlled ionic strength and may be used as a complement to mica in AFM investigations.

A novel design of a scanning probe microscope integrated with an ultramicrotome for serial block-face nanotomography

We present a new concept of a combined scanning probe microscope (SPM)/ultramicrotome apparatus. It enables "slice-and-view" scanning probe nanotomography measurements and 3D reconstruction of the bulk sample nanostructure from series of SPM images after consecutive ultrathin sections. The sample is fixed on a flat XYZ scanning piezostage mounted on the ultramicrotome arm. The SPM measuring head with a cantilever tip and a laser-photodiode tip detection system approaches the sample for SPM measurements of the block-face surface immediately after the ultramicrotome sectioning is performed. The SPM head is moved along guides that are also fixed on the ultramicrotome arm. Thereby, relative dysfunctional displacements of the tip, the sample, and the ultramicrotome knife are minimized. The design of the SPM head enables open frontal optical access to the sample block-face adapted for high-resolution optical lenses for correlative SPM/optical microscopy applications. The new system can be used in a wide range of applications for the study of 3D nanostructures of biological objects, biomaterials, polymer nanocomposites, and nanohybrid materials in various SPM and optical microscopy measuring modes.

Cryo scanning probe nanotomography study of the structure of alginate microcarriers

Nanostructure of microparticles of decellularized rat liver ECM on spherical alginate hydrogel microcarriers is analyzed by cryo scanning probe nanotomography.

Nanotemplate-directed DNA segmental thermal motion

Nanotemplate directed DNA segmental thermal motion on molecular nanotemplates on graphite was directly observed and characterized using AFM in a liquid.

Novel imaging technologies for characterization of microbial extracellular polysaccharides

Understanding of biology is underpinned by the ability to observe structures at various length scales. This is so in a historical context and is also valid today. Evolution of novel insight often emerges from technological advancement. Recent developments in imaging technologies that is relevant for characterization of extraceullar microbiological polysaccharides are summarized. Emphasis is on scanning probe and optical based techniques since these tools offers imaging capabilities under aqueous conditions more closely resembling the physiological state than other ultramicroscopy imaging techniques. Following the demonstration of the scanning probe microscopy principle, novel operation modes to increase data capture speed toward video rate, exploitation of several cantilever frequencies, and advancement of utilization of specimen mechanical properties as contrast, also including their mode of operation in liquid, have been developed on this platform. Combined with steps in advancing light microscopy with resolution beyond the far field diffraction limit, non-linear methods, and combinations of the various imaging modalities, the potential ultramicroscopy toolbox available for characterization of exopolysaccharides (EPS) are richer than ever. Examples of application of such ultramicroscopy strategies range from imaging of isolated microbial polysaccharides, structures being observed when they are involved in polyelectrolyte complexes, aspects of their enzymatic degradation, and cell surface localization of secreted polysaccharides. These, and other examples, illustrate that the advancement in imaging technologies relevant for EPS characterization supports characterization of structural aspects.

Statistical analysis of molecular nanotemplate driven DNA adsorption on graphite

In this work, we have studied the conformation of DNA molecules aligned on the nanotemplates of octadecylamine, stearyl alcohol, and stearic acid on highly oriented pyrolytic graphite (HOPG). For this purpose, fluctuations of contours of adsorbed biopolymers obtained from atomic force microscopy (AFM) images were analyzed using the wormlike chain model. Moreover, the conformations of adsorbed biopolymer molecules were characterized by the analysis of the scaling exponent ν, which relates the mean squared end-to-end distance and contour length of the polymer. During adsorption on octadecylamine and stearyl alcohol nanotemplates, DNA forms straight segments, which order along crystallographic axes of graphite. In this case, the conformation of DNA molecules can be described using two different length scales. On a large length scale (at contour lengths l > 200-400 nm), aligned DNA molecules have either 2D compact globule or partially relaxed 2D conformation, whereas on a short length scale (at l ≤ 200-400 nm) their conformation is close to that of rigid rods. The latter type of conformation can be also assigned to DNA adsorbed on a stearic acid nanotemplate. The different conformation of DNA molecules observed on the studied monolayers is connected with the different DNA-nanotemplate interactions associated with the nature of the functional group of the alkane derivative in the nanotemplate (amine, alcohol, or acid). The persistence length of λ-DNA adsorbed on octadecylamine nanotemplates is 31 ± 2 nm indicating the loss of DNA rigidity in comparison with its native state. Similar values of the persistence length (34 ± 2 nm) obtained for 24-times shorter DNA molecules adsorbed on an octadecylamine nanotemplate demonstrate that this rigidity change does not depend on biopolymer length. Possible reasons for the reduction of DNA persistence length are discussed in view of the internal DNA structure and DNA-surface interaction.

Analysis of the conformation of the androgen receptor in spinal bulbar muscular atrophy by atomic force microscopy

Spinal bulbar muscular atrophy (SBMA) (also known as Kennedy's disease) is a motor degenerative disease caused by an amplification of the polyglutamine stretch at the N-terminus of the human androgen receptor (AR). Amplifications larger than 40 glutamine residues are thought to lead to the disease. A characteristic feature of this disease is a ligand-dependent misfolding and aggregation of the mutant receptor that lead to the death of motor neurons. Initially, large cytoplasmic and nuclear aggregates reaching sizes of 6 μm were thought to be the pathogenic agents. Later studies have suggested that oligomeric species with sizes of less than 1 μm that occur prior to the formation of the larger aggregates are the toxic agents. However, there have been disagreements regarding the shape of these oligomers, as most studies have been carried out with peptide fragments of the androgen receptor containing different lengths of polyglutamine stretch. We have isolated the wild-type AR with a polyglutamine stretch of 22 (ARQ22) and a mutant receptor with a stretch of 65 (ARQ65) using a baculovirus system and have analyzed the oligomeric structures formed by these receptors with atomic force microscopy. This method has allowed us to determine the conformations of the full-length wild-type and mutant AR and revealed the conformation of the mutant AR that causes SBMA.

Cyclodextrin insulation prevents static quenching of conjugated polymer fluorescence at the single molecule level

Conjugated polymers (CPs) are promising materials for fluorescence imaging application. However, a significant problem in this field is the unexplained abnormally low fluorescence brightness (or number of fluorescence photons detected per one excitation photon) exhibited by most of CP single chains in solid polymer hosts. Here it is shown that this detrimental effect can be fully avoided for short chains of polyfluorene-bis-vinylphenylene (PFBV) embedded in a host polymer matrix of PMMA, if the conjugated backbone is insulated by cyclodextrin rings to form a polyrotaxane (PFBV-Rtx). Fluorescence kinetics and quantum yields are measured for the polymers in liquid solutions, pristine films, and solid PMMA blends. The fluorescence brightness of PFBV-Rtx single chains dispersed in a solid PMMA is very close to that expected for a chain with 100% fluorescence quantum yield, while the unprotected PFBV chains of the same length possess 4 times lower brightness. Despite this, the fluorescence decay kinetics are the same for both polymers, suggesting the presence of static or ultrafast fluorescence quenching in the unprotected polymer. About 80% of an unprotected PFBV chain is estimated to be completely quenched. The hypothesis is that the cyclodextrin rings prevent the quenching by working as 'bumpers' reducing the mechanical forces applied by the host polymer to the conjugated backbone and help retaining its conformational freedom. While providing a recipe for making CP fluorescence bright at the single-molecule level, these results identify a lack of fundamental understanding in the community of the influence of the environment on excited states in conjugated materials.

Conformational transitions of flexible hydrophobic polyelectrolytes in solutions of monovalent and multivalent salts and their mixtures

Conformations of cationic polyelectrolytes (PEs), a weak poly(2-vinylpyridine) (P2VP) and a strong poly(N-methyl-2-vinylpyridinium iodide) (qP2VP), adsorbed on mica from saline solutions in the presence of counterions of different valences are studied using in situ atomic force microscopy (AFM). Quantitative characteristics of chain conformations are analyzed using AFM images of the adsorbed molecules. The results of the statistical analysis of the chain contour reveal collapse of the PE coils when ionic strength is in a range from tens to hundreds of millimoles per kilogram and re-expansion of the coils with a further increase of ionic strength up to a region of the saturated saline solutions. The competition between monovalent and multivalent counterions simultaneously present in solutions strongly affects conformations of PE chains even at a very small fraction of multivalent counterions. Shrinkage of PE coils is steeper for multivalent counterions than for monovalent counterions. However, the re-expansion is only incremental in the presence of multivalent counterions. Extended adsorbed coils at low salt concentrations and at very high concentrations of monovalent salt exhibit conformation corresponding to a 2D coil with 0.95 fraction of bound segments (segments in "trains") in the regime of diluted surface concentration of the PE. Shrunken coils in the intermediate range of ionic strength resemble 3D-globules with 0.8 fraction of trains. The incrementally re-expanded PE coils at a high ionic strength remain unchanged at higher multivalent salt concentrations up to the solubility limit of the salt. The formation of a strong PE complex with multivalent counterions at high ionic strength is not well understood yet. A speculative explanation of the observed experimental result is based on possible stabilization of the complex due to hydrophobic interactions of the backbone.

AFM imaging of adsorbed Nafion polymer on mica and graphite at molecular level

Perfluorosulfonic acid ionomer (PFSA, specifically Nafion at EW = 975 g/mol) was visualized at the single molecule level using atomic force microscopy (AFM) in liquid. The diluted commercial Nafion dispersion shows an apparent M(w) = 1430 kg/mol and M(w)/M(n) = 3.81, which is assigned to chain aggregation. PFSA aggregates, imaged on mica and HOPG during adsorption from EtOH-H(2)O solvent at pH(e) 3.0 (below isoelectric point), showed a stable, segmented rod-like conformation. This structure is consistent with earlier NMR, SAXS/SANS, and TEM results that support a stiff helical Nafion conformation with long persistence length, a sharp solvent-polymer interface, and an extension of the sulfonated side chain into solution. Adsorption of Nafion structures on HOPG was observed at even higher pH(e) from EtOH due to screening of the repulsive electrostatic interaction in lower dielectric constant solvent, while the chain adopted an expanded coil conformation. These measurements provided direct evidence of the chain aggregation in EtOH-H(2)O solution and revealed their equilibrium conformations for adsorption on two model surfaces, highly ordered pyrolitic graphite (HOPG) and mica. The commercial Nafion dispersion was autoclaved at 0.10% w/w in nPrOH/H(2)O = 4:1 v/v solvent at 230 °C for 6 h to give a single-chain dispersion with M(w) = 310 kg/mol and M(w)/M(n) = 1.60. The autoclaved chains adopt an electrostatically stabilized compact globule conformation as observed by AFM imaging of the single PFSA molecules after rapid deposition on mica and HOPG at a low surface coverage.