Single-molecule imaging of the dynamic interactions between macromolecules

In recent years, the development of single-molecule detection techniques has allowed the dynamic properties of biomolecules, which are normally obscured in conventional ensemble measurements, to be measured. One of these single-molecule detection techniques allows the measurement of dissociation and association events of individual molecules to be measured. This technique is based on the unique premise that the mobility between molecules that are bound and the mobility between those that are free in solution are different. The binding of ATP at the beginning and its dissociation at the end of the hydrolysis reaction were detected at the single-molecule level in real time. In this study, we extended this technique to image the dynamic interactions between large biomolecules (protein/protein and protein/polysaccharide). The binding and dissociation of fluorescently labeled macromolecules to partner molecules fixed on a glass surface were visualized by total internal reflection fluorescence microscopy. The dynamic interactions between the proteins in two energy conversion systems, that is, signaling proteins and enzyme molecules moving on dextran, have been measured. In these systems, the dynamic interactions were sensitive to the factors determining the chemical reactions. Thus, the dynamic interactions monitored in the single-molecule measurements provided useful information to further the understanding of the underlying mechanisms of energy conversion systems.     

Single-molecule resolution and fluorescence imaging of mixed-mode sorption of a dye at the interface of C18 and acetonitrile/water.

Single-molecule imaging is used for the first time to study the cationic dye, 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI), at the chromatographic interface consisting of acetonitrile/water and a hydrocarbon monolayer (C18) covalently bound to silica. Autocorrelations of burst data agree with our previous single-molecule counting results, showing that most dye molecules are diffusing and that there is a rare specific adsorption site associated with a 0.07-s desorption time. These autocorrelations go further in detecting an even rarer specific adsorption event associated with a 2.6-s desorption time. The latter desorption time would contribute much more significantly to peak tailing in chromatography. In water, the populations of DiI at these two specific adsorption sites are shown to be 11% and 4%, respectively, for the weaker and stronger sites, relative to the diffusing population of DiI. In 60% acetonitrile/water, the relative populations of the specific adsorption sites are 11% and 17%, showing that acetonitrile enhances the population of the stronger specific adsorption site. Fluorescence movies of single and multiple molecules link the stronger specific adsorption sites to specific locations on the surface. The imaging makes rare observations frequent by pinpointing where the events occur spatially. This ability to observe rare events by imaging reveals the presence of a third type of specific adsorption site, for which DiI has a desorption time in excess of 20 s.     

Raman spectroscopy and imaging of graphene

Graphene has many unique properties that make it an ideal material for fundamental studies as well as for potential applications. Here we review recent results on the Raman spectroscopy and imaging of graphene. We show that Raman spectroscopy and imaging can be used as a quick and unambiguous method to determine the number of graphene layers. The strong Raman signal of single layer graphene compared to graphite is explained by an interference enhancement model. We have also studied the effect of substrates, the top layer deposition, the annealing process, as well as folding (stacking order) on the physical and electronic properties of graphene. Finally, Raman spectroscopy of epitaxial graphene grown on a SiC substrate is presented and strong compressive strain on epitaxial graphene is observed. The results presented here are highly relevant to the application of graphene in nano-electronic devices and help in developing a better understanding of the physical and electronic properties of graphene. This article is published with open access at Springerlink.com     

Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami

DNA origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on DNA origami. We find that the kinetics of hybridization to single-stranded extensions on DNA origami is similar to isolated substrate-immobilized DNA with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to DNA nanostructures for PAINT (points accumulation for imaging in nanoscale topography) imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures.     

Increasing the sensitivity of magnetic resonance spectroscopy and imaging

Nuclear magnetic resonance and magnetic resonance imaging are two of the most important techniques in analytical chemistry and noninvasive medical imaging, respectively. They share a common physical basis, one aspect of which is a low intrinsic sensitivity relative to complementary techniques. Encouragingly, recent advances in physics, chemistry, engineering, and data processing have enabled significant increases in sensitivity, as measured by both increased signal-to-noise and reduced data acquisition times, allowing previously unattainable data to be acquired and also new types of experiments to be designed.     

Nondestructive evaluation of cork enclosures using terahertz/millimeter wave spectroscopy and imaging

Natural cork enclosures, due to their cell structure, composition, and low moisture are fairly transparent to terahertz (THz) and millimeter waves enabling nondestructive evaluation of the cork's surface and interior. It is shown that the attenuation coefficient of the defect-free cork can be modeled with a Mie scattering model in the weakly scattering limit. Contrast in the THz images is a result of enhanced scattering of THz radiation by defects or voids as well as variations in the cork cell structure. The presence of voids, defects, and changes in grain structure can be determined with roughly 100-300 microm resolution.     

Size-correlated spectroscopy and imaging of rare-earth-doped nanocrystals

Isolated europium-doped metal-oxide nanoparticles were probed by size-correlated high-numerical-aperture (far-field) imaging techniques. A modified Digital Instruments Bioscope atomic force microscope mounted upon a Nikon TE300 inverted microscope was used to interrogate (dry) particles ranging in size from 2 to 150 nm on the surface of a glass or quartz coverslip. These experiments revealed several interesting features of doped-nanoparticle luminescence such as Poissonian occupation statistics, size-dependent luminescence efficiency enhancement for particle sizes of <10 nm, and correlation of interesting transient behavior at particle sizes of <5 nm.     

Sub-surface imaging with the magnetic resonance force microscope

The magnetic resonance force microscope (MRFM) is based on mechanical detection of magnetic resonance signals. The force between the field gradient due to a small permanent magnet and the spin magnetization in the sample is used to drive the oscillation of a high Q, low spring-constant micro-mechanical resonator (e.g. atomic force microscope cantilever). This same field gradient also enables microscopic magnetic resonance imaging. We will discuss the characteristics and capabilities of the electron spin MRFM we have fabricated. Our MRFM has a sensitivity of 3×10¹¹ electron spins at room temperature in an applied field of 253 Gauss. Its vertical resolution is 1 micron. One- and two-dimensional scans of a particle beneath the silicon cantilever have been performed which demonstrate the sub-surface spatial imaging capabilities. We also discuss recent advances in the miniaturization of two crucial MRFM components: the micromechanical resonator and the micromagnetic tip.     

Peeling force spectroscopy: exposing the adhesive nanomechanics of one-dimensional nanostructures

The physics of adhesion and stiction of one-dimensional nanostructures such as nanotubes, nanowires, and biopolymers on different material substrates is of great interest for the study of biological adhesion and the development of nanoelectronics and nanocomposites. Here, we combine theoretical models and a new mode in the atomic force microscope to investigate quantitatively the physics of nanomechanical peeling of carbon nanotubes and nanocoils on different substrates. We demonstrate that when an initially straight nanotube is peeled from a surface, small perturbations can trigger sudden transitions between different geometric configurations of the nanotube with vastly different interfacial energies. This opens up the possibility of quantitative comparison and control of adhesion between nanotubes or nanowires on different substrates.     

Sequencing DNA by dynamic force spectroscopy: limitations and prospects

Using a well established model, we systematically analyze fundamental limitations on the viability of using mechanical unzipping of DNA as a fast and inexpensive sequencing method. Standard unzipping techniques, where double-stranded DNA is unzipped through the application of a force at one end of the molecule, are shown to be inadequate. Emerging techniques that unzip DNA by local force application are more promising, and we establish the necessary experimental requirements that must be met for these techniques to succeed as single molecule sequencing tools.     

Application of dynamic impedance spectroscopy to atomic force microscopy

Abstract

Atomic force microscopy (AFM) is a universal imaging technique, while impedance spectroscopy is a fundamental method of determining the electrical properties of materials. It is useful to combine those techniques to obtain the spatial distribution of an impedance vector. This paper proposes a new combining approach utilizing multifrequency scanning and simultaneous AFM scanning of an investigated surface.     

Intermolecular force between monoamine oxidase B and Pseudarthria viscida (L.) using atomic force spectroscopy

Inhibition of monoamine oxidase B (MAO-B) activity by deprenyl hydrochloride (drug) and methanolic extract of Pseudarthria viscida (L.) have been studied using atomic force microscopy force–distance (AFM F–D) curves. Attractive force measured between MAO-B and kynuramine dihydrobromide (substrate) was 56.12?pN?±?8.9, between MAO-B (inhibited by drug) and substrate was 11.25?pN?±?2.6 and MAO-B (inhibited by plant extract) and substrate was 18.61?pN?±?2.9. Phytochemical analysis revealed catechin as one of the compounds in P. viscida (L.) extract and MAO-B–catechin binding sites were confirmed using in silico methods. This study is perhaps the first report of combining three techniques, namely AFM F–D curves, phytochemical and in silico analysis to measure enzyme–substrate attractive force, constituents of plant extract and position of binding sites, respectively.     

Point-contact spectroscopy of the electron-phonon interaction in single-crystal LaB6

Point-contact spectra of single-crystal LaB₆ are obtained, yielding the energy positions of all the phonon modes up to 160 meV. A relatively strong anisotropy of the spectra is observed. It is related to the anisotropy of the phonon system. The point-contact electron-phonon interaction function and the point-contact electron-phonon interaction parameter are compared with published calculated data and a qualitative agreement is found. From the measured spectra the temperature dependence of the LaB₆ electrical resistivity and heat capacity are calculated.     

Atomic force spectroscopy evidence of non-specific adhesion of Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is a gram-negative periodontopathogen found within the subgingival plaque on the tooth surface. It is associated with localized aggressive periodontitis, a severe form of periodontitis in adolescents, and is the cause various extra-oral infections. The ability of this organism to tenaciously adhere to abiotic surfaces has been attributed to bundle-forming type IVb-like fimbriae whose major component is the fimbrial lower molecular weight protein (Flp). In this study the adhesion of purified Flp fimbriae isolated from A. actinomycetemcomitans to materials with different surface chemistries was measured using atomic force microscopy (AFM). The adhesion of Flp fimbriae to uncoated and saliva-coated tooth, hydroxylapatite, and glass surfaces was compared. Force data were used to quantify the magnitude of adhesion of the fimbriae and force-distance profiles were used to predict the mechanisms of adhesion. The results of this study confirm that non-specific interactions likely dominate the adhesion of these fimbriae to the surfaces used in this study. However, force data indicate that non-specific electrostatic interactions may be more significant under the conditions used in this study. Salivary coatings did affect both the hydrophobicity and adhesion of these fimbriae to the surfaces used in this study. Additionally, these data demonstrate the affect of salivary proteins on bacterial adhesion in the oral cavity.     

Adhesion force during microcontact interaction between cylindrical-segment-on-flat and flat bodies

Adhesion force including its both attractive and repulsive components during microcontact interaction between cylindrical-segment-on-flat and flat bodies is formulated using the volumetric integration of interactions among the atoms. Thenceforth the corresponding formulation for cylinder-on-flat and flat-on-flat is developed and compared with the available counterpart attractive force and they are in excellent agreement with each other. However, the present study provides also the repulsive component of adhesion force for these contact geometries. The formulation is also extended for a cylindrical segment with two radii to model the elastic–plastic deformation. Several phenomena related to adhesion during microcontact are then studied leading to the following salient observations. The adhesion force during microcontact interaction can be of the same order as the applied force, and thus causes the plastic deformation. The attractive force from the cylindrical segment is the major component of adhesion force for its radius/height ratios smaller than 1000 while that from the bulk body is the major for the larger ratios, i.e. when the cylindrical segment is similar to an asperity. There is considerable difference in the attractive force between a cylinder and a cylindrical-segment-on-flat for the smaller values of radius. The difference between attractive and total adhesion force is significant (∼60%) when adhesion force is the maximum, but it rapidly decreases with increasing separation distance and can be neglected at the separation distance larger than the twice of inter-atomic equilibrium distance. The equilibrium separation distance is about 60% of the inter-atomic equilibrium distance and adhesion force is maximum at about 80% of the inter-atomic equilibrium separation distance for both deformed and undeformed configurations. The adhesion force also increased with the deformation of cylindrical segment. The views expressed in this article are those of the authors and do not reflect the official policy or position of the United State Air Force, Department of Defense, or the U.S. Government.     

Sample-tip interaction of piezoresponse force microscopy in ferroelectric nanostructures

We report on qualitative and quantitative implications of the sample-tip interaction in piezoresponse force microscopy. Our finite-element analysis of adsorbate effects, sample heterogeneities, and tip asymmetries is in agreement with experimental observation of ferroelectric nanostructures. Qualitative discrepancies arise from locally asymmetric tip-sample interaction. Any quantitative determination of field-related material parameters as required for the verification of semiempirical models of the ferroelectric limit typically relies on an overestimated field across the sample. Our findings indicate that adsorbates reduce the actual field across the nanograin by roughly one order of magnitude.     

利用粘度法和二维红外相关光谱法研究胶原/羟丙甲基纤维素共混物的相互作用

采用粘度法和二维红外相关光谱法对胶原/羟丙甲基纤维素共混体系的相容性及相互作用进行了研究。粘度法测定结果表明,羟丙甲基纤维素含量<30%时共混体系相容,超过50%则不相容。二维红外相关光谱法的分析结果表明,当羟丙甲基纤维素含量<30%时,归属于羟丙甲基纤维素的C—O(H)伸缩振动峰1061cm-1与归属于胶原酰胺带的CO对称伸缩振动峰1660cm-1、N—H摇摆振动峰1553cm-1和N—H面内变形振动峰1238cm-1之间存在同步负交叉峰,表明胶原和羟丙甲基纤维素之间存在氢键作用;而当羟丙甲基纤维素含量>30%时,同步图中负交叉峰强度减小的同时同步峰1061cm-1的强度明显变大,表明此时羟丙甲基纤维素与胶原之间的氢键作用变弱,羟丙甲基纤维素更倾向于在自身分子之间形成氢键。     

Effects of nonlinear forces on dynamic mode atomic force microscopy and spectroscopy

In this paper, we describe the effects of nonlinear tip-sample forces on dynamic mode atomic force microscopy and spectroscopy. The jumps and hysteresis observed in the vibration amplitude (A) versus tip-sample distance (h) curves have been traced to bistability in the resonance curve. A numerical analysis of the basic dynamic equation was used to explain the hysteresis in the experimental curve. It has been found that the location of the hysteresis in the A-h curve depends on the frequency of the forced oscillation relative to the natural frequency of the cantilever.