Atomic force microscopy in mechanical measurements of single nanowires

In this paper, we present the results of mechanical measurement of single nanowires (NWs) in a repeatable manner. Substrates with specifically designed mechanical features were used for NW placement and localization for measurements of properties such as Young's modulus or tensile strength of NW with an atomic force microscopy (AFM) system. Dense arrays of zinc oxide (ZnO) nanowires were obtained by one-step anodic oxidation of metallic Zn foil in a sodium bicarbonate electrolyte and thermal post-treatment. ZnO NWs with a hexagonal wurtzite structure were fixed to the substrates using focused electron beam-induced deposition (FEBID) and were annealed at different temperatures in situ. We show a 10-fold change in the properties of annealed materials as well as a difference in the properties of the NW materials from their bulk values with pre-annealed Young modulus at the level of 20 GPa and annealed reaching 200 GPa. We found the newly developed method to be much more versatile, allowing for in situ operations of NWs, including measurements with different methods of scanning probe microscopy.

Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay

The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.

Experimental extraction of Young's modulus of MCF-7 tissue using atomic force microscopy and the spherical contact models

The study of mechanical properties of tissues can be considered as biomarkers for early detection of cancer and help in new treatments. In this study, the Young's modulus of MCF-7 breast cancer tissue was extracted using atomic force microscopy (AFM) by measuring the interaction force of the sample and performing a simulation. The force-indentation depth diagram was plotted by averaging the experimental results. In this paper, the modulus of elasticity of breast cancer tissue has been extracted with complex models such as DMT, MD, BCP, and SUN. By comparing the experimental and theoretical results and by changing the amount of hypothetical Young's modulus in the spherical contact models, the Young's modulus of the cancer tissue is considered to be between 300 and 400 Pa. The geometry of the cell was also assumed to be spherical according to the images obtained by atomic force microscopy.

Probing single molecule mechanical interactions of syntaxin 1A with native synaptobrevin 2 residing on a secretory vesicle

Interactive mechanical forces between pairs of individual SNARE proteins synaptobrevin 2 (Sb2) and syntaxin 1A (Sx1A) may be sufficient to mediate vesicle docking. This notion, based on force spectroscopy single molecule measurements probing recombinant Sx1A an Sb2 in silico, questioned a predominant view of docking via the ternary SNARE complex formation, which includes an assembly of the intermediate cis binary complex between Sx1A and SNAP25 on the plasma membrane to engage Sb2 on the vesicle. However, whether a trans binary Sx1A-Sb2 complex alone could mediate vesicle docking in a cellular environment remains unclear. To address this issue, we used atomic force microscopy (AFM) in the force spectroscopy mode combined with fluorescence imaging. Using AFM tips functionalized with the full Sx1A cytosolic domain, we probed native Sb2 studding the membrane of secretory vesicles docked at the plasma membrane patches, referred to as "inside-out lawns", identified based on fluorescence stains and prepared from primary culture of lactotrophs. We recorded single molecule Sx1A-Sb2 mechanical interactions and obtained measurements of force (∼183 pN) and extension (∼21.6 nm) necessary to take apart Sx1A-Sb2 binding interactions formed at tip-vesicle contact. Measured interactive force between a single pair of Sx1A-Sb2 molecules is sufficient to hold a single secretory vesicle docked at the plasma membrane within distances up to that of the measured extension. This finding further advances a notion that native vesicle docking can be mediated by a single trans binary Sx1A-Sb2 complex in the absence of SNAP25.

Analysis of Lipids in Single Cells and Organelles Using Nanomanipulation-Coupled Mass Spectrometry

The ability to discriminately analyze the chemical constituents of single cells and organelles is highly sought after and necessary to establish true biomarkers. Some major challenges of individual cell analysis include requirement and expenditure of a large sample of cells as well as extensive extraction and separation techniques. Here, we describe methods to perform individual cell and organelle extractions of both tissues and cells in vitro using nanomanipulation coupled to mass spectrometry. Lipid profiles display heterogeneity from extracted adipocytes and lipid droplets, demonstrating the necessity for single cell analysis. The application of these techniques can be applied to other cell and organelle types for selective and thorough monitoring of disease progression and biomarker discovery.

Modeling and simulation of contact parameters of elliptical and cubic nanoparticles to be used in nanomanipulation based on atomic force microscope

Regarding the contact mechanics of smooth nanoparticles, two new geometries, specifically elliptical and cubic are chosen for nanoparticles. The results of elliptical contact simulation show that the JKR theory induces a greater indentation depth in both contact geometries since it includes the adhesion forces. Moreover, the Jamari theory shows a lesser indentation depth because it assumes larger contact area. The results of cubic nanoparticles simulation exhibit a significant difference between the contact of tip and nanoparticle compared to the contact of nanoparticle and surface. This can be attributed to the large contact area between the cubic nanoparticle and the reference surface. The JKR and DMT theories, however, show greater indentation depths in the tip contact with nanoparticle. Furthermore, the Lundberg theory yields the maximum indentation depth in the nanoparticle contact with reference surface. Finally, in order to validate the results, experimental and FEM approaches are incorporated. Concerning the experimental results, a certain number of silver nanoparticles are placed on a polystyrene surface. After obtaining the experimental force-displacement curves, the results of presented models are compared with them. The experimental results indicate that for silver nanoparticles and polystyrene surface, the Hertz theory with 1.11% of error and the JKR theory with 8.7% of error show the best output, respectively. Regarding rough nanoparticles contact, the geometry of roughness are taken as elliptical. Meanwhile, analytical relations are presented to solve force and contact area integrals while noting the problem dimensions. The results of simulation show that the JKR theory yields the highest roughness force, followed by the Hertz and Jamari theories, and regarding rough contact area, the Hertz theory creates the largest contact area, followed by the Jamari and JKR theories. The presented analytical method is compared with numerical results as a means of validation.

Noncalssical multiscale modeling of ssDNA manipulation using a CNT-nanocarrier based on AFM

Nanocarriers are useful tools in biological and medical research fields. In nanomanipulation, a nondestructive and successful process can be achieved by using nanocarriers. In this paper, a nonclassical multiscale approach has been presented for modeling a single strand DNA (ssDNA) manipulation based on AFM. To achieve a nondestructive nanomanipulation process, carbon nanotube (CNT) has been used as a nanocarrier. AFM setup has been separated into a Micro field (MF) and a Nano field (NF). The governing equations of the MF have been derived based on Kirchhoff plate model and a modified couple stress theory. The NF has been modeled by molecular dynamics (MD) method. A set of nanomanipulations has been performed for the free ssDNA and the ssDNA inside the nanocarrier (shielded ssDNA) on three types of substrates. The exerted forces on the free ssDNA and the shielded ssDNA have been compared for manipulation on various substrates. The results show that using the nanocarrier reduces the manipulation force considerably. The results of RMSD as a general geometrical criterion have illustrated that the maximum damage occurs on the golden substrate for free ssDNA. Elongation and curvature criteria have been presented to investigate the ssDNA deformation in detail. The elongation and curvature criteria have been shown that using a nanocarrier is a good approach for a successful and nondestructive nanomanipulation. Finally it can be concluded that the manipulation process of free ssDNA on silicon substrate is successful as well as the manipulation process of the shielded ssDNA on all three types of substrates.

DAPNe with micro-capillary separatory chemistry-coupled to MALDI-MS for the analysis of polar and non-polar lipid metabolism in one cell

The cellular metabolome is considered to be a representation of cellular phenotype and cellular response to changes to internal or external events. Methods to expand the coverage of the expansive physiochemical properties that makeup the metabolome currently utilize multi-step extractions and chromatographic separations prior to chemical detection, leading to lengthy analysis times. In this study, a single-step procedure for the extraction and separation of a sample using a micro-capillary as a separatory funnel to achieve analyte partitioning within an organic/aqueous immiscible solvent system is described. The separated analytes are then spotted for MALDI-MS imaging and distribution ratios are calculated. Initially, the method is applied to standard mixtures for proof of partitioning. The extraction of an individual cell is non-reproducible; therefore, a broad chemical analysis of metabolites is necessary and will be illustrated with the one-cell analysis of a single Snu-5 gastric cancer cell taken from a cellular suspension. The method presented here shows a broad partitioning dynamic range as a single-step method for lipid analysis demonstrating a decrease in ion suppression often present in MALDI analysis of lipids. Graphical Abstract ᅟ.

Analysis the effect of different geometries of AFM's cantilever on the dynamic behavior and the critical forces of three-dimensional manipulation

An important challenge when using an atomic force microscope (AFM) is to be able to control the force exerted by the AFM for performing various tasks. Nevertheless, the exerted force is proportional to the deflection of the AFM cantilever, which itself is affected by a cantilever's stiffness coefficient. Many papers have been published so far on the methods of obtaining the stiffness coefficients of AFM cantilevers in 2D; however, a comprehensive model is yet to be presented on 3D cantilever motion. The discrepancies between the equations of the 2D and 3D analysis are due to the number and direction of forces and moments that are applied to a cantilever. Moreover, in the 3D analysis, contrary to the 2D analysis, due to the interaction between the forces and moments applied on a cantilever, its stiffness values cannot be separately expressed for each direction; and instead, a stiffness matrix should be used to correctly derive the relevant equations. In this paper, 3D stiffness coefficient matrices have been obtained for three common cantilever geometries including the rectangular, V-shape and dagger-shape cantilevers. The obtained equations are validated by two methods. In the first approach, the Finite Element Method is combined with the cantilever deflection values computed by using the obtained stiffness matrices. In the second approach, by reducing the problem's parameters, the forces applied on a cantilever along different directions are compared with each other in 2D and 3D cases. Then the 3D manipulation of a stiff nanoparticle is modeled and simulated by using the stiffness matrices obtained for the three cantilever geometries. The obtained results indicate that during the manipulation process, the dagger-shaped and rectangular cantilevers exert the maximum and minimum amounts of forces on the stiff nanoparticle, respectively. Also, by examining the effects of different probe tip geometries, it is realized that a probe tip of cylindrical geometry exerts the smallest force on a biological nanoparticle. Therefore, the rectangular cantilever is a more suitable geometry for preventing the exertion of excessive force and the possible damage of such nanoparticle.

Nanomanipulation-Coupled Matrix-Assisted Laser Desorption/ Ionization-Direct Organelle Mass Spectrometry: A Technique for the Detailed Analysis of Single Organelles

We describe a novel technique combining precise organelle microextraction with deposition and matrix-assisted laser desorption/ionization (MALDI) for a rapid, minimally invasive mass spectrometry (MS) analysis of single organelles from living cells. A dual-positioner nanomanipulator workstation was utilized for both extraction of organelle content and precise co-deposition of analyte and matrix solution for MALDI-direct organelle mass spectrometry (DOMS) analysis. Here, the triacylglycerol (TAG) profiles of single lipid droplets from 3T3-L1 adipocytes were acquired and results validated with nanoelectrospray ionization (NSI) MS. The results demonstrate the utility of the MALDI-DOMS technique as it enabled longer mass analysis time, higher ionization efficiency, MS imaging of the co-deposited spot, and subsequent MS/MS capabilities of localized lipid content in comparison to NSI-DOMS. This method provides selective organellar resolution, which complements current biochemical analyses and prompts for subsequent subcellular studies to be performed where limited samples and analyte volume are of concern. Graphical Abstract ᅟ.

Framed carbon nanostructures: synthesis and applications in functional SPM tips

We present a synthesis method to fabricate framed carbon-based nanostructures having highly anisotropic shapes, in particular, the nanofork and nanoscalpel structures which are obtained systematically under optimized growth conditions. A theoretical model is developed to explain the formation of such nanostructures on Si cantilevers and W etched wires exposed to a focused electron beam. We then demonstrate the potentials of these nanostructures as functional tips for scanning probe microscopy. Owing to their anisotropic shapes, such tips can be very useful for nanolithography, nanosurgery of biological objects, and precise manipulation with surface particles. Overall, our method provides a simple and robust way to produce functional scanning probe microscopy tips with variable shapes and enhanced capabilities for different applications compared to standard cantilevers.

Nanomanipulation-coupled to nanospray mass spectrometry applied to document and ink analysis

A method for the extraction and analysis of ink samples was developed using microscopy with direct analyte probe nanoextraction coupled to nanospray ionization mass spectrometry (DAPNe-NSI-MS) for localized chemical analysis of document inks. Nanomanipulation can be effectively coupled to nanospray ionization mass spectrometry providing picomolar sensitivity, and the capability to analyze ultra-trace amounts of material and reduce the required sample volume to as low as 300 nL. This new and innovative technique does not leave destructive footprints on the surface of a document. To demonstrate the breadth of this technique, analysis of inks from various eras were tested, iron gall ink and modern inks, as well as the capability to detect the oxidative products of polyethylene glycol (PEG), a common binding agent. The experimental results showed that DAPNe-NSI-MS was able to chelate iron(II) and manganese(II) ions of iron gall ink and organic components of modern and carbon-based inks. Regardless of whether the ink composition is modern or ancient, organic or inorganic, this new instrumental approach is able to identify and characterize the ingredients by modifying the extraction solvent, illustrating the potential diversity of the DAPNe technique.

Some aspects of formation and tribological properties of silver nanodumbbells

In this paper, metal nanodumbbells (NDs) formed by laser-induced melting of Ag nanowires (NWs) on an oxidized silicon substrate and their tribological properties are investigated. The mechanism of ND formation is proposed and illustrated with finite element method simulations. Tribological measurements consist in controllable real-time manipulation of NDs inside a scanning electron microscope (SEM) with simultaneous force registration. The geometry of NDs enables to distinguish between different types of motion, i.e. rolling, sliding and rotation. Real contact areas are calculated from the traces left after the displacement of NDs and compared to the contact areas predicted by the contact mechanics and frozen droplet models.

PACS

81.07.-b; 62.25.-g; 62.23.Hj.