Force spectroscopy 101: how to design, perform, and analyze an AFM-based single molecule force spectroscopy experiment

Quantitative measurement of cation-mediated adhesion of DNA to anionic surfaces

Anionic polyelectrolytes, such as DNA, are attracted to anionic surfaces in the presence of multivalent cations. A major barrier toward molecular-level understanding of these attractive interactions is the paucity of measurements of the binding strength. Here, atomic force microscopy-based single molecule force spectroscopy was used to quantify the binding free energy of double-stranded DNA to an anionic surface, with complementary density functional theory calculations of the binding energies of metal ion-ligand complexes. The results support both electrostatic attraction and ion-specific binding. Our study suggests that the correlated interactions between counterions are responsible for attraction between DNA and an anionic surface, but the strength of this attraction is modulated by the identity of the metal ion. We propose a mechanism in which the strength of metal-ligand binding, as well as the preference for particular binding sites, influence both the concentration dependence and the strength of the DNA-surface interactions.

Atomic Force Microscopy for the Study of Cell Mechanics in Pharmaceutics

Cell mechanics is gaining attraction in drug screening, but the applicable methods have not yet become part of the standardized norm. This review presents the current state of the art for atomic force microscopy, which is the most widely available method. The field is first motivated as a new way of tracking pharmaceutical effects, followed by a basic introduction targeted at pharmacists on how to measure cellular stiffness. The review then moves on to the current state of the knowledge in terms of experimental results and supplementary methods such as fluorescence microscopy that can give relevant additional information. Finally, rheological approaches as well as the theoretical interpretations are presented before ending on additional methods and outlooks.

Single-Chain Inherent Elasticity of Macromolecules: From Concept to Applications

"The Tao begets the One. One begets all things of the world." These words of wisdom from Tao Te Ching are of great inspiration to scientists in polymer materials science and engineering: The "One" means an individual polymer chain while polymer materials consist of numerous chains. The understanding of the single-chain mechanics of polymers is crucial for the bottom-up rational design of polymer materials. With a backbone and side chains, a polymer chain is more complex than a small molecule. Moreover, an individual polymer chain is usually placed in a complicated environment (such as solvent, cosolute, and solid surface), which significantly affects the behaviors of the chain. With all these factors, it is hard to fully understand the elastic behaviors of polymers. Herein, we will first introduce the concept of the single-chain inherent elasticity of polymers, which is a fundamental property determined by the polymer backbone. Then, the applications of inherent elasticity in quantifying the effects of side chains and surrounding environment will be summarized. Finally, the challenges in related fields at present and potential research directions in the future will be discussed.

Highly glycosylated MUC1 mediates high affinity L-selectin binding at the human endometrial surface

Background

Sialyl-Lewis X/L-selectin high affinity binding interactions between transmembrane O-glycosylated mucins proteins and the embryo have been implicated in implantation processes within the human reproductive system. However, the adhesive properties of these mucins at the endometrial cell surface are difficult to resolve due to known discrepancies between in vivo models and the human reproductive system and a lack of sensitivity in current in vitro models. To overcome these limitations, an in vitro model of the human endometrial epithelial was interrogated with single molecule force spectroscopy (SMFS) to delineate the molecular configurations of mucin proteins that mediate the high affinity L-selectin binding required for human embryo implantation.

Results

This study reveals that MUC1 contributes to both the intrinsic and extrinsic adhesive properties of the HEC-1 cellular surface. High expression of MUC1 on the cell surface led to a significantly increased intrinsic adhesion force (148 pN vs. 271 pN, p < 0.001), whereas this adhesion force was significantly reduced (271 pN vs. 118 pN, p < 0.001) following siRNA mediated MUC1 ablation. Whilst high expression of MUC1 displaying elevated glycosylation led to strong extrinsic (> 400 pN) L-selectin binding at the cell surface, low expression of MUC1 with reduced glycosylation resulted in significantly less (≤200 pN) binding events.

Conclusions

An optimal level of MUC1 together with highly glycosylated decoration of the protein is critical for high affinity L-selectin binding. This study demonstrates that MUC1 contributes to cellular adhesive properties which may function to facilitate trophoblast binding to the endometrial cell surface through the L-selectin/sialyl-Lewis x adhesion system subsequent to implantation.

Investigation of the interaction between MeCP2 methyl-CpG binding domain and methylated DNA by single molecule force spectroscopy

MeCP2 is an essential transcriptional repressor that mediates transcriptional inhibition by binding to methylated DNA. The binding specificity of MeCP2 protein to methylated DNA was considered to depend on its methyl-CpG binding domain (MBD). In this study, we used atomic force microscope based single-molecular force spectroscopy to investigate the interaction of MeCP2 MBD and methylated DNA. The specific interaction forces of the MeCP2 MBD-methylated DNA complexes were measured for the first time. The dynamics was also investigated by measuring the unbinding force of the complex at different loading rates. In addition, the distribution of unbinding forces and binding probabilities of MeCP2 MBD and different DNA were studied at the same loading rate. It was found that MeCP2 MBD had weak interaction with hemi-methylated and unmethylated DNA compared to methylated DNA. This work revealed the binding characteristics of MeCP2 MBD and methylated DNA at the single-molecule level. It provides a new idea for exploring the molecular mechanism of MeCP2 in regulating methylation signals.

Unzipping Mechanism of Free and Polyarginine-Conjugated DNA-PNA Duplexes, Preconfined Inside the α-Hemolysin Nanopore

In this work, comparative studies on DNA-PNA and polyarginine-conjugated DNA-PNA duplexes unzipping inside the α-hemolysin nanopore (α-HL) are presented. We identified significant differences in the blockade currents, as the applied voltage across the nanopore facilitated the duplex capture inside the nanopore's vestibule against the constriction region, subsequent cDNA strand insertion inside the nanopore's β-barrel past the constriction site, its complete unzip from the duplex, and translocation. We observed that inside the voltage-biased nanopore, polyarginine-conjugated DNA-PNA duplexes dehybridize faster than their DNA-PNA counterparts and proposed a model to describe the duplex unzipping. This study identifies key particularities of DNA-PNA duplex unzipping as it takes place inside the nanopore and being preceded by entrapment in the vestibule domain of the α-HL. Our results are a crucial step toward understanding the nucleic acids duplexes unzipping kinetics variability, in confined, variable geometries.

Micro-Cantilever Displacement Detection Based in Optical Fiber Tip

This work demonstrates the potential of combining a microsphere with a tip for the functionality of the contact sensor. This sensor consists of a tip aligned with the fiber core and a microsphere, which appears during tip formation. This new structure was produced using the electric arc machine. The sensor operation consists of the variation of the tip curvature, which causes a variation of the optical paths and, consequently, a change in the output signal. The study of this micro-cantilever consisted of an exploration of the contact mode. In addition, the sensor was characterized by temperature, which shows very low sensitivity and vibration. This last characterization was performed with two configurations parallel and perpendicular to the oscillating surface. The perpendicular case showed higher sensitivity and has an operating band of 0 Hz to 20 kHz. In this configuration, for frequencies up to 2 Hz, the intensity varies linearly with the frequencies and with a sensitivity of 0.032 ± 0.001 (Hz^-1). For the parallel case, the operating band was from 1.5 kHz to 7 kHz.

Detection of streptavidin-biotin intermediate metastable states at the single-molecule level using high temporal-resolution atomic force microscopy

Although the streptavidin-biotin intermolecular bond has been extensively used in many applications due to its high binding affinity, its exact nature and interaction mechanism have not been well understood. Several reports from previous studies gave a wide range of results in terms of the system's energy potential landscape because of bypassing some short-lived states in the detection process. We employed a quasi-static process of slowly loading force onto the bond (loading rate = 20 pN s-1) to minimize the force-induced disruption and to provide a chance to explore the system in near-equilibrium. Therein, by utilizing a fast sampling rate for the detection of force by atomic force microscopy (20 μs per data point), several transient states of the system were clearly resolved in our force spectroscopy measurements. These key strategies allow the determination of the states' relative positions and free energy levels along the pulling reaction coordinate for the illustration of an energy landscape of the system.

Using Force Spectroscopy to Probe Coiled-Coil Assembly and Membrane Fusion

Force spectroscopy allows the manipulation of single molecules and the characterization of their properties and interactions thereby rendering it a powerful tool for biological sciences. Force spectroscopy at the level of individual molecules requires force resolution in the piconewton regime as achieved by optical tweezers (OT), magnetic tweezers (MT), and atomic force microscopy (AFM) with AFM providing the largest force range from tenth of piconewton to several micronewton. In membrane probe spectroscopy the commonly used sharp cantilever tip is replaced by a lipid-coated glass sphere. This technique expands the scope of force spectroscopy to processes at and between lipid bilayers, like the formation of coiled coils between SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) proteins as well as subsequent membrane fusion. To this end, two solid-supported membranes equipped with SNARE proteins or fusion peptides are separately deposited on a flat glassy surface and on a micrometer glass sphere attached to the end of a tipless AFM cantilever. These two membranes are rapidly brought into contact until a defined force is reached. The AFM deflection readout is used to monitor the distance between the two bilayers, which allows to observe and identify fusion processes of the two lipid membranes, while the forces needed to separate the two surfaces give insights into the formation of SNARE complexes. By changing the contact pressure one can access fusion kinetics and to some extent reconstruct the energy landscape of membrane fusion. In this chapter we describe the preparation of membrane-coated colloidal probes attached to AFM cantilevers, experimental procedures, and necessary data analysis to perform membrane probe spectroscopy in the presence of fusogenic peptides or proteins.

Valsartan impedes epinephrine-induced ICAM-4 activation on normal, sickle cell trait and sickle cell disease red blood cells

Abnormal red blood cell (RBC) adhesion to endothelial αvβ3 plays a crucial role in triggering vaso-occlusive episodes in sickle cell disease (SCD). It is known that epinephrine, a β-adrenergic receptor (β-AR) stimulator, increases the RBC surface density of active intercellular adhesion molecule-4 (ICAM-4) which binds to the endothelial αvβ3. It has also been demonstrated that in human embryonic kidney 293 cells, mouse cardiomyocytes, and COS-7 cell lines, the β-adrenergic and renin-angiotensin systems are interrelated and that there is a direct interaction and cross-regulation between β-AR and angiotensin II type 1 receptor (AT1R). Selective blockade of AT1R reciprocally inhibits the downstream signaling of β-ARs, similar to the inhibition observed in the presence of a β-AR-blocker. However, it is not known if this mechanism is active in human RBCs. Here, we studied the effect of valsartan, an AT1R blocker, on the surface density of active ICAM-4 receptors in normal, sickle cell trait, and homozygous sickle RBCs. We applied single molecule force spectroscopy to detect active ICAM-4 receptors on the RBC plasma membrane with and without the presence of valsartan and epinephrine. We found that epinephrine significantly increased whereas valsartan decreased their surface density. Importantly, we found that pretreatment of RBCs with valsartan significantly impeded the activation of ICAM-4 receptors induced by epinephrine. The observed reduced expression of active ICAM-4 receptors on the RBC plasma membrane leads us to conjecture that valsartan may be used as a supporting remedy for the prevention and treatment of vaso-occlusive crisis in SCD.

B cell mechanosensing: A mechanistic overview

B cells are essential to the adaptive immune system for providing the humoral immunity against cohorts of pathogens. The presentation of antigen to the B cell receptor (BCR) leads to the initiation of B cell activation, which is a process sensitive to the stiffness features of the substrates presenting the antigens. Mechanosensing of the B cells, potentiated through BCR signaling and the adhesion molecules, efficiently regulates B cell activation, proliferation and subsequent antibody responses. Defects in sensing of the antigen-presenting substrates can lead to the activation of autoreactive B cells in autoimmune diseases. The use of high-resolution, high-speed live-cell imaging along with the sophisticated biophysical materials, has uncovered the mechanisms underlying the initiation of B cell activation within seconds of its engagement with the antigen presenting substrates. In this chapter, we reviewed studies that have contributed to uncover the molecular mechanisms of B cell mechanosensing during the initiation of B cell activation.

Goodness of fit testing in dynamic single-molecule force spectroscopy

Dynamic single-molecule force spectroscopy (SMFS) is a powerful method to characterize the mechanical stability of biomolecules. We address the problem that the standard manner of reporting the extracted energy landscape parameters does not reveal the intrinsic statistical errors associated with them. This problem becomes particularly relevant when SMFS is used to compare two or more different molecular systems. Here, we propose two methods that allow for a straightforward test of statistical significance. We illustrate the power of the methods by applying them to the experimental results obtained for three dimeric coiled coils of different lengths. Both methods are general and may be applied to any problem involving the fit of models with two correlated parameters.

Ligand-Receptor Binding on Cell Membrane: Dynamic Force Spectroscopy Applications

Ligand-receptor recognition on the cell membrane enables the communication of cells with the extracellular environment. Atomic force microscopy (AFM)-based single-molecule dynamic force spectroscopy represents one of the most powerful techniques available to directly investigate ligand-receptor recognition under physiological conditions without considerable disruption to cells. It provides important information for research on biological processes, disease pathogenesis, and mechanism of drugs. Here we describe an example of applying single-molecule dynamic force spectroscopy to study the binding of epidermal growth factor (EGF) to its receptor EGFR, as well as the effect of two clinical drugs, Pertuzumab and Trastuzumab, on the interaction of EGF and EGFR.

Label-free determination of adenosine and mercury ions according to force mapping-based force-to-color variety

Single molecule force spectroscopy based on atomic force microscopy (AFM) is a simple and sensitive technique to probe molecular recognition forces. Here we demonstrate that visual color-intensity analysis of single molecule force mapping (SMFM) can be employed as a quick and convenient force-to-color detection towards the presence of various dissolved analytes in very low concentrations. To achieve this aim, analyte-specific single-strand DNA aptamers are first bound to an AFM tip. The measured forces between the functionalized tip and a suitable substrate, namely either a clean surface or a surface functionalized with the complementary DNA oligomer, change when a critical concentration of the analyte is reached. The current SMFM-based visual biosensing shows improved developments like higher sensitivity, lower detection limits, quicker detection, and much simple readout. The color of the obtained force maps reveals the force intensity, which gives a highly selective and immediate visual force-to-color response towards the presence of adenosine (above ∼0.1 nM) and Hg²⁺ (∼10 pM). The strategies shown in this work will be helpful to design and fabricate aptasensors for biomedical analysis as well as to understand the molecular interactions between DNA hybridization.

Langmuir-Blodgett Procedure to Precisely Control the Coverage of Functionalized AFM Cantilevers for SMFS Measurements: Application with Cellulose Nanocrystals

Atomic force microscopy (AFM) experiments with functionalized tips are currently one of the most powerful tools to locally measure adhesion forces via single-molecule force spectroscopy (SMFS) measurements. The main difficulty is to precisely control the attachment of biomolecules to the cantilever. Different chemistry procedures have been developed including the use of spacer molecules. Even if a process works well for small biomolecules such as antibodies, issues remain regarding nanoparticles or larger objects such as cellulose nanocrystals because it is difficult to precisely control their coverage and homogeneity. In this work, an original procedure based on the Langmuir-Blodgett (LB) technique was implemented for lever functionalization with cellulose nanocrystals and compared with classical chemical strategies. LB shows to be almost 6.0-fold more efficient than chemical procedure in terms of cellulose nanocrystals coverage attachment. Moreover, the LB technology provides advantage of not requiring linker molecules, which could have detrimental effects such as overestimation of the interaction force. The structural characterization and SMFS measurements of lignocellulosic polymers show that this strategy enables the precise control of the lever coverage, which improves the accuracy of the adhesion measurements. Such methodology is expected to strongly impact the AFM tip/tipless functionalization and SMFS measurements in different fields.

The role of hydrophobic, aromatic and electrostatic interactions between amino acid residues and a titanium dioxide surface

Understanding the nature of interactions between inorganic surfaces and biomolecules, such as amino acids and peptides, can enhance the development of new materials.

Dynamic force spectroscopy of synthetic oligorotaxane foldamers

Wholly synthetic molecules involving both mechanical bonds and a folded secondary structure are one of the most promising architectures for the design of functional molecular machines with unprecedented properties. Here, we report dynamic single-molecule force spectroscopy experiments that explore the energetic details of donor-acceptor oligorotaxane foldamers, a class of molecular switches. The mechanical breaking of the donor-acceptor interactions responsible for the folded structure shows a high constant rupture force over a broad range of loading rates, covering three orders of magnitude. In comparison with dynamic force spectroscopy performed during the past 20 y on various (bio)molecules, the near-equilibrium regime of oligorotaxanes persists at much higher loading rates, at which biomolecules have reached their kinetic regime, illustrating the very fast dynamics and remarkable rebinding capabilities of the intramolecular donor-acceptor interactions. We focused on one single interaction at a time and probed the stochastic rupture and rebinding paths. Using the Crooks fluctuation theorem, we measured the mechanical work produced during the breaking and rebinding to determine a free-energy difference, ΔG, of 6 kcal·mol^-1 between the two local conformations around a single bond.

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20-40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10^-3 s^-1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s^-1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies.

Regulation of Active ICAM-4 on Normal and Sickle Cell Disease RBCs via AKAPs Is Revealed by AFM

Human healthy (wild-type (WT)) and homozygous sickle (SS) red blood cells (RBCs) express a large number of surface receptors that mediate cell adhesion between RBCs, and between RBCs and white blood cells, platelets, and the endothelium. In sickle cell disease (SCD), abnormal adhesion of RBCs to endothelial cells is mediated by the intercellular adhesion molecule-4 (ICAM-4), which appears on the RBC membrane and binds to the endothelial αvβ3 integrin. This is a key factor in the initiation of vaso-occlusive episodes, the hallmark of SCD. A better understanding of the mechanisms that control RBC adhesion to endothelium may lead to novel approaches to both prevention and treatment of vaso-occlusive episodes in SCD. One important mechanism of ICAM-4 activation occurs via the cyclic adenosine monophosphate-protein kinase A (cAMP-PKA)-dependent signaling pathway. Here, we employed an in vitro technique called single-molecule force spectroscopy to study the effect of modulation of the cAMP-PKA-dependent pathway on ICAM-4 receptor activation. We quantified the frequency of active ICAM-4 receptors on WT-RBC and SS-RBC membranes, as well as the median unbinding force between ICAM-4 and αvβ3. We showed that the collective frequency of unbinding events in WT-RBCs is not significantly different from that of SS-RBCs. This result was confirmed by confocal microscopy experiments. In addition, we showed that incubation of normal RBCs and SS-RBCs with epinephrine, a catecholamine that binds to the β-adrenergic receptor and activates the cAMP-PKA-dependent pathway, caused a significant increase in the frequency of active ICAM-4 receptors in both normal RBCs and SS-RBCs. However, the unbinding force between ICAM-4 and the corresponding ligand αvβ3 remained the same. Furthermore, we demonstrated that forskolin, an adenylyl cyclase activator, significantly increased the frequency of ICAM-4 receptors in WT-RBCs and SS-RBCs, confirming that the activation of ICAM-4 is regulated by the cAMP-PKA pathway. Finally, we showed that A-kinase anchoring proteins play an essential role in ICAM-4 activation.

Single versus dual-binding conformations in cellulosomal cohesin-dockerin complexes

Cohesins and dockerins are complementary interacting protein modules that form stable and highly specific receptor-ligand complexes. They play a crucial role in the assembly of cellulose-degrading multi-enzyme complexes called cellulosomes and have potential applicability in several technology areas, including biomass conversion processes. Here, we describe several exceptional properties of cohesin-dockerin complexes, including their tenacious biochemical affinity, remarkably high mechanostability and a dual-binding mode of recognition that is contrary to the conventional lock-and-key model of receptor-ligand interactions. We focus on structural aspects of the dual mode of cohesin-dockerin binding, highlighting recent single-molecule analysis techniques for its explicit characterization.

Revealing the role of catechol moieties in the interactions between peptides and inorganic surfaces

Catechol (1,2-dihydroxy benzene) moieties are being widely used today in new adhesive technologies. Understanding their mechanism of action is therefore of high importance for developing their applications in materials science. This paper describes a single-molecule study of the interactions between catechol-related amino acid residues and a well-defined titanium dioxide (TiO2) surface. It is the first quantified measurement of the adhesion of these residues with a well-defined TiO2 surface. Single-molecule force spectroscopy measurements with AFM determined the role of different substitutions of the catechol moiety on the aromatic ring in the adhesion to the surface. These results shed light on the nature of interactions between these residues and inorganic metal oxide surfaces. This information is important for the design and fabrication of catechol-based materials such as hydrogels, coatings, and composites. Specifically, the interaction with TiO2 is important for the development of solar cells.

Force distribution in a semiflexible loop

Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed "phase-space sampling," we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.

Interaction of the Hydrophobic Tip of an Atomic Force Microscope with Oligopeptides Immobilized Using Short and Long Tethers

We report an investigation of the adhesive force generated between the hydrophobic tip of an atomic force microscope (AFM) and surfaces presenting oligopeptides immobilized using either short (∼1 nm) or long (∼60 nm) tethers. Specifically, we used either sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SSMCC) or 10 kDa polyethylene glycol (PEG) end-functionalized with maleimide and N-hydroxysuccinimide groups to immobilize helical oligomers of β-amino acids (β-peptides) to mixed monolayers presenting tetraethylene glycol (EG4) and amine-terminated EG4 (EG4N) groups. When SSMCC was used to immobilize the β-peptides, we measured the adhesive interaction between the AFM tip and surface to rupture through a single event with magnitude consistent with the interaction of a single β-peptide with the AFM tip. Surprisingly, this occurred even when, on average, multiple β-peptides were located within the interaction area between the AFM tip and surface. In contrast, when using the long 10 kDa PEG tether, we observed the magnitude of the adhesive interaction as well as the dynamics of the rupture events to unmask the presence of the multiple β-peptides within the interaction area. To provide insight into these observations, we formulated a simple mechanical model of the interaction of the AFM tip with the immobilized β-peptides and used the model to demonstrate that adhesion measurements performed using short tethers (but not long tethers) are dominated by the interaction of single β-peptides because (i) the mechanical properties of the short tether are highly nonlinear, thus causing one β-peptide to dominate the adhesion force at the point of rupture, and (ii) the AFM cantilever is mechanically unstable following the rupture of the adhesive interaction with a single β-peptide. Overall, our study reveals that short tethers offer the basis of an approach that facilitates measurement of adhesive interactions with single molecules presented at surfaces.

Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for ‘lab-on-a-chip’ type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored.

The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy

The cell membrane is one of the most complicated biological complexes, and long-term fierce debates regarding the cell membrane persist because of technical hurdles. With the rapid development of nanotechnology and single-molecule techniques, our understanding of cell membranes has substantially increased. Atomic force microscopy (AFM) has provided several unprecedented advances (e.g., high resolution, three-dimensional and in situ measurements) in the study of cell membranes and has been used to systematically dissect the membrane structure in situ from both sides of membranes; as a result, novel models of cell membranes have recently been proposed. This review summarizes the new progress regarding membrane structure using in situ AFM and single-molecule force spectroscopy (SMFS), which may shed light on the study of the structure and functions of cell membranes.

Molecular Mechanisms of Ultrafiltration Membrane Fouling in Polymer-Flooding Wastewater Treatment: Role of Ions in Polymeric Fouling

Polymer (i.e., anionic polyacrylamide (APAM)) fouling of polyvinylidene fluoride (PVDF) ultrafiltration (UF) membranes and its relationships to intermolecular interactions were investigated using atomic force microscopy (AFM). Distinct relations were obtained between the AFM force spectroscopy measurements and calculated fouling resistance over the concentration polarization layer (CPL) and gel layer (GL). The measured maximum adhesion forces (Fad,max) were closely correlated with the CPL resistance (Rp), and the proposed molecular packing property (largely based on the shape of AFM force spectroscopy curve) of the APAM chains was related to the GL resistance (Rg). Calcium ions (Ca(2+)) and sodium ions (Na(+)) caused more severe fouling. In the presence of Ca(2+), the large Rp corresponded to high foulant-foulant Fad,max, resulting in high flux loss. In addition, the Rg with Ca(2+) was minor, but the flux recovery rate after chemical cleaning was the lowest, indicating that Ca(2+) created more challenges in GL cleaning. With Na(+), the fouling behavior was complicated and concentration-dependent. The GL structures with Na(+), which might correspond to the proposed molecular packing states among APAM chains, played essential roles in membrane fouling and GL cleaning.

AFM-based force spectroscopy for bioimaging and biosensing

AFM-based force spectroscopy shows wide bio-related applications especially for bioimaging and biosensing.

Elucidating the mechanism of interaction between peptides and inorganic surfaces

Understanding the mechanism of interaction between peptides and inorganic materials is of high importance for the development of new composite materials. Here, we combined an experimental approach along with molecular simulations in order to gain insights into this binding process. Using single molecule force spectroscopy by atomic force microscopy and molecular simulations we studied the binding of a peptide towards an inorganic substrate. By performing alanine scan we examined the propensity of each amino acid in the peptide sequence to bind the substrate (mica). Our results indicate that this binding is not controlled by the specific sequence of the peptide, but rather by its conformational freedom in solution versus its freedom when it is in proximity to the substrate. When the conformational freedom of the peptide is identical in both environments, the peptide will not adhere to the substrate. However, when the conformational freedom is reduced, i.e., when the peptide is in close proximity to the substrate, binding will occur. These results shed light on the interaction between peptides and inorganic materials.

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

Multivalent biomolecular interactions allow for a balanced interplay of mechanical stability and malleability, and nature makes widely use of it. For instance, systems of similar thermal stability may have very different rupture forces. Thus it is of paramount interest to study and understand the mechanical properties of multivalent systems through well-characterized model systems. We analyzed the rupture behavior of three different bivalent pyridine coordination complexes with Cu²⁺ in aqueous environment by single-molecule force spectroscopy. Those complexes share the same supramolecular interaction leading to similar thermal off-rates in the range of 0.09 and 0.36 s⁻¹, compared to 1.7 s⁻¹ for the monovalent complex. On the other hand, the backbones exhibit different flexibility, and we determined a broad range of rupture lengths between 0.3 and 1.1 nm, with higher most-probable rupture forces for the stiffer backbones. Interestingly, the medium-flexible connection has the highest rupture forces, whereas the ligands with highest and lowest rigidity seem to be prone to consecutive bond rupture. The presented approach allows separating bond and backbone effects in multivalent model systems.

Laser actuation of cantilevers for picometre amplitude dynamic force microscopy

As nanoscale and molecular devices become reality, the ability to probe materials on these scales is increasing in importance. To address this, we have developed a dynamic force microscopy technique where the flexure of the microcantilever is excited using an intensity modulated laser beam to achieve modulation on the picoscale. The flexure arises from thermally induced bending through differential expansion and the conservation of momentum when the photons are reflected and absorbed by the cantilever. In this study, we investigated the photothermal and photon pressure responses of monolithic and layered cantilevers using a modulated laser in air and immersed in water. The developed photon actuation technique is applied to the stretching of single polymer chains.

Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography

We report direct, concurrent measurements of the forces and currents associated with the translocation of a single-stranded DNA molecule tethered to the tip of an atomic force microscope (AFM) cantilever through synthetic pores with topagraphies comparable to the DNA. These measurements were performed to gauge the signal available for sequencing and the electric force required to impel a single molecule through synthetic nanopores ranging from 1.0 to 3.5 nm in diameter in silicon nitride membranes 6-10 nm thick. The measurements revealed that a molecule can slide relatively frictionlessly through a pore, but regular fluctuations are observed intermittently in the force (and the current) every 0.35-0.72 nm, which are attributed to individual nucleotides translating through the nanopore in a turnstile-like motion.

Applications of biosensing atomic force microscopy in monitoring drug and nanoparticle delivery

INTRODUCTION

The therapeutic effects of medicinal drugs not only depend on their properties, but also on effective transport to the target receptor. Here we highlight recent developments in this discipline and show applications of atomic force microscopy (AFM) that enable us to track the effects of drugs and the effectiveness of nanoparticle delivery at the single molecule level.

AREAS COVERED

Physiological AFM imaging enables visualization of topographical changes to cells as a result of drug exposure and allows observation of cellular responses that yield morphological changes. When we upgrade the regular measuring tip to a molecular biosensor, it enables investigation of functional changes at the molecular level via single molecule force spectroscopy.

EXPERT OPINION

Biosensing AFM techniques have generated powerful tools to monitor drug delivery in (living) cells. While technical developments in actual AFM methods have simplified measurements at relevant physiological conditions, understanding both the biological and technical background is still a crucial factor. However, due to its potential impact, we expect the number of application-based biosensing AFM techniques to further increase in the near future.

Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

Single-chain mechanics of poly(N,N-diethylacrylamide) and poly(N-isopropylacrylamide): comparative study reveals the effect of hydrogen bond donors

The single-chain mechanics of two similar thermosensitive polymers, poly(N,N-diethylacrylamide) (PDEAM) and poly(N-isopropylacrylamide) (PNIPAM), have been studied by atomic force microscopy-based single-molecule force spectroscopy (SMFS). In a typical nonpolar organic solvent, octane, both of the polymers show the same inherent elasticity, although they have different substitutional groups. However, the mechanics of the two polymers presents large differences in water. The energies needed for the rearrangement of the bound water during elongation at room temperature are estimated by the SMFS method at the single-chain level, which is ~1.13 ± 0.10 and ~5.19 ± 0.10 kJ/mol for PDEAM and PNIPAM, respectively. In addition, PNIPAM shows a temperature-dependent single-chain mechanics when the temperature is increased across the lower critical solution temperature (LCST), while PDEAM does not. These differences observed in aqueous solution originate from the different structures of the two polymers. With a hydrogen bond donor in the amide group, PNIPAM will be more hydrated when T < LCST. When T > LCST, PNIPAM will have larger changes in both conformation and hydration. These findings also suggest that PNIPAM is a good candidate for a thermo-driven single-molecule motor, while PDEAM is not.

Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy

This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands

Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding.

Inherent stretching elasticity of a single polymer chain with a carbon-carbon backbone

We study the single-chain elasticities of three kinds of neutral polymers with a carbon-carbon (C-C) backbone by atomic force microscopy-based single-molecule force spectroscopy in a nonpolar solvent (octane), aiming at measuring the inherent chain elasticity of this very important class of polymers. The finding that the single-chain elasticities of all three polymers in octane are virtually identical in the entire force region implies that the side chains of the polymers have no detectable effects on the single-chain elasticity. By utilizing the single-chain elasticity from quantum mechanics calculations, the freely rotating chain model can provide the best fitting curve when each C-C bond is set to be the rotating unit. Although there are some exceptions when the side chain is very huge, our work provides a general result for the inherent elasticity of single neutral flexible polymer chains with C-C backbones.