Supramolecular chemistry at the single-molecule level

Inner and Interfacial Environmental Nanoarchitectonics of Supramolecular Assemblies Formed by Amphiphiles: from Emergence to Application

The inner and interfacial environments of self-assemblies provide fascinating nano-space for selective and efficient chemical reactions and processes. In biological systems, various chemical reactions, molecular recognition, and transport occur precisely and selectively by virtue of effective molecular interactions on biological membranes and proteins. Considering these advantages and the concept of nanoarchitectonics, we demonstrated that the photochromism of a lophine dimer was accelerated by using confined nano-spaces formed by surfactant micelles. The photoresponsive micelles were used for the rapid controlled release of a model drug upon ultraviolet light irradiation. Furthermore, selective ion recognition inside the self-assembled molecular films at the interfaces was investigated. The anion-π interaction between the anion and an electron-deficient aromatic ring was evaluated on a solid substrate modified with a naphthalenediimide (NDI) analog. Force curve measurements afforded a quantitative analysis of anion-π interactions on the NDI film. The strength of anion-π interactions is regulated by the electric fields on the electrode. An optical probe was developed to visualize the distribution of Cs ions in the soil, plant bodies, and aqueous media using an optode system. Advances in the development of molecular functional systems are expected based not only on molecular structures but also on the spaces and environments produced by them.

Determination of protein-protein interactions at the single-molecule level using optical tweezers

Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (k_off, k_on), affinity values (K_D), energy to the transition state ΔG^≠, distance to the transition state Δx^≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

Evidenced cucurbit[n]uril-based host-guest interactions using single-molecule force spectroscopy

In this work, enhanced guest-pair interactions in the cavity of cucurbit[8]uril (CB[8]) are quantitatively determined using single-molecule force spectroscopy (SMFS). Significantly, the light-driven dynamic conformational change of guest pairs leads to a rupture force switching between the connected and broken CB[8]-mediated heteroternary complexation with viologen and bis(azobenzene) derivatives. SMFS is further utilized to detect methyl viologen based on the competitive host-guest interaction toward the guest in CB[8] or CB[7]. These findings highlight the extraordinary power of SMFS in supramolecular chemistry and will contribute to the fundamental understanding of the mechanochemical behavior of host-guest interactions.

Anion-π interaction at the solid/water interfaces

Anion-π interaction has been found to play a key role in interfacial phenomena. In this study, we evaluated the anion-π interactions at the solid/water interface. Anion adsorption originating from anion-π interaction at the interfaces followed the hydration energy and the presence of conjugated systems of the anions by the QCM measurements. Force curve measurements revealed that the single-molecule force of anion-π interaction between an NDI unit and the negatively charged surface of the cantilever was ∼40 pN. To the best of our knowledge, this is the first example of obtaining a single-molecule force for anion-π interactions.

Exploring the Sulfatase 1 Catch Bond Free Energy Landscape using Jarzynski's Equality

In non-covalent biological adhesion, molecular bonds commonly exhibit a monotonously decreasing life time when subjected to tensile forces (slip bonds). In contrast, catch bonds behave counter intuitively, as they show an increased life time within a certain force interval. To date only a hand full of catch bond displaying systems have been identified. In order to unveil their nature, a number of structural and phenomenological models have been introduced. Regardless of the individual causes for catch bond behavior, it appears evident that the free energy landscapes of these interactions bear more than one binding state. Here, we investigated the catch bond interaction between the hydrophilic domain of the human cell surface sulfatase 1 (Sulf1HD) and its physiological substrate heparan sulfate (HS) by atomic force microscopy based single molecule force spectroscopy (AFM-SMFS). Using Jarzynski’s equality, we estimated the associated Gibbs free energy and provide a comprehensive thermodynamic and kinetic characterization of Sulf1HD/HS interaction. Interestingly, the binding potential landscape exhibits two distinct potential wells which confirms the recently suggested two state binding. Even though structural data of Sulf1HD is lacking, our results allow to draft a detailed picture of the directed and processive desulfation of HS.

Perioperative Comparison of Hip Arthroplasty Using the Direct Anterior Approach with the Posterolateral Approach

Purpose

The aim of the current study is to report the advantage and disadvantage of total hip arthroplasty performed in direct anterior approach (DAA) by comparing it to the posterolateral approach (PLA).

Materials and Methods

Twenty-five hip arthroplasty done in DAA (12 total hip arthroplasty [THA] and 13 bipolar hemiarthroplasty [BHA]) were compared with the same number done in PLA (13 THA and 12 BHA). Intraoperative assessments including operation time, anesthetic time, bleeding amount were recorded with intraoperative complications. Immediate postoperatively, position of the prosthesis and leg length discrepancy were measured and were compared between the two approaches.

Results

The operation time was 22 minutes and 19 minutes longer in DAA for THA and BHA respectively while the anesthetic time difference was 26 and 10 respectively. However, these parameters showed no statistical difference. No significance was found when bleeding amount was compared. For DAA, cup alignment was within safe zone in 100% both for inclination and for anteversion while this was 83.3% and 75.0% respectively in PLA. Leg length difference was 3 mm in DAA and 5 mm in PLA but had no significant difference. Tensor fascia lata tear was the most common complication occurring in 9 patients.

Conclusion

Although significant was not reached there was trend toward more operation time and anesthetic time when DAA was used. However, the trend also showed that cup and stem were likely to be in more accurate position and in adequate size which is likely due to the accurate use of fluoroscopy.

Direct measurement of interaction forces between a platinum dichloride complex and DNA molecules

The interaction forces between a platinum dichloride complex and DNA molecules have been studied using atomic force microscopy (AFM). The platinum dichloride complex, di-dimethylsulfoxide-dichloroplatinum (II) (Pt(DMSO)₂Cl₂), was immobilized on an AFM probe by coordinating the platinum to two amino groups to form a complex similar to Pt(en)Cl₂, which is structurally similar to cisplatin. The retraction forces were measured between the platinum complex and DNA molecules immobilized on mica plates using force curve measurements. The histogram of the retraction force for λ-DNA showed several peaks; the unit retraction force was estimated to be 130 pN for a pulling rate of 60 nm/s. The retraction forces were also measured separately for four single-base DNA oligomers (adenine, guanine, thymine, and cytosine). Retraction forces were frequently observed in the force curves for the DNA oligomers of guanine and adenine. For the guanine DNA oligomer, the most frequent retraction force was slightly lower than but very similar to the retraction force for λ-DNA. A higher retraction force was obtained for the adenine DNA oligomer than for the guanine oligomer. This result is consistent with a higher retraction activation energy of adenine with the Pt complex being than that of guanine because the kinetic rate constant for retraction correlates to exp(FΔx - ΔE) where ΔE is an activation energy, F is an applied force, and Δx is a displacement of distance.

Observing Single Molecules Complexing with Cucurbit[7]uril through Nanogap Surface-Enhanced Raman Spectroscopy

In recent years, single-molecule sensitivity achievable by surface-enhanced Raman spectroscopy (SERS) has been widely reported. We use this to investigate supramolecular host-guest chemistry with the macrocyclic host cucurbit[7]uril, on a few-to-single-molecule level. A nanogap geometry, comprising individual gold nanoparticles on a planar gold surface spaced by a single layer of molecules, gives intense SERS signals. Plasmonic coupling between the particle and the surface leads to strongly enhanced optical fields in the gap between them, with single-molecule sensitivity established using a modification of the well-known bianalyte method. Changes in the Raman modes of the host molecule are observed when single guests included inside its cavity internally stretch it. Anisotropic intermolecular interactions with the guest are found which show additional distinct features in the Raman modes of the host molecule.

Catch bond interaction between cell-surface sulfatase Sulf1 and glycosaminoglycans

In biological adhesion, the biophysical mechanism of specific biomolecular interaction can be divided in slip and catch bonds, respectively. Conceptually, slip bonds exhibit a reduced bond lifetime under increased external force and catch bonds, in contrast, exhibit an increased lifetime (for a certain force interval). Since 2003, a handful of biological systems have been identified to display catch bond properties. Upon investigating the specific interaction between the unique hydrophilic domain (HD) of the human cell-surface sulfatase Sulf1 against its physiological glycosaminoglycan (GAG) target heparan sulfate (HS) by single molecule force spectroscopy (SMFS), we found clear evidence of catch bond behavior in this system. The HD, ∼320 amino acids long with dominant positive charge, and its interaction with sulfated GAG-polymers were quantitatively investigated using atomic force microscopy (AFM) based force clamp spectroscopy (FCS) and dynamic force spectroscopy (DFS). In FCS experiments, we found that the catch bond character of HD against GAGs could be attributed to the GAG 6-O-sulfation site whereas only slip bond interaction can be observed in a GAG system where this site is explicitly lacking. We interpreted the binding data within the theoretical framework of a two state two path model, where two slip bonds are coupled forming a double-well interaction potential with an energy difference of ΔE ≈ 9 kBT and a compliance length of Δx ≈ 3.2 nm. Additional DFS experiments support this assumption and allow identification of these two coupled slip-bond states that behave consistently within the Kramers-Bell-Evans model of force-mediated dissociation.

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.

Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it?

Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.

Applications of supramolecular capsules derived from resorcin[4]arenes, calix[n]arenes and metallo-ligands: from biology to catalysis

This review summarizes supramolecular capsules based on resorcin[4]arenes, calix[n]arenes and metal–ligands, having concrete applications in biomedical field, catalysis and material science.

Selectivity assessment in host–guest complexes from single-crystal X-ray diffraction data: the cavitand–alcohol case

The solid-state selectivity of a cavitand receptor towards short alkyl chain alcohols was evaluated by analysis of X-ray diffraction data of isomorphous single crystals grown in competition binding experiments.

Single-molecule force spectroscopic study on chiral recognition of cysteine derivatives immobilized on a gold substrate by using AFM tips chemically modified with optically active crown ethers

The chiral recognition of cysteine derivatives on a gold substrate was investigated using AFM tips modified with optically active crown ethers.

Single-molecule force spectroscopy of selenium-containing amphiphilic block copolymer: toward disassembling the polymer micelles

Selenium-containing polymers are a new type of responsive polymer material. Here, a selenium-containing amphiphilic block copolymer (PEG-PUSe-PEG) has been investigated using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS). The deviation between force-extension curves of PEG-PUSe-PEG in water and in DMSO is found to be related to the disassembly of the micellar structures in water. SMFS experiments on PEG-PUSeox-PEG suggest that the change from selenide to oxidized selenone contributes significantly to the change in amphiphilicity, without obviously influencing the single-chain elasticity.

Long lifetime of hydrogen-bonded DNA basepairs by force spectroscopy

Electron-tunneling data suggest that a noncovalently-bonded complex of three molecules, two recognition molecules that present hydrogen-bond donor and acceptor sites via a carboxamide group, and a DNA base, remains bound for seconds. This is surprising, given that imino-proton exchange rates show that basepairs in a DNA double helix open on millisecond timescales. The long lifetime of the three-molecule complex was confirmed using force spectroscopy, but measurements on DNA basepairs are required to establish a comparison with the proton-exchange data. Here, we report on a dynamic force spectroscopy study of complexes between the bases adenine and thymine (A-T, two-hydrogen bonds) and 2-aminoadenine and thymine (2AA-T, three-hydrogen bonds). Bases were tethered to an AFM probe and mica substrate via long, covalently linked polymer tethers. Data for bond-survival probability versus force and the rupture-force distributions were well fitted by the Bell model. The resulting lifetime of the complexes at zero pulling force was ~2 s for two-hydrogen bonds (A-T) and ~4 s for three-hydrogen bonds (2AA-T). Thus, DNA basepairs in an AFM pulling experiment remain bonded for long times, even without the stabilizing influence of base-stacking in a double helix. This result suggests that the pathways for opening, and perhaps the open states themselves, are very different in the AFM and proton-exchange measurements.

Functional characterization of a supramolecular affinity switch at the single molecule level

Surface-immobilized and switchable resorcin[4]arene receptor molecules were quantitatively investigated with atomic force microscopy (AFM) and AFM-single molecule force spectroscopy (AFM-SMFS). The upper rim of the supramolecular receptor cavities was modified with two photodimerizable anthracene moieties. The molecular constitution can be externally switched and controlled by exposure to ultraviolet (UV) light and heat. The topography as well as the complexation affinity against small ammonium guest ions of the two isomers were investigated at the single molecule level. Our results demonstrate the feasibility to externally control the supramolecular receptor's affinity and simultaneously quantify and associate these binding properties with the structural change of the resorcin[4]arenes structure on the basis of the measured molecule corrugation height.

Distance dependence of near-field fluorescence enhancement and quenching of single quantum dots

In fluorescence microscopy and spectroscopy, energy transfer processes between single fluorophores and fluorophore quencher pairs play an important role in the investigation of molecular distances or orientations. At distances larger than about 3 nm these effects originate predominantly from dipolar coupling. As these experiments are commonly performed in homogenous media, effects at the interface boundaries can be neglected. Nevertheless, the combination of such assays with single-molecule manipulation techniques such as atomic force microscopy (AFM) requires a detailed understanding of the influence of interfaces on dipolar coupling effects. In the presented work we used a combined total internal reflection fluorescence microscopy (TIRFM)-AFM setup to elucidate this issue. We measured the fluorescence emission emanating from single quantum dots as a function of distance from the apex of a gold-coated cantilever tip. As well as fluorescence quenching at close proximity to the tip, we found a nonlinear and nonmonotonic distance dependence of the fluorescence emission. To confirm and interpret our findings we performed calculations on the basis of a simplified multiple multipole (MMP) approach, which successfully supports our experimental data. Moreover, we revealed and quantified the influence of interfering processes such as field enhancement confined at interface boundaries, mirror dipoles and (resonant) dipolar coupling.

Study on intercalations between double-stranded DNA and pyrene by single-molecule force spectroscopy: toward the detection of mismatch in DNA

Intercalation interactions between planar aromatic molecules and double-stranded DNA (dsDNA) relate to not only the structure of the guest molecules but also the structure of the dsDNA. In this letter, we have comparatively studied the intercalation between pyrene and fully matched or mismatched dsDNA using single-molecule force spectroscopy (SMFS). The significant difference in rupture forces, upon pyrene unbinding from 25-mer dsDNA with or without mismatches, is observed at the single-molecule level, indicating the influence of mismatches on the interaction between pyrene and dsDNA. In the analysis of the dynamic force spectra, two transition barriers are revealed for pyrene unbinding from matched sites in dsDNA and for pyrene unbinding from mismatched sites as well. These results suggest that SMFS is a useful single-molecule method for the detection of mismatches in dsDNA by the intercalation of pyrene.

AFM force mapping for characterizing patterns of electrostatic charges on SiO2 electrets

To characterize patterns of charges on electrets, Kelvin probe force microscopy (KFM) usually serves as a very useful tool to measure the electrostatic potential through an electric cycle; however, it is limited to electrets supported on conductive substrates. In this article, we demonstrate the use of atomic force microscopy (AFM) force mapping to visualize the pattern of charges on SiO(2) electrets. In contrast to KFM, AFM force mapping can be used for characterizing electrets that are formed not only on conductive substrates but also on nonconductive substrates. Functional groups can be introduced to the AFM tip to achieve the force mapping and to improve the resolution. Our study clearly indicates that AFM force mapping can serve as an optional method for the characterization of electrets.

Single-molecule force spectroscopy: a method for quantitative analysis of ligand–receptor interactions

The quantitative analysis of molecular interactions is of high interest in medical research. Most methods for the investigation of ligand–receptor complexes deal with huge ensembles of biomolecules, but often neglect interactions with low affinity or small subpopulations with different binding properties. Single-molecule force spectroscopy offers fascinating possibilities for the quantitative analysis of ligand–receptor interactions in a wide affinity range and the sensitivity to detect point mutations. Furthermore, this technique allows one to address questions about the related binding energy landscape. In this article, we introduce single-molecule force spectroscopy with a focus on novel developments in both data analysis and theoretical models for the technique. We also demonstrate two examples of the capabilities of this method.

A tripod molecular tip for single molecule ligand-receptor force spectroscopy by AFM

Tripod-shaped molecules were designed for chemical modification of the surface of probes used for atomic force microscopy (AFM). These chemically functionalized tips were used for chemical force spectroscopy (CFS) measurements of the ligand-protein receptor interaction in a biotin-NeutrAvidin model system. We demonstrate that by using this unique tripodal system, we can achieve significantly lower density of ligand on the AFM tip apex, which is optimal for true single molecule measurements. Furthermore, the molecular tripods form highly stable bonds to the AFM probes, leading to more robust and reproducible unbinding force data, thereby addressing one of the challenges in CFS studies. Histogram analysis of the hundreds of collected unbinding forces showed a specific distribution with a peak force maximum at approximately 165 pN, in good agreement with the previously reported data of single rupture events of biotin-avidin. We compared these molecular tripod tips with a molecular monopod. The results showed that the molecular tripods are more robust for repeated measurements. The distinct biotin-avidin force maximum was not observed in the control experiments. This indicated that the force distribution observed for molecular tripods corresponds to the specific rupture force between biotin and avidin. The improved robustness of molecular tripods for CFS will provide benefits in other ligand-receptor unbinding studies, including those of transmembrane receptor systems, which require high resolution, sensitivity, and reproducibility in force spectroscopy measurements.

Full view of single-molecule force spectroscopy of polyaniline in oxidized, reduced, and doped states

The macroscopic mechanical properties of polyaniline (PANI) lie mainly on two factors, the structure of molecular aggregations of polymers and the mechanical properties of a single polymer chain. The former factor is well revealed; however, the latter is rarely studied. In this article, we have employed atomic force microscopy-based single-molecule force spectroscopy to investigate the mechanical properties of a kind of water-soluble PANI at a single-molecular level. We have carried out the study comparatively on single-chain-stretching experiments of oxidized, reduced, and doped PANI and obtained a full view of the single-chain elasticity of PANI in all these states. It is found that oxidized and reduced PANI chains are rigid, and the oxidized PANI is more rigid than the reduced PANI. Such a difference in single-chain elasticity can be rationalized by the molecular structures that are composed of benzenoid diamine and quinoid diimine in different proportions. The doped PANI has been found to be more flexible than the oxidized and reduced PANI, and the modified freely jointed chain parameters of doped PANI are similar with those of a common flexible-chain polymer. The results have explained the molecular-level origin of the outstanding flexibilities of materials made of doped PANI.

Quantitative analysis of single-molecule RNA-protein interaction

RNA-binding proteins impact gene expression at the posttranscriptional level by interacting with cognate cis elements within the transcripts. Here, we apply dynamic single-molecule force spectroscopy to study the interaction of the Arabidopsis glycine-rich RNA-binding protein AtGRP8 with its RNA target. A dwell-time-dependent analysis of the single-molecule data in combination with competition assays and site-directed mutagenesis of both the RNA target and the RNA-binding domain of the protein allowed us to distinguish and quantify two different binding modes. For dwell times <0.21 s an unspecific complex with a lifetime of 0.56 s is observed, whereas dwell times >0.33 s result in a specific interaction with a lifetime of 208 s. The corresponding reaction lengths are 0.28 nm for the unspecific and 0.55 nm for the specific AtGRP8-RNA interactions, indicating formation of a tighter complex with increasing dwell time. These two binding modes cannot be dissected in ensemble experiments. Quantitative titration in RNA bandshift experiments yields an ensemble-averaged equilibrium constant of dissociation of KD = 2 x 10(-7) M. Assuming comparable on-rates for the specific and nonspecific binding modes allows us to estimate their free energies as DeltaG0 = -42 kJ/mol and DeltaG0 = -28 kJ/mol for the specific and nonspecific binding modes, respectively. Thus, we show that single-molecule force spectroscopy with a refined statistical analysis is a potent tool for the analysis of protein-RNA interactions without the drawback of ensemble averaging. This makes it possible to discriminate between different binding modes or sites and to analyze them quantitatively. We propose that this method could be applied to complex interactions of biomolecules in general, and be of particular interest for the investigation of multivalent binding reactions.

Binding mechanisms in supramolecular complexes

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force

The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins. Here, we report a molecular design based on oligo calix[4]arene catenanes-calixarene dimers held together by 16 hydrogen bridges-in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual nanocapsules. Experimental evidence, supported by molecular dynamics simulations, reveals the presence of an intermediate state involving the concerted rupture of the 16 hydrogen bridges. Stochastic modelling using a three-well potential under external load allows reconstruction of the energy landscape.

Interaction force of chitin-binding domains onto chitin surface

Interaction force of chitin-binding domains (ChBD1 and ChBD2) from a thermostable chitinase onto chitin surface was directly measured by atomic force microscopy (AFM) in a buffer solution. In the force curve measurement, multiple pull-off events were observed for the AFM tips functionalized with either ChBD1 or ChBD2, whereas the AFM tips terminated with nitrilotriacetic acid groups without ChBD showed no interaction peak, suggesting that the detected forces are derived from the binding functions of ChBDs onto the chitin surface. The force curve analyses indicate that the binding force of ChBD2 is stronger than that of ChBD1. This result suggests that ChBD1 and ChBD2 play different roles in adsorption onto chitin surface.

Refined procedure of evaluating experimental single-molecule force spectroscopy data

Dynamic force spectroscopy is a well-established tool to study molecular recognition in a wide range of binding affinities on the single-molecule level. The theoretical interpretation of these data is still very challenging and the models describe the experimental data only partly. In this paper we reconsider the basic assumptions of the models on the basis of an experimental data set and propose an approach of analyzing and quantitatively evaluating dynamic force spectroscopy data on single ligand-receptor complexes. We present our procedure to process and analyze the force-distance curves, to detect the rupture events in an automated manner, and to calculate quantitative parameters for a biophysical characterization of the investigated interaction.

Intercalation interactions between dsDNA and acridine studied by single molecule force spectroscopy

In this letter, we report on the direct measurement of the intercalation interactions between acridine and double-stranded DNA (dsDNA) using single molecule force spectroscopy. The interaction between acridine and dsDNA is broken by force of 36 pN at a loading rate of 5.0 nN/s. The most probable rupture force between acridine and dsDNA is dependent on the loading rate, indicating that the binding of acridine and dsDNA is a dynamic process. The combination of SMFS experimental data with the theoretical model clearly suggests the presence of two energy barriers along with an unbinding trajectory of acridine-dsDNA.

Direct measurements of the interaction between pyrene and graphite in aqueous media by single molecule force spectroscopy: understanding the pi-pi interactions

Pyrene derivatives can absorb onto the surface of carbon nanotubes and graphite particles through pi-pi interactions to functionalize these inorganic building blocks with organic surface moieties. Using single molecule force spectroscopy, we have demonstrated the first direct measurement of the interaction between pyrene and a graphite surface. In particular, we have connected a pyrene molecule onto an AFM tip via a flexible poly(ethylene glycol) (PEG) chain to ensure the formation of a molecular bridge. The pi-pi interaction between pyrene and graphite is thus indicated to be approximately 55 pN with no hysteresis between the desorption and adhesion forces.

Developing scanning probe–based nanodevices—stepping out of the laboratory into the clinic

This report focuses on nanotools based on the scanning force microscope (SFM) for imaging, measuring, and manipulating biological matter at the sub-micron scale. Because pathophysiological processes often occur at the (sub-) cellular scale, the SFM has opened the exciting possibility to spot diseases at a stage before they become symptomatic and cause functional impairments in the affected part of the body. Such presymptomatic detection will be key to developing effective therapies to slow or halt disease progression.

Optimized Biorecognition of Cytochrome c 551 and Azurin Immobilized on Thiol-Terminated Monolayers Assembled on Au(111) Substrates

Molecular recognition between two redox partners, azurin and cytochrome c 551, is studied at the single-molecule level by means of atomic force spectroscopy, after optimizing azurin adsorption on gold via sulfhydryl-terminated alkanethiol spacers. Our experiments provide evidence of specific interaction between the two partners, thereby demonstrating that azurin preserves biorecognition capability when assembled on gold via these spacers. Additionally, the measured single-molecule kinetic reaction rate results are consistent with a likely transient nature of the complex. Interestingly, the immobilization strategy adopted here, which was previously demonstrated to favor electrical coupling between azurin (AZ) and the metal electrode, is also found to facilitate AZ interaction with the redox partner, if compared to the case of AZ directly adsorbed on bare gold. Our findings confirm the key role of a well-designed immobilization strategy, capable of optimizing both biorecognition capabilities and electrical coupling with the conductive substrate at the single-molecule level, as a starting point for advanced applications of redox proteins for ultrasensitive biosensing.

The characterisation of rough particle contacts by atomic force microscopy

An Atomic Force Microscopy (AFM) reverse imaging technique has been used to determine the contact zone topography of glass and UO3 particles in contact with flat mica substrates. A method is proposed that uses this topography to determine an effective asperity radius of curvature for the contacting particle. Application of the method has been found to be consistent with established contact mechanics models, for both glass and UO3 particle probes that present significantly different surface roughness. The method proposed is straightforward to apply and offers a greater insight into the influence of particle micro- and nano-roughness on adhesion. This is important for applications that rely on the control of granular flow such as pellet or tablet manufacture.