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.     

Multivalent Interactions of Polyamide Based Sequence‐Controlled Glycomacromolecules with Concanavalin A

Binding of mannose presenting macromolecules to the protein receptor concanavalin A (ConA) is investigated by means of single‐molecule atomic force spectroscopy (SMFS) in combination with dynamic light scattering and molecular modeling. Oligomeric (M_w ≈ 1.5–2.5 kDa) and polymeric (M_w ≈ 22–30 kDa) glycomacromolecules with controlled number and positioning of mannose units along the scaffolds accessible by combining solid phase synthesis and thiol–ene coupling are used as model systems to assess the molecular mechanisms that contribute to multivalent ConA–mannose complexes. SMFS measurements show increasing dissociation force from monovalent (≈57 pN) to pentavalent oligomers (≈75 pN) suggesting subsite binding to ConA. Polymeric glycomacromolecules with larger hydrodynamic diameters compared to the binding site spacing of ConA exhibit larger dissociation forces (≈80 pN), indicating simultaneous dissociation from multiple ConA binding sites. Nevertheless, although simultaneous dissociation of multiple ligands could be expected for such multivalent systems, predominantly single dissociation events are observed. This is rationalized by strong coiling of the macromolecules' polyamide backbone due to intramolecular hydrogen bonding hindering unfolding of the coil. Therefore, this study shows that the design of glycopolymers for multivalent receptor binding and clustering must consider 3D structure and intramolecular interactions of the scaffold.     

Single-molecule force spectroscopy of bimolecular reactions: system homology in the mechanical activation of ligand substitution reactions

The mechanochemistry of the bimolecular nucleophilic substitution of DMSO for substituted pyridines at a square-planar pincer Pd(II) center was investigated using single-molecule force spectroscopy (SMFS). The SMFS data are interpreted in terms of the Bell-Evans model, which gives thermal off-rates for two reactions that agree well with previous, stress-free measurements. The characteristic force dependency of the rupture rate, fbeta, is effectively constant for the two reactions examined (22 +/- 2 and 24 +/- 2 pN), and the system homology in the mechanical response is consistent with expected similarities in the reaction potential energy surfaces.     

Antigen binding forces of single antilysozyme Fv fragments explored by atomic force microscopy

We used atomic force microscopy (AFM) to explore the antigen binding forces of individual Fv fragments of antilysozyme antibodies (Fv). To detect single molecular recognition events, genetically engineered histidine-tagged Fv fragments were coupled onto AFM tips modified with mixed self-assembled monolayers (SAMs) of nitrilotriacetic acid- and tri(ethylene glycol)-terminated alkanethiols while lysozyme (Lyso) was covalently immobilized onto mixed SAMs of carboxyl- and hydroxyl-terminated alkanethiols. The quality of the functionalization procedure was validated using X-ray photoelectron spectroscopy (surface chemical composition), AFM imaging (surface morphology in aqueous solution), and surface plasmon resonance (SPR, specific binding in aqueous solution). AFM force-distance curves recorded at a loading rate of 5000 pN/s between Fv- and Lyso-modified surfaces yielded a distribution of unbinding forces composed of integer multiples of an elementary force quantum of approximately 50 pN that we attribute to the rupture of a single antibody-antigen pair. Injection of a solution containing free Lyso caused a dramatic reduction of adhesion probability, indicating that the measured 50 pN unbinding forces are due to the specific antibody-antigen interaction. To investigate the dynamics of the interaction, force-distance curves were recorded at various loading rates. Plots of unbinding force vs log(loading rate) revealed two distinct linear regimes with ascending slopes, indicating multiple barriers were present in the energy landscape. The kinetic off-rate constant of dissociation (k(off) approximately = 1 x 10(-3) s(-1)) obtained by extrapolating the data of the low-strength regime to zero force was in the range of the k(off) estimated by SPR.     

分子间相互作用力的直接测量

结合我们近期的研究工作,着重介绍如何将分子组装与单分子力谱相结合,从单分子水平直接研究分子间相互作用力,包括π-π相互作用、多价作用及嵌入作用.在实验中,将一个相互作用单元通过高分子间隔基共价连接到原子力显微镜针尖上,并将另一相互作用单元共价修饰到基底上,通过压电陶瓷管的移动获得力与拉伸长度的曲线.高分子柔性间隔基团的引入既可用来作为判别单链拉伸的"内标",又可避免非特异相互作用对待测的特异相互作用的影响.研究表明,结合静态和动态力学谱,不仅能够实现分子间相互作用力的直接测量,而且还可获得解离速率和相互作用的距离等参数.     

Force spectroscopy of quadruple H-bonded dimers by AFM: dynamic bond rupture and molecular time-temperature superposition

We report on the application of the time-temperature superposition principle to supramolecular bond-rupture forces on the single-molecule level. The construction of force-loading rate master curves using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) experiments carried out in situ at different temperatures allows one to extend the limited range of the experimentally accessible loading rates and hence to cross from thermodynamic nonequilibrium to quasi-equilibrium states. The approach is demonstrated for quadruple H-bonded ureido-4[1H]-pyrimidinone (UPy) moieties studied by variable-temperature SMFS in organic media. The unbinding forces of single quadruple H-bonding (UPy)2 complexes, which were identified based on a polymeric spacer strategy, were found to depend on the loading rate in the range of 5 nN/s to 500 nN/s at 301 K in hexadecane. By contrast, these rupture forces were independent of the loading rate from 5 to 200 nN/s at 330 K. These results indicate that the unbinding behavior of individual supramolecular complexes can be directly probed under both thermodynamic nonequilibrium and quasi-equilibrium conditions. On the basis of the time-temperature superposition principle, a master curve was constructed for a reference temperature of 301 K, and the crossover force (from loading-rate independent to -dependent regimes) was determined as approximately 145 pN (at a loading rate of approximately 5.6 nN/s). This approach significantly broadens the accessible loading-rate range and hence provides access to fine details of potential energy landscape of supramolecular complexes based on SMFS experiments.     

Effects of contact force and salt concentration on the unbinding of a DNA duplex by force spectroscopy

We report that varying the contact force in force spectroscopy results in a significant shift in DNA unbinding forces, measured from short oligonucleotides using a PicoForce microscope. The contact force between a 30-mer complementary DNA-coated probe and surface was varied from 100 pN to 10 nN, resulting in a significant shift in the most abundant unbinding force measured between the duplex. When contact forces were set at 200 pN or less, which is generally considered to be a low contact force region for biomolecular force spectroscopy studies, the shift in DNA unbinding forces was significant with changes in contact force. The effect of the salt concentration on the DNA unbinding forces was also examined for a range of salt concentrations from 5 to 500 mM because the presence of salt ions is necessary to facilitate the hybridization process. Although an increase in salt concentration resulted in the facilitation of DNA multiple binding events during force spectroscopy measurements, no significant shift in unbinding forces was observed. Our experiment demonstrates that the wide variation in DNA unbinding forces reported in the literature (50-600 pN) for short oligonucleotides can be accounted for by the different contact forces used and shows little or no effect of the salt concentration used in those studies. Furthermore, this study demonstrates the importance of reporting contact forces in force spectroscopy measurements for quantitative comparisons between different biomolecular systems, especially for noncovalent-type interactions.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

Electromagnetophoretic force measurement of a single binding interaction between lectin and yeast cell surfaces.

A novel measurement method of the binding force between a micrometer-sized particle and a solid surface in an electrolyte solution has been established by using the electromagnetophoretic buoyancy on the particle. By this method, we investigated the binding force between a yeast cell surface and an oligosaccharide-binding protein, concanavalin A (Con A), fixed on a silica capillary wall. The force measurement was carried out up to 60 pN. In a lower surface concentration of Con A, yeast cells could be desorbed by a force less than 60 pN. However, in a higher surface concentration after treated by 1 mg ml(-1) solution, yeast cells were adsorbed with a force stronger than 60 pN. In this case, the addition of 10 mg ml(-1) D-mannose solution to the medium reduced the binding force to less than 60 pN. The observed adsorption force of yeast cells ranged within 30 - 40 pN, regardless of the interfacial amount of Con A. This force was thought to be the single binding force between a mannose group of the cell surface and an active site of Con A. Moreover, the dissociation rate constant of the single binding of yeast cell and Con A complex was determined as 4.6 x 10(-3) s(-1) and the increment of the binding distance at the transition state as 0.33 nm from the desorption kinetic experiments of yeast cell under the constant pulling conditions of 10, 20 and 30 pN. Such satisfactory results demonstrate the novel advantages of the present method.     

EMSA and single-molecule force spectroscopy study of interactions between Bacillus subtilis single-stranded DNA-binding protein and single-stranded DNA

In this article, interactions between Bacillus subtilis single-stranded DNA binding proteins (BsSSB) and single-stranded DNA (ssDNA) were systematically studied. The effect of different molar ratios between BsSSB and ssDNA on their binding modes was first investigated by electrophoretic mobility shift assays (EMSAs). It is found that a high molar ratio of BsSSB to ssDNA can produce BsSSB-ssDNA complexes formed in the mode of two proteins binding one 65-nt (nucleotide) ssDNA whereas a low molar ratio facilitates the formation of BsSSB-ssDNA complexes in the mode of one protein binding one 65-nt ssDNA. Furthermore, two binding modes are in dynamic equilibrium. The unbinding force of BsSSB-ssDNA complexes was measured quantitatively in solutions with different salt concentrations by using AFM-based single-molecule force spectroscopy (SMFS). Our results show that the unbinding force is about 10 pN higher at high salt concentration (0.5 M NaCl) than at low salt concentration (0.1 M NaCl) and the lifetime of BsSSB-ssDNA complexes at high salt concentration is twice as long as that at low salt concentration. These results indicate that more tightly packed BsSSB-ssDNA complexes can form at high salt (0.5 M NaCl) concentration. In addition, the results of EMSA show that ssDNA, which is bound to BsSSB, can dissociate from BsSSB in the presence of the cDNA strand, indicating the dynamic nature of BsSSB-ssDNA interactions.     

Stretching single polysaccharides and proteins using atomic force microscopy

The past years have witnessed remarkable advances in our use of atomic force microscopy (AFM) for stretching single biomolecules, thereby contributing to answering many outstanding questions in biophysics and chemical biology. In these single-molecule force spectroscopy (SMFS) experiments, the AFM tip is continuously approached to and retracted from the biological sample, while monitoring the interaction force. The obtained force-extension curves provide key insight into the molecular elasticity and localization of single molecules, either on isolated systems or on cellular surfaces. In this tutorial review, we describe the principle of such SMFS experiments, and we survey remarkable breakthroughs made in manipulating single polysaccharides and proteins, including understanding the conformational properties of sugars and controlling them by force, measuring the molecular elasticity of mechanical proteins, unfolding and refolding individual proteins, probing protein-ligand interactions, and tuning enzymatic reactions by force. In addition, we show how SMFS with AFM tips bearing specific bioligands has enabled researchers to stretch and localize single molecules on live cells, in relation with cellular functions.     

Surface plasmon resonance imaging studies of protein-carbohydrate interactions

Carbohydrate arrays fabricated on gold films were used to study carbohydrate-protein interactions with surface plasmon resonance (SPR) imaging. An immobilization scheme consisting of the formation of a surface disulfide bond was used to attach thiol-modified carbohydrates onto gold films and to fabricate carbohydrate arrays. The carbohydrate attachment steps were characterized using polarization modulation Fourier transform infrared reflection absorption spectroscopy; and poly(dimethylsiloxane) microchannels were used to immobilize probe compounds at discrete locations on a gold film. The binding of the carbohydrate-binding proteins concanavalin A (ConA) and jacalin to arrays composed of the monosaccharides mannose and galactose was monitored with SPR imaging. SPR imaging measurements were employed to accomplish the following: (i) construct adsorption isotherms for the interactions of ConA and jacalin to the carbohydrate surfaces, (ii) monitor protein binding to surfaces presenting different compositions of the immobilized carbohydrates, and (iii) measure the solution equilibrium dissociation constants for ConA and jacalin toward mannose and galactose, respectively. Adsorption coefficients (K(ADS)) of 2.2 +/- 0.8 x 10(7) M(-)(1) and 5.6 +/- 1.7 x 10(6) M(-)(1) were obtained for jacalin adsorbing to a galactose surface and ConA adsorbing to a mannose surface, respectively. The solution equilibrium dissociation (K(D)) constant for the interaction of jacalin and galactose was found to be 16 +/- 5 microM, and for ConA and mannose was found to be 200 +/- 50 microM.     

Supramolecular research by single molecule force spectroscopy

Single molecule force spectroscopy (SMFS) is a new kind of technique based on atomic force microscope, which allows detecting force as low as pico-newtons directly. Herein based on our recent work, we want to demonstrate the investigation of supramolecular structures and interactions in polymer systems by SMFS, such as desorption force between polymer and substrate, identifiability of polymer micelle and its interaction with surfactant, splitting force of ion-induced helical structure in polysaccharide. It shows well that SMFS is a powerful tool in the study of supramolecular science.     

Rupture force of single supramolecular bonds in associative polymers by AFM at fixed loading rates

Atomic-force-microscopy-based single-molecule force spectroscopy (AFM-SMFS) was used to study the bond strength of self-complementary hydrogen-bonded complexes based on the 2-ureido-4[1H]-pyrimidinone (UPy) quadruple H-bond motif in hexadecane (HD). The unbinding force corresponding to single UPy-UPy dimers was investigated at a fixed piezo retraction rate in the nonequilibrium loading rate regime. The rupture force of bridging supramolecular polymer chains formed between UPy-functionalized substrates and AFM tips in the presence of a bis-UPy derivative was found to decrease with increasing rupture length. The rupture length was identified as the chain length of single, associating polymers, which allowed us to determine the number of supramolecular bonds (N) at rupture. The rupture force observed as a function of N was in quantitative agreement with the theory on uncooperative bond rupture for supramolecular linkages switched in a series. Hence, the value of the dimer equilibrium constant Keq=(1.3+/-0.5) x 10(9) M(-1), which is in good agreement with previously estimated values, was obtained by SMFS of supramolecular polymers at a single loading rate.     

Mechanical unfolding of ensemble biomolecular structures by shear force

Mechanical unfolding of biomolecular structures has been exclusively performed at the single-molecule level by single-molecule force spectroscopy (SMFS) techniques. Here we transformed sophisticated mechanical investigations on individual molecules into a simple platform suitable for molecular ensembles. By using shear flow inside a homogenizer tip, DNA secondary structures such as i-motifs are unfolded by shear force up to 50 pN at a 77 796 s⁻¹ shear rate. We found that the larger the molecules, the higher the exerted shear forces. This shear force approach revealed affinity between ligands and i-motif structures. It also demonstrated a mechano-click reaction in which a Cu(i) catalyzed azide–alkyne cycloaddition was modulated by shear force. We anticipate that this ensemble force spectroscopy method can investigate intra- and inter-molecular interactions with the throughput, accuracy, and robustness unparalleled to those of SMFS methods.

Shear force in a homogenizer mechanically unfolds an ensemble set of biomolecular structures.     

Interaction between poly[(R)-3-hydroxybutyrate] depolymerase and biodegradable polyesters evaluated by atomic force microscopy

Adsorption of PHB depolymerase from Ralstonia pickettii T1 to biodegradable polyesters such as poly[(R)-3-hydroxybutyrate] (PHB) and poly(l-lactic acid) (PLLA) was investigated by atomic force microscopy (AFM). The substrate-binding domain (SBD) with histidines within the N-terminus was prepared and immobilized on the AFM tip surface via a self-assembled monolayer with a nitrilotriacetic acid group. Using the functionalized AFM tips, the force-distance measurements for polyesters were carried out at room temperature in a buffer solution. In the case of AFM tips with immobilized SBD and their interaction with polyesters, multiple pull-off events were frequently recognized in the retraction curves. The single rupture force was estimated at approximately 100 pN for both PLLA and PHB. The multiple pull-off events were recognized even in the presence of a surfactant, which will prevent nonspecific interactions, but reduced when using polyethylene instead of polyesters as a substrate. The present results provide that the PHB depolymerase adsorbs specifically to the surfaces of polyesters and that the single unbinding event evaluated here is mainly associated with the interaction between one molecule of SBD and the polymer surface.     

Collective and single-molecule interactions of alpha5beta1 integrins

A novel biomimetic system was used to study collective and single-molecule interactions of the alpha5beta1 receptor-GRGDSP ligand system with an atomic force microscope (AFM). Bioartificial membranes, which display peptides that mimic the cell adhesion domain of the extracellular matrix protein fibronectin, are constructed from peptide-amphiphiles. The interaction measured with the immobilized alpha5beta1 integrins and GRGDSP peptide-amphiphiles is specifically related to the integrin-peptide binding. It is affected by divalent cations in a way that accurately mimics the adhesion function of the alpha5beta1 receptor. The recognition of the immobilized receptor was significantly increased for a surface that presented both the primary recognition site (GRGDSP) and the synergy site (PHSRN) compared to the adhesion measured with surfaces that displayed only the GRGDSP peptide. At the collective level, the separation process of the receptor-ligand pairs is a combination of multiple unbinding and stretching events that can accurately be described by the wormlike chain (WLC) model of polymer elasticity. In contrast, stretching was not observed at the single-molecule level. The dissociation of single alpha5beta1-GRGDSP pairs under loading rates of 1-305 nN/s revealed the presence of two activation energy barriers in the unbinding process. The high-strength regime above 59 nN/s maps the inner barrier at a distance of 0.09 nm along the direction of the force. Below 59 nN/s a low-strength regime appears with an outer barrier at 2.77 nm and a much slower transition rate that defines the dissociation rate (off-rate) in the absence of force (k(off) degrees = 0.015 s(-1)).     

Polymer-based photocoupling agent for the efficient immobilization of nanomaterials and small molecules

A highly efficient photocoupling agent, based on perfluorophenylazide (PFPA)-conjugated polyallylamine (PAAm), was developed for the efficient immobilization of polymers, nanoparticles, graphene, and small molecules. The conjugate, PAAm-PFPA, was synthesized, and the percentage of the photoactive moiety, PFPA, can be controlled by the ratio of the two components in the synthesis. By treating epoxy-functionalized wafers with PAAm-PFPA, photoactive surfaces were generated. Compared with the PFPA surface, these polymer-based photocoupling matrix resulted in significantly enhanced immobilization efficiencies, especially for nanomaterials and small molecules. Thus, polystyrene nanoparticles (PS NPs) and alkyl-functionalized silica nanoparticles (SNPs) were successfully immobilized on the PAAm-PFPA surface, resulting in a high material density. Graphene flakes patterned on the PAAm-PFPA surface showed improved feature resolution in addition to a higher material density compared to that of flakes immobilized on the PFPA surface. Furthermore, 2-O-α-D-mannopyranosyl-D-mannopyranose (Man2) immobilized on the PAAm-PFPA surface exhibited significantly enhanced signals when treated with lectin concanavalin A (Con A).     

Dynamic force spectroscopy of the specific interaction between the PDZ domain and its recognition peptides

To characterize the molecular basis of specific interactions of PDZ proteins, dynamic force spectroscopy (DFS) for the PDZ protein Tax-interacting protein-1 (TIP-1) and its recognition peptide (PDZ-pep) derived from beta-catenin was performed using an atomic force microscope (AFM), together with measurement of thermodynamic and kinetic parameters using surface plasmon resonance (SPR). The unbinding force of this pair was measured under different conditions of AFM tip-retraction velocity. The relationship between the unbinding force and the logarithmic force-loading rate, that is, the dynamic force spectrum, exhibited two different rate regimes, for each of which the forces increased linearly with the force-loading rate. On the basis of the theoretical treatment of the Bell-Evans model, the positions of two different activation barriers in the reaction coordinate and dissociation rate constants in each barrier were evaluated from slopes and x-intercepts of the two linear regimes (first barrier: 0.04 nm and 1.10 x 10 s(-1); second barrier: 0.21 nm and 2.77 x 10(-2) s(-1), respectively). Although two-step unbinding kinetics between TIP-1 and PDZ-pep was suggested from the DFS analysis, SPR results showed single-step dissociation kinetics with a rate constant of 2.89 x 10(-1) s(-1). Different shapes of the free energy profile of the unbinding process were deduced from each result of DFS and SPR. The reason for such topographic differences in the energy landscape is discussed in relation to the differences in the pathways of forced unbinding and spontaneous dissociation.     

Nonlinearly additive forces in multivalent ligand binding to a single protein revealed with force spectroscopy

We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between concanavalin A (ConA) and alpha-D-mannose but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 68, and 85 pN at a loading rate of 650 +/- 25 pN/s, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and nonspecific binding. We analyze the binding configuration (i.e., serial vs parallel connections) through fitting the polymer stretching data with modified wormlike chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.