Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy

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.

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.

Evaluating the effect of aminoglycosides on the interaction between bovine serum albumins by atomic force microscopy

Characterization and determination of protein-protein interactions (PPIs) plays an important role in molecular biological science. In this study, the effect of aminoglycosides (AGs: streptomycin, gentamycin, lincomycin and clindamycin) on interactions between bovine serum albumin (BSA) was evaluated employing imaging and probing adhesion event by AFM. Multi-spectroscopy and molecular docking were supplementary to investigate the acting forces of the effect. AFM measurements revealed the aggregation of BSA grains and changes of adhesion forces at single molecule level. With adhesion forces between BSA pairs decomposed by Poisson method, specific forces in streptomycin, gentamycin, lincomycin and climdamycin were obviously decreased with the rate of 33.1%, 26.4%, 32.3% and 31.3% while non-specific forces slightly decreased with 5.5%, 3.3%, 4.0% and 7.7%. Combined with results of multi-spectroscopy as well as molecular docking, the whole determination showed AGs affected PPIs by multiple forces, where the hydrogen bonding and hydration effect were the main reasons. The binding of drugs and proteins acted by hydrogen bonding affected the interaction forces between BSA. Consequently, AFM was proposed to be an effective and precise tool in application including evaluating the effects of exogenous compounds on biomacromolecular interactions and rapid screening of drug candidates to avoid potential damages in disease treatment.

Dronpa: A Light-Switchable Fluorescent Protein for Opto-Biomechanics

Since the development of the green fluorescent protein, fluorescent proteins (FP) are indispensable tools in molecular biology. Some FPs change their structure under illumination, which affects their interaction with other biomolecules or proteins. In particular, FPs that are able to form switchable dimers became an important tool in the field of optogenetics. They are widely used for the investigation of signaling pathways, the control of surface recruitment, as well as enzyme and gene regulation. However, optogenetics did not yet develop tools for the investigation of biomechanical processes. This could be leveraged if one could find a light-switchable FP dimer that is able to withstand sufficiently high forces. In this work, we measure the rupture force of the switchable interface in pdDronpa1.2 dimers using atomic force microscopy-based single molecule force spectroscopy. The most probable dimer rupture force amounts to around 80 pN at a pulling speed of 1600 nm/s. After switching of the dimer using illumination at 488 nm, there are hardly any measurable interface interactions, which indicates the successful dissociation of the dimers. Hence this Dronpa dimer could expand the current toolbox in optogenetics with new opto-biomechanical applications like the control of tension in adhesion processes.

Reversibly Switching Molecular Spectra

Manipulation of light transmission/absorbance and reflection/emission has a great significance in smart windows and displaying media like liquid crystal. Here, we report the usage of an external electric field to reversibly switch the molecular spectra of a model molecule on the basis of its interaction with an electroresponsible polymer brush. Both the UV-vis absorbance spectrum and the fluorescence emission spectrum of the model molecule were confirmed to be electroswitchable. The electroswitchable spectra were experimentally demonstrated to be induced by the electroswitchable statuses of medium anionic poly-allyloxy hydroxypropyl sulfonate (poly-AHPS) brush. Insightfully, the molecular aggregated status of model proflavine molecules could be electrically controlled via the electroresponsible poly-AHPS brushes and then the molecular spectra of the model proflavine molecule also could be electrically and controllably shifted. The success in the manipulation of molecular spectra opens up a wide range of applications not only for displaying but also for nonlinear optics, in vivo imaging, sensors, and environmental inspection.

Single molecular recognition force spectroscopy study of a DNA aptamer with the target epithelial cell adhesion molecule

The epithelial cell adhesion molecule (EpCAM) is a tumor-specific antigen for malignancies of the epithelialis lineage. In this study the interaction between the DNA-based EpCAM aptamer (SYL3C) and EpCAM was explored using single molecular recognition force spectroscopy (SMFS). The capability of aptamer SYL3C to recognize the EpCAM protein and the kinetic parameters were investigated.

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.

Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair

Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.

Analysis of DNA interactions using single-molecule force spectroscopy

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

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.

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.

Photocycloaddition of anthracene-functionalized monolayers on silicon(100) surface

Here we present detailed investigations of UV-photoinduced dimerization of anthracene substructures without solvent environment at the level of molecular monolayers prepared on a surface. Monolayers prepared on silicon(100) substrates were analyzed by means of X-ray photoelectron spectroscopy (XPS) in the valence band region revealing significant changes in the carbon C 2s region (11-20 eV). SVWN DFT calculations were performed to understand the influence of the structural changes by dimerization. The geometric structure of the functionality was retrieved through B3LYP DFT calculations, which were performed ahead of the SVWN DFT ones, and the result of these calculations matches with the measured vibration signature. FTIR investigations of polybutadiene (PBD) volume backboned functionality were performed before and after irradiation.

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.