Search results for "Force spectroscopy"

Stability of a Split Streptomycin Binding Aptamer

2016

Here we investigated the stability of an aptamer, which is formed by two RNA strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystal structure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycin binding with a free energy of ΔGbind° = −101.7 kJ mol–1. Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (koff-COMPLEX = 0.22 ± 0.16 s–1) for the …

Resveratrol-Induced Temporal Variation in the Mechanical Properties of MCF-7 Breast Cancer Cells Investigated by Atomic Force Microscopy

2019

Atomic force microscopy (AFM) combined with fluorescence microscopy has been used to quantify cytomechanical modifications induced by resveratrol (at a fixed concentration of 50 &micro

Searching events in AFM force-extension curves: A wavelet approach

2016

An algorithm, based on the wavelet scalogram energy, for automatically detecting events in force-extension AFM force spectroscopy experiments is introduced. The events to be detected are characterized by a discontinuity in the signal. It is shown how the wavelet scalogram energy has different decay rates at different points depending on the degree of regularity of the signal, showing faster decay rates at regular points and slower rates at singular points (jumps). It is shown that these differences produce peaks in the scalogram energy plot at the event points. Finally, the algorithm is illustrated in a tether analysis experiment by using it for the detection of events in the AFM force-exte…

AFM study of interaction forces in supported planar DPPC bilayers in the presence of general anesthetic halothane

2006

International audience; In spite of numerous investigations, the molecular mechanism of general anesthetics action is still not well understood. It has been shown that the anesthetic potency is related to the ability of an anesthetic to partition into the membrane. We have investigated changes in structure, dynamics and forces of interaction in supported dipalmitoylphosphatidylcholine (DPPC) bilayers in the presence of the general anesthetic halothane. In the present study, we measured the forces of interaction between the probe and the bilayer using an atomic force microscope. The changes in force curves as a function of anesthetic incorporation were analyzed. Force measurements were in go…

Measuring single small molecule binding via rupture forces of a split aptamer.

2011

The rupture force of a split (bipartite) aptamer that forms binding pockets for adenosine monophosphate (AMP) was measured by atomic force spectroscopy. Changes in the rupture force were observed in the presence of AMP, while this effect was absent when mutant aptamers or inosine were used. Thus, changes in the rupture force were a direct consequence of specific binding of AMP to the split aptamer. The split aptamer concept allowed the detection of nonlabeled AMP and enabled us to determine the dissociation constant on a single-molecule level.

Energy landscapes of ligand-receptor couples probed by dynamic force spectroscopy.

2013

Playing a dominant role in many biochemical processes are the dynamic properties of molecular linkages; examples include cell adhesion, enzyme-catalyzed reactions, and molecular recognition by antibodies. Dynamic force spectroscopy, namely separating molecular bonds under external force ramps has rapidly become a powerful tool to study the rugged energy landscape of noncovalent ligand-receptor bonds. The picture shows a surface and tip-bound pair being pulled apart and the derived potential energy diagram.

Rupture Force of Single Small Drug Molecule Binding a Split Aptamer

2012

Aptamers are specific oligonucleotides (DNA or RNA) which bind small inorganic or organic molecules, large proteins or cells. In particular, the high affinity of aptamers is expected to lead to a new class of therapeutic reagents. Thus the detection and characterization of binding strength of small molecules is important for drug and medical research. Atomic force spectroscopy (AFS) with a force resolution in the piconewton range is a valuable tool for studying interactions on a single molecular level. The detection of very small target molecules less than 500 Dalton is characterized by only a few hydrogen interactions between the aptamer and the target molecules. Thus tiny rupture forces w…

2019

Atomic force microscopy (AFM) is today an established tool in imaging and determination of mechanical properties of biomaterials. Due to their complex organization, those materials show intricate properties such as viscoelasticity. Therefore, one has to consider that the loading rate at which the sample is probed will lead to different mechanical response (properties). In this work, we studied the dependence of the mechanical properties of endothelial cells on the loading rate using AFM in force spectroscopy mode. We employed a sharp, four-sided pyramidal indenter and loading rates ranging from 0.5 to 20 μm/s. In addition, by variation of the load (applied forces from 100 to 10,000 pN), the…

Measuring (biological) materials mechanics with atomic force microscopy. 2. Influence of the loading rate and applied force (colloidal particles)

2020

Atomic force microscopy (AFM) is the most often used tool to study the mechanical properties of eukaryotic cells. Due to their complex assembly, cells show viscoelastic properties. When performing experiments, one has to consider the influence of both loading rate and maximum load on the measured mechanical properties. Here, we employed colloidal particles of various sizes (from 2 to 20 μm diameter) to perform force spectroscopy measurements on endothelial cells at loading rates varying from 0.1 to 50 μm/s, and maximum loads ranging from 1 to 25 nN. We were able to determine the non-linear dependence of cell viscoelastic properties on the loading rate which followed a weak power law. In add…

Reversible hydrogen bond network dynamics: molecular dynamics simulations of calix[4]arene-catenanes.

2011

We present detailed molecular dynamics (MD) simulations of mechanically interlocked calix[4]arene-catenanes under external force. Single-molecule force spectroscopy experiments revealed that the separation of dimers with two aliphatic loops results in reversible hydrogen bond breakage through an intermediate in a triple-well potential, while the tetra-loop species separates in a one-step manner (Janke, M.; et al. Nat. Nanotechnol. 2009, 4, 225). MD simulations show that calix[4]arenes interlocked by four loops (1) display a complete restructuring of the hydrogen bond network under mechanical force. All hydrogen bonds of the closed structure open, and new ones are formed in the extended stru…