On the way to supramolecular photochemistry at the single-molecule level

2006 ◽  
Vol 78 (12) ◽  
pp. 2247-2259 ◽  
Author(s):  
Christian Schäfer ◽  
Björn Decker ◽  
Matthias Letzel ◽  
Francesca Novara ◽  
Rainer Eckel ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Pocket ◽  
Ion Cyclotron Resonance ◽  
Dynamic Force ◽  
Fticr Mass Spectrometry ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Molecular Length ◽  
First Time

Two examples of artificial supramolecular host-guest systems derived from resorc[4]arenes (calix[n]arenes based on resorcinol) and ammonium ions as guests have been studied by atomic force microscopy (AFM). For the first time, real single-molecule events have been determined for this type of supramolecular complexes and off-rates as well as molecular parameters of single-molecule aggregates such as the depths of the binding pocket (molecular length parameter) could be measured by applying the methods of dynamic force spectroscopy. In addition, this technique was also applied to differentiate between the two states (open and closed) of a photoswitchable resorc[4]arene-anthracene tweezer. An investigation of the exchange rates of various complexes in the gas phase by means of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry confirmed the results of the AFM study.

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single Molecule Level

2013 ◽  
pp. 102-112
Author(s):  
Memed Duman ◽  
Andreas Ebner ◽  
Christian Rankl ◽  
Jilin Tang ◽  
Lilia A. Chtcheglova ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single-Molecule Level

2018 ◽  
pp. 1-14
Author(s):  
Memed Duman ◽  
Yoo Jin Oh ◽  
Rong Zhu ◽  
Michael Leitner ◽  
Andreas Ebner ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

scholarly journals How Microbes Use Force To Control Adhesion

2020 ◽  
Vol 202 (12) ◽  
Author(s):  
Albertus Viljoen ◽  
Johann Mignolet ◽  
Felipe Viela ◽  
Marion Mathelié-Guinlet ◽  
Yves F. Dufrêne
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Flow Chamber ◽  
Microbial Adhesion ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Adhesive Interactions ◽  
And Function ◽  
Mechanisms Of Adhesion

ABSTRACT Microbial adhesion and biofilm formation are usually studied using molecular and cellular biology assays, optical and electron microscopy, or laminar flow chamber experiments. Today, atomic force microscopy (AFM) represents a valuable addition to these approaches, enabling the measurement of forces involved in microbial adhesion at the single-molecule level. In this minireview, we discuss recent discoveries made applying state-of-the-art AFM techniques to microbial specimens in order to understand the strength and dynamics of adhesive interactions. These studies shed new light on the molecular mechanisms of adhesion and demonstrate an intimate relationship between force and function in microbial adhesins.

scholarly journals Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs

2020 ◽  
Vol 21 (11) ◽  
pp. 4142
Author(s):  
Aleksandra Kaczorowska ◽  
Weronika Lamperska ◽  
Kaja Frączkowska ◽  
Jan Masajada ◽  
Sławomir Drobczyński ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Regulatory Elements ◽  
Dna Molecules ◽  
Anthracycline Antibiotics ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Analysis ◽  
Dna Regulatory Elements

In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.

scholarly journals Nonspecific Protein Adsorption at the Single Molecule Level Studied by Atomic Force Microscopy

Langmuir ◽  
2007 ◽  
Vol 23 (20) ◽  
pp. 9921-9923 ◽  
Author(s):  
Peter Schön ◽  
Martin Görlich ◽  
Michiel J. J. Coenen ◽  
Hans A. Heus ◽  
Sylvia Speller
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Adsorption ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Nonspecific Protein Adsorption

scholarly journals Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shintaroh Kubo ◽  
Suguru Kato ◽  
Kazuyuki Nakamura ◽  
Noriyuki Kodera ◽  
Shoji Takada
Keyword(s):  
Atomic Force Microscopy ◽  
Kalman Filter ◽  
Single Molecule ◽  
High Speed ◽  
Ground Truth ◽  
Bayesian Filtering ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Kalman Smoother ◽  
Atomic Force

Abstract High-speed atomic force microscopy (HS-AFM) is a scanning probe microscopy that can capture structural dynamics of biomolecules in real time at single molecule level near physiological condition. Albeit much improvement, while scanning one frame of HS-AFM movies, biomolecules often change their conformations largely. Thus, the obtained frame images can be hampered by the time-difference, the asynchronicity, in the data acquisition. Here, to resolve this data asynchronicity in the HS-AFM movie, we developed Kalman filter and smoother methods, some of the sequential Bayesian filtering approaches. The Kalman filter/smoother methods use alternative steps of a short time-propagation by a linear dynamical system and a correction by the likelihood of AFM data acquired pixel by pixel. We first tested the method using a toy model of a diffusing cone, showing that the Kalman smoother method outperforms to reproduce the ground-truth movie. We then applied the Kalman smoother to a synthetic movie for conformational change dynamics of a motor protein, i.e., dynein, confirming the superiority of the Kalman smoother. Finally, we applied the Kalman smoother to two real HS-AFM movies, FlhAC and centralspindlin, reducing distortion and noise in the AFM movies. The method is general and can be applied to any HS-AFM movies.

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

RSC Advances ◽  
2019 ◽  
Vol 9 (39) ◽  
pp. 22705-22712 ◽  
Author(s):  
Evan Angelo Mondarte ◽  
Tatsuhiro Maekawa ◽  
Takashi Nyu ◽  
Hiroyuki Tahara ◽  
Ganchimeg Lkhamsuren ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Temporal Resolution ◽  
Single Molecule ◽  
Energy Landscape ◽  
Metastable States ◽  
High Temporal Resolution ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Biotin Binding

Energy landscape illustration from the streptavidin–biotin binding dynamics observed in high temporal-resolution AFM.

Determining structural and chemical heterogeneities of surface species at the single-bond limit

Science ◽  
2021 ◽  
Vol 371 (6531) ◽  
pp. 818-822
Author(s):  
Jiayu Xu ◽  
Xiang Zhu ◽  
Shijing Tan ◽  
Yao Zhang ◽  
Bin Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Scanning Tunneling ◽  
Surface Species ◽  
Tunneling Microscopy ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Chemical Structures ◽  
Atomic Force ◽  
Surface Catalysis ◽  
Enhanced Raman Scattering

The structure determination of surface species has long been a challenge because of their rich chemical heterogeneities. Modern tip-based microscopic techniques can resolve heterogeneities from their distinct electronic, geometric, and vibrational properties at the single-molecule level but with limited interpretation from each. Here, we combined scanning tunneling microscopy (STM), noncontact atomic force microscopy (AFM), and tip-enhanced Raman scattering (TERS) to characterize an assumed inactive system, pentacene on the Ag(110) surface. This enabled us to unambiguously correlate the structural and chemical heterogeneities of three pentacene-derivative species through specific carbon-hydrogen bond breaking. The joint STM-AFM-TERS strategy provides a comprehensive solution for determining chemical structures that are widely present in surface catalysis, on-surface synthesis, and two-dimensional materials.

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