scholarly journals Analyzing DNA Structure Quantitatively at a Single-Molecule Level by Atomic Force Microscopy

10.5772/35796 ◽  
2012 ◽  
Author(s):  
Yong Jiang ◽  
Yuan Yi
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Dna Structure ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force

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 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.

scholarly journals Mobility of nucleosomes is regulated by their binding partners

2022 ◽  
Author(s):  
Daniel P Melters ◽  
Keir C Neuman ◽  
Tatini Rakshit ◽  
Yamini Dalal
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Diffusion Constant ◽  
Chromatin Accessibility ◽  
Chromatin Dynamics ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force

Chromatin accessibility is modulated in a variety of ways, both to create open and closed chromatin states which are critical for eukaryotic gene regulation. At the mechanistic single molecule level, how accessibility is regulated remains a fundamental question in the field. Here, we use single molecule tracking by high-speed atomic force microscopy to investigate this question using chromatin arrays and extend our findings into the nucleus. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and observed that the essential kinetochore protein CENP-C reduces the diffusion constant of CENP-A nucleosomes and the linker H1.5 protein restricts H3 nucleosome mobility. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. These data suggest a model in which inner kinetochore proteins are critically involved in modulating chromatin accessibility and consequently, noncoding transcription at human centromeres.

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