Single-Molecule Visualization of Biomolecules in the Designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy

2016 ◽  
pp. 403-427
Author(s):  
Masayuki Endo
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Quantitative Assessment of Tip Effects in Single‐Molecule High‐Speed Atomic Force Microscopy Using DNA Origami Substrates

2020 ◽  
Vol 132 (34) ◽  
pp. 14442-14447 ◽  
Author(s):  
Charlotte Kielar ◽  
Siqi Zhu ◽  
Guido Grundmeier ◽  
Adrian Keller
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Quantitative Assessment ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4798
Author(s):  
Yang Xin ◽  
Amir Ardalan Zargariantabrizi ◽  
Guido Grundmeier ◽  
Adrian Keller
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Pure Water ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force ◽  
The Individual ◽  
Individual Strategies ◽  
Phosphate Buffered Saline

DNA origami nanostructures (DONs) are promising substrates for the single-molecule investigation of biomolecular reactions and dynamics by in situ atomic force microscopy (AFM). For this, they are typically immobilized on mica substrates by adding millimolar concentrations of Mg2+ ions to the sample solution, which enable the adsorption of the negatively charged DONs at the like-charged mica surface. These non-physiological Mg2+ concentrations, however, present a serious limitation in such experiments as they may interfere with the reactions and processes under investigation. Therefore, we here evaluate three approaches to efficiently immobilize DONs at mica surfaces under essentially Mg2+-free conditions. These approaches rely on the pre-adsorption of different multivalent cations, i.e., Ni2+, poly-l-lysine (PLL), and spermidine (Spdn). DON adsorption is studied in phosphate-buffered saline (PBS) and pure water. In general, Ni2+ shows the worst performance with heavily deformed DONs. For 2D DON triangles, adsorption at PLL- and in particular Spdn-modified mica may outperform even Mg2+-mediated adsorption in terms of surface coverage, depending on the employed solution. For 3D six-helix bundles, less pronounced differences between the individual strategies are observed. Our results provide some general guidance for the immobilization of DONs at mica surfaces under Mg2+-free conditions and may aid future in situ AFM studies.

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 Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Akinori Kuzuya ◽  
Yusuke Sakai ◽  
Takahiro Yamazaki ◽  
Yan Xu ◽  
Makoto Komiyama
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force

In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami

Nanoscale ◽  
2011 ◽  
Vol 3 (6) ◽  
pp. 2481 ◽  
Author(s):  
Na Wu ◽  
Xingfei Zhou ◽  
Daniel M. Czajkowsky ◽  
Ming Ye ◽  
Dongdong Zeng ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Time Lapse ◽  
Dna Origami ◽  
In Situ Monitoring ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Single-Molecule Dynamics of the DNA−EcoRII Protein Complexes Revealed with High-Speed Atomic Force Microscopy

Biochemistry ◽  
2009 ◽  
Vol 48 (44) ◽  
pp. 10492-10498 ◽  
Author(s):  
Jamie L. Gilmore ◽  
Yuki Suzuki ◽  
Gintautas Tamulaitis ◽  
Virginijus Siksnys ◽  
Kunio Takeyasu ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
High Speed ◽  
Protein Complexes ◽  
Force Microscopy ◽  
Atomic Force ◽  
Single Molecule Dynamics ◽  
Molecule Dynamics

Real‐Time Observation of Superstructure‐Dependent DNA Origami Digestion by DNase I Using High‐Speed Atomic Force Microscopy

ChemBioChem ◽  
2019 ◽  
Vol 20 (22) ◽  
pp. 2818-2823 ◽  
Author(s):  
Saminathan Ramakrishnan ◽  
Boxuan Shen ◽  
Mauri A. Kostiainen ◽  
Guido Grundmeier ◽  
Adrian Keller ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Real Time ◽  
High Speed ◽  
Dnase I ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force ◽  
Time Observation ◽  
Real Time Observation
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