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

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.

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

Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template

ACS Nano ◽  
2010 ◽  
Vol 4 (12) ◽  
pp. 7475-7480 ◽  
Author(s):  
Sarah Helmig ◽  
Alexandru Rotaru ◽  
Dumitru Arian ◽  
Larisa Kovbasyuk ◽  
Jacob Arnbjerg ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Singlet Oxygen ◽  
Single Molecule ◽  
Dna Origami ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Direct Visualization of Protein Kinase A Activation on DNA Origami using Fast-Scan Atomic Force Microscopy

2020 ◽  
Author(s):  
Ioanna Mela ◽  
Daniel Ladant ◽  
Hiroshi Sugiyama ◽  
Masayuki Endo ◽  
J. Michael Edwardson ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Kinase ◽  
Protein Kinase A ◽  
Adenylyl Cyclase ◽  
Single Molecule ◽  
Dna Origami ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Kinase A

ABSTRACTDNA origami nanostructures provide a unique platform for the direct observation of protein-protein interactions at the single-molecule level. Here, we used DNA origami in combination with fast-scan atomic force microscopy to observe the activation-induced dissociation of individual protein kinase A (PKA) holoenzymes. The PKA holoenzyme consists of two regulatory (R) and two catalytic (C) subunits. When cAMP binds to the R subunits it causes dissociation of the C subunits from the R subunit dimer and activation of the enzyme. Using a DNA origami platform, we were able to observe the activation of PKA in response to photolysis of caged cAMP. Furthermore, exploiting the potential of DNA origami for precise positioning of biomolecules, we were able to position the catalytic subunit of adenylyl cyclase in close proximity to PKA and to observe the activation of PKA in response to cAMP produced by adenylyl cyclase. We provide tools for the observation of signalling pathways at the single-molecule level and show that the C subunits of PKA dissociate from the holoenzyme but stay within ~10 nm of the R subunit dimer upon activation.

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
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