Quantitative Measurement of Spatial Effects of DNA Origami on Molecular Binding Reactions Detected using Atomic Force Microscopy

2019 ◽  
Vol 11 (24) ◽  
pp. 21973-21981 ◽  
Author(s):  
Ping Zhang ◽  
Fei Wang ◽  
Wenjing Liu ◽  
Xiuhai Mao ◽  
Changchun Hao ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Quantitative Measurement ◽  
Dna Origami ◽  
Spatial Effects ◽  
Molecular Binding ◽  
Force Microscopy ◽  
Atomic Force

Visualization of molecular binding sites at the nanoscale in the lift-up mode by amplitude-modulation atomic force microscopy

Nanoscale ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 4213-4220
Author(s):  
Tatsuhiro Maekawa ◽  
Takashi Nyu ◽  
Evan Angelo Quimada Mondarte ◽  
Hiroyuki Tahara ◽  
Kasinan Suthiwanich ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Recognition ◽  
Amplitude Modulation ◽  
Binding Sites ◽  
Local Distribution ◽  
New Approach ◽  
Molecular Binding ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Sites

We report a new approach to visualize the local distribution of molecular recognition sites with nanoscale resolution by amplitude-modulation atomic force microscopy.

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 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

Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami

Nanoscale ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 4707-4711 ◽  
Author(s):  
Lin Li ◽  
Ping Zhang ◽  
Jiang Li ◽  
Ying Wang ◽  
Yuhui Wei ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Dna Origami ◽  
Dna Molecules ◽  
Force Microscopy ◽  
Nanomechanical Properties ◽  
Atomic Force ◽  
Dna Strands

Characterization of the stiffness of thin DNA strands remains difficult.

Manipulation of DNA origami nanotubes in liquid using programmable tapping‐mode atomic force microscopy

2013 ◽  
Vol 8 (10) ◽  
pp. 641-645 ◽  
Author(s):  
Longhai Li ◽  
Xiaojun Tian ◽  
Zaili Dong ◽  
Lianqing Liu ◽  
Osamu Tabata ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Dna Origami ◽  
Tapping Mode ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mode Atomic Force Microscopy
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