Direct Observation of Dynamic Movement of DNA Molecules in DNA Origami Imaged Using High-Speed AFM

2018 ◽  
pp. 213-224 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Direct Observation ◽  
High Speed ◽  
Dna Origami ◽  
Dna Molecules ◽  
Dynamic Movement

A DNA prism for high-speed continuous fractionation of large DNA molecules

2002 ◽  
Vol 20 (10) ◽  
pp. 1048-1051 ◽  
Author(s):  
Lotien Richard Huang ◽  
Jonas O. Tegenfeldt ◽  
Jessica J. Kraeft ◽  
James C. Sturm ◽  
Robert H. Austin ◽  
...  
Keyword(s):  
High Speed ◽  
Dna Molecules

Direct observation of surfactant aggregate behavior on a mica surface using high-speed atomic force microscopy

2011 ◽  
Vol 47 (17) ◽  
pp. 4974 ◽  
Author(s):  
Shigeto Inoue ◽  
Takayuki Uchihashi ◽  
Daisuke Yamamoto ◽  
Toshio Ando
Keyword(s):  
Atomic Force Microscopy ◽  
Direct Observation ◽  
High Speed ◽  
Mica Surface ◽  
Force Microscopy ◽  
Atomic Force ◽  
Aggregate Behavior

Direct observation of individual RecA filaments assembling on single DNA molecules

Nature ◽  
2006 ◽  
Vol 443 (7113) ◽  
pp. 875-878 ◽  
Author(s):  
Roberto Galletto ◽  
Ichiro Amitani ◽  
Ronald J. Baskin ◽  
Stephen C. Kowalczykowski
Keyword(s):  
Direct Observation ◽  
Dna Molecules ◽  
Single Dna Molecules

Direct observation of G-quadruplexes using DNA origami nanoscaffold

2015 ◽  
pp. 38-54
Author(s):  
Arivazhagan Rajendran ◽  
Yue Li ◽  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Direct Observation ◽  
Dna Origami

Direct Observation of Dynamic Interactions between Orientation‐Controlled Nucleosomes in a DNA Origami Frame

2020 ◽  
Vol 26 (66) ◽  
pp. 15282-15289
Author(s):  
Yihong Feng ◽  
Fumitaka Hashiya ◽  
Kumi Hidaka ◽  
Hiroshi Sugiyama ◽  
Masayuki Endo
Keyword(s):  
Direct Observation ◽  
Dna Origami ◽  
Dynamic Interactions

scholarly journals Self-assembly of highly ordered DNA origami lattices at solid-liquid interfaces by controlling cation binding and exchange

Nano Research ◽  
2020 ◽  
Vol 13 (11) ◽  
pp. 3142-3150 ◽  
Author(s):  
Yang Xin ◽  
Salvador Martinez Rivadeneira ◽  
Guido Grundmeier ◽  
Mario Castro ◽  
Adrian Keller
Keyword(s):  
Correlation Length ◽  
Self Assembly ◽  
High Speed ◽  
Time Course ◽  
Divalent Cations ◽  
Topological Analysis ◽  
Monovalent Cation ◽  
Cation Binding ◽  
Dna Origami ◽  
Lattice Order

Abstract The surface-assisted hierarchical self-assembly of DNA origami lattices represents a versatile and straightforward method for the organization of functional nanoscale objects such as proteins and nanoparticles. Here, we demonstrate that controlling the binding and exchange of different monovalent and divalent cation species at the DNA-mica interface enables the self-assembly of highly ordered DNA origami lattices on mica surfaces. The development of lattice quality and order is quantified by a detailed topological analysis of high-speed atomic force microscopy (HS-AFM) images. We find that lattice formation and quality strongly depend on the monovalent cation species. Na+ is more effective than Li+ and K+ in facilitating the assembly of high-quality DNA origami lattices, because it is replacing the divalent cations at their binding sites in the DNA backbone more efficiently. With regard to divalent cations, Ca2+ can be displaced more easily from the backbone phosphates than Mg2+ and is thus superior in guiding lattice assembly. By independently adjusting incubation time, DNA origami concentration, and cation species, we thus obtain a highly ordered DNA origami lattice with an unprecedented normalized correlation length of 8.2. Beyond the correlation length, we use computer vision algorithms to compute the time course of different topological observables that, overall, demonstrate that replacing MgCl2 by CaCl2 enables the synthesis of DNA origami lattices with drastically increased lattice order.

scholarly journals Direct Observation of Rotary Catalysis of Rotorless F1-ATPase by High-Speed Atomic Force Microscopy

2012 ◽  
Vol 102 (3) ◽  
pp. 600a
Author(s):  
Ryota Iino ◽  
Takayuki Uchihashi ◽  
Toshio Ando ◽  
Hiroyuki Noji
Keyword(s):  
Atomic Force Microscopy ◽  
Direct Observation ◽  
High Speed ◽  
Force Microscopy ◽  
F1 Atpase ◽  
Atomic Force ◽  
Rotary Catalysis

scholarly journals Direct observation and analysis of TET-mediated oxidation processes in a DNA origami nanochip

2020 ◽  
Vol 48 (8) ◽  
pp. 4041-4051 ◽  
Author(s):  
Xiwen Xing ◽  
Shinsuke Sato ◽  
Nai-Kei Wong ◽  
Kumi Hidaka ◽  
Hiroshi Sugiyama ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Speed ◽  
Excision Repair ◽  
Regulation Of Gene Expression ◽  
Dna Demethylation ◽  
Dna Origami ◽  
Enzymatic Reactions ◽  
Oxidation Reactions ◽  
Methyl Cytosine ◽  
Tet Enzymes

Abstract DNA methylation and demethylation play a key role in the epigenetic regulation of gene expression; however, a series of oxidation reactions of 5-methyl cytosine (5mC) mediated by ten-eleven translocation (TET) enzymes driving demethylation process are yet to be uncovered. To elucidate the relationship between the oxidative processes and structural factors of DNA, we analysed the behavior of TET-mediated 5mC-oxidation by incorporating structural stress onto a substrate double-stranded DNA (dsDNA) using a DNA origami nanochip. The reactions and behaviors of TET enzymes were systematically monitored by biochemical analysis and single-molecule observation using atomic force microscopy (AFM). A reformative frame-like DNA origami was established to allow the incorporation of dsDNAs as 5mC-containing substrates in parallel orientations. We tested the potential effect of dsDNAs present in the tense and relaxed states within a DNA nanochip on TET oxidation. Based on enzyme binding and the detection of oxidation reactions within the DNA nanochip, it was revealed that TET preferred a relaxed substrate regardless of the modification types of 5-oxidated-methyl cytosine. Strikingly, when a multi-5mCG sites model was deployed to further characterize substrate preferences of TET, TET preferred the fully methylated site over the hemi-methylated site. This analytical modality also permits the direct observations of dynamic movements of TET such as sliding and interstrand transfer by high-speed AFM. In addition, the thymine DNA glycosylase-mediated base excision repair process was characterized in the DNA nanochip. Thus, we have convincingly established the system's ability to physically regulate enzymatic reactions, which could prove useful for the observation and characterization of coordinated DNA demethylation processes at the nanoscale.

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
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