Direct Observation of the Formation and Dissociation of Double-Stranded DNA Containing G-Quadruplex/i-Motif Sequences in the DNA Origami Frame Using High-Speed AFM

2019 ◽  
pp. 299-308
Author(s):  
Masayuki Endo ◽  
Xiwen Xing ◽  
Hiroshi Sugiyama
Keyword(s):  
Direct Observation ◽  
High Speed ◽  
Dna Origami ◽  
Double Stranded Dna ◽  
G Quadruplex

Direct observation of the dual-switching behaviors corresponding to the state transition in a DNA nanoframe

2014 ◽  
Vol 50 (32) ◽  
pp. 4211-4213 ◽  
Author(s):  
Yangyang Yang ◽  
Masayuki Endo ◽  
Yuki Suzuki ◽  
Kumi Hidaka ◽  
Hiroshi Sugiyama
Keyword(s):  
Atomic Force Microscopy ◽  
Direct Observation ◽  
High Speed ◽  
State Transition ◽  
The State ◽  
Force Microscopy ◽  
Atomic Force ◽  
G Quadruplex

The dual-switching behaviors of photoresponsive DNAs and the G-quadruplex in the DNA nanoframe were successfully visualized by high-speed atomic force microscopy.

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

Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA

2018 ◽  
Vol 10 (30) ◽  
pp. 25166-25173 ◽  
Author(s):  
Ming Jin ◽  
Xiangjun Liu ◽  
Xin Zhang ◽  
Linlin Wang ◽  
Tao Bing ◽  
...  
Keyword(s):  
Fluorescence Detection ◽  
Carbon Dots ◽  
Thiazole Orange ◽  
Ratiometric Fluorescence ◽  
Double Stranded Dna ◽  
G Quadruplex

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 Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40255-40262 ◽  
Author(s):  
Shikhar Tyagi ◽  
Sarika Saxena ◽  
Nikita Kundu ◽  
Taniya Sharma ◽  
Amlan Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synthetic Peptide ◽  
High Selectivity ◽  
Selective Recognition ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna ◽  
G Quadruplex ◽  
Guanine Base

A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.

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
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