scholarly journals Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure

ACS Nano ◽  
2015 ◽  
Vol 9 (10) ◽  
pp. 9922-9929 ◽  
Author(s):  
Masayuki Endo ◽  
Xiwen Xing ◽  
Xiang Zhou ◽  
Tomoko Emura ◽  
Kumi Hidaka ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Nanostructure ◽  
G Quadruplex ◽  
Motif Site ◽  
Duplex Formation ◽  
Single Molecule Manipulation

scholarly journals Voltammetry and molecular assembly of G-quadruplex DNAzyme on single-crystal Au(111)-electrode surfaces – hemin as an electrochemical intercalator

2016 ◽  
Vol 193 ◽  
pp. 99-112 ◽  
Author(s):  
Ling Zhang ◽  
Jens Ulstrup ◽  
Jingdong Zhang
Keyword(s):  
Single Crystal ◽  
Single Molecule ◽  
Electrode Surface ◽  
Molecular Assembly ◽  
Electrode Surfaces ◽  
Potential Control ◽  
G Quadruplex ◽  
Tunnelling Microscopy ◽  
Dna Quadruplexes

DNA quadruplexes (qs) are a class of “non-canonical” oligonucleotides (OGNs) composed of stacked guanine (G) quartets stabilized by specific cations. Metal porphyrins selectively bind to G-qs complexes to form what is known as DNAzyme, which can exhibit peroxidase and other catalytic activity similar to heme group metalloenzymes. In the present study we investigate the electrochemical properties and the structure of DNAzyme monolayers on single-crystal Au(111)-electrode surfaces using cyclic voltammetry and scanning tunnelling microscopy under electrochemical potential control (in situ STM). The target DNAzyme is formed from a single-strand OGN with 12 guanines and iron(iii) porphyrin IX (hemin), and assembles on Au(111) through a mercapto alkyl linker. The DNAzyme monolayers exhibit a strong pair of redox peaks at 0.0 V (NHE) at pH 7 in acetate buffer, shifted positively by about 50 mV compared to free hemin weakly physisorbed on the Au(111)-electrode surface. The voltammetric hemin signal of DNAzyme is enhanced 15 times compared with that of hemin adsorbed directly on the Au(111)-electrode surface. This is indicative of both the formation of a close to dense DNAzyme monolayer and that hemin is strongly bound to the immobilized 12G-qs in well-defined orientation favorable for interfacial ET with a rate constant of 6.0 ± 0.4 s−1. This is supported by in situ STM which discloses single-molecule G-quartet structures with a size of 1.6 ± 0.2 nm.

Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level

2010 ◽  
Vol 39 (9) ◽  
pp. 1343-1350 ◽  
Author(s):  
A. C. Krüger ◽  
M. K. Raarup ◽  
M. M. Nielsen ◽  
M. Kristensen ◽  
F. Besenbacher ◽  
...  
Keyword(s):  
Single Molecule ◽  
Hnrnp A1 ◽  
Single Molecule Level ◽  
G Quadruplex

scholarly journals In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

2014 ◽  
Vol 10 (2) ◽  
pp. e1003456 ◽  
Author(s):  
Pascal Carrivain ◽  
Maria Barbi ◽  
Jean-Marc Victor
Keyword(s):  
Rigid Body ◽  
Single Molecule ◽  
In Silico ◽  
Rigid Body Dynamics ◽  
Body Dynamics ◽  
Single Molecule Manipulation

scholarly journals New Tool for Single Molecule Manipulation: Optical Pushing

2012 ◽  
Vol 102 (3) ◽  
pp. 385a-386a
Author(s):  
Gerrit Sitters ◽  
Niels Laurens ◽  
Emile J. de Rijk ◽  
Erwin J.G. Peterman ◽  
Gijs J.L. Wuite
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation

scholarly journals The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope

2014 ◽  
Vol 5 ◽  
pp. 202-209 ◽  
Author(s):  
Christian Wagner ◽  
Norman Fournier ◽  
F Stefan Tautz ◽  
Ruslan Temirov
Keyword(s):  
Frequency Shift ◽  
Single Molecule ◽  
Oscillation Amplitude ◽  
Surface Corrugation ◽  
Atomic Force ◽  
Data Points ◽  
Atomic Surface ◽  
Tetracarboxylic Dianhydride ◽  
Single Molecule Manipulation

Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule–surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.

A Universal Assay for Making DNA, RNA, and RNA–DNA Hybrid Configurations for Single-Molecule Manipulation in Two or Three Steps without Ligation

2019 ◽  
Vol 8 (7) ◽  
pp. 1663-1672 ◽  
Author(s):  
Ya-Jun Yang ◽  
Lun Song ◽  
Xiao-Cong Zhao ◽  
Chen Zhang ◽  
Wen-Qiang Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation

A thin permeable-membrane device for single-molecule manipulation

2016 ◽  
Vol 87 (1) ◽  
pp. 014301 ◽  
Author(s):  
Chang-Young Park ◽  
David R. Jacobson ◽  
Dan T. Nguyen ◽  
Sam Willardson ◽  
Omar A. Saleh
Keyword(s):  
Single Molecule ◽  
Permeable Membrane ◽  
Single Molecule Manipulation
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