Combined single-molecule manipulation and localization for the study of lac Repressor 1D-diffusion along DNA

2013 ◽  
Author(s):  
G. Belcastro ◽  
C. Mónico ◽  
M. Capitanio ◽  
F. Vanzi ◽  
F. S. Pavone
Keyword(s):  
Single Molecule ◽  
Lac Repressor ◽  
Single Molecule Manipulation

scholarly journals Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

2008 ◽  
Vol 36 (8) ◽  
pp. 2505-2513 ◽  
Author(s):  
Davide Normanno ◽  
Francesco Vanzi ◽  
Francesco Saverio Pavone
Keyword(s):  
Single Molecule ◽  
Lac Repressor ◽  
Dna Looping ◽  
Single Molecule Manipulation

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

Single-molecule manipulation

2012 ◽  
pp. 709-764
Author(s):  
Igor N. Serdyuk ◽  
Nathan R. Zaccai ◽  
Joseph Zaccai
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation
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