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

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 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

PRINCIPLES OF SINGLE-MOLECULE MANIPULATION AND ITS APPLICATION IN BIOLOGICAL PHYSICS

2012 ◽  
Vol 26 (13) ◽  
pp. 1230006 ◽  
Author(s):  
WEI-HUNG CHEN ◽  
JONATHAN D. WILSON ◽  
SITHARA S. WIJERATNE ◽  
SARAH A. SOUTHMAYD ◽  
KUAN-JIUH LIN ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Biological Molecules ◽  
Force Detection ◽  
Biomolecular Systems ◽  
Single Molecule Level ◽  
Detection Techniques ◽  
Atomic Force ◽  
Manipulation System ◽  
Single Molecule Manipulation

Recent advances in nanoscale manipulation and piconewton force detection provide a unique tool for studying the mechanical and thermodynamic properties of biological molecules and complexes at the single-molecule level. Detailed equilibrium and dynamics information on proteins and DNA have been revealed by single-molecule manipulation and force detection techniques. The atomic force microscope (AFM) and optical tweezers have been widely used to quantify the intra- and inter-molecular interactions of many complex biomolecular systems. In this article, we describe the background, analysis, and applications of these novel techniques. Experimental procedures that can serve as a guide for setting up a single-molecule manipulation system using the AFM are also presented.

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