scholarly journals Configuration Transitions of Free Circular DNA System Induced by Nicks

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Chao Ji ◽  
Lingyun Zhang ◽  
Pengye Wang
Keyword(s):  
Physical Mechanism ◽  
Effective Length ◽  
Base Pairs ◽  
Circular Dna ◽  
Force Microscopy ◽  
System A ◽  
Atomic Force ◽  
Torsional Energy ◽  
Dna Base ◽  
Quantitative Results

Nicks have important functions in the biological functions of DNA-mediated systems. However, the configuration transitions of DNA molecules induced by the presence of nicks have not been quantitatively investigated. This study aims to analyze the configuration transitions of free circular DNA system induced by nicks. Using atomic force microscopy, two configuration states were observed in the free circular DNA system with different nick numbers. To understand the transmission of torsional energy among DNA base pairs, we defined the effective length and nicking angle. In the free DNA system, a torsional energy of 233 bp can be completely released by nicks. Based on the experimental and quantitative results, we propose a physical mechanism to explain the configuration transitions of the free circular DNA system induced by nicks. This study and the presented method are very useful in understanding the physical mechanism of nicks in DNA-mediated systems.

scholarly journals Studies of the Antiproliferative Activity of Ruthenium (II) Cyclopentadienyl-Derived Complexes with Nitrogen Coordinated Ligands

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Virtudes Moreno ◽  
Julia Lorenzo ◽  
Francesc X. Aviles ◽  
M. Helena Garcia ◽  
João P. Ribeiro ◽  
...  
Keyword(s):  
Plasmid Dna ◽  
Antitumor Agents ◽  
Tertiary Structure ◽  
Base Pairs ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Pbr322 Plasmid ◽  
Ct Dna

Four cationic ruthenium(II) complexes with the formula[Ru(η5-C5H5)(PPh3)2]+, withL=5-phenyl-1H-tetrazole (TzH)1, imidazole (ImH)2, benzo[1,2-b;4,3-b′] dithio-phen-2-carbonitrile (Bzt)3, and [5-(2-thiophen-2-yl)-vinyl]-thiophene-2-carbonitrile] (Tvt)4were prepared and characterized in view to evaluate their potentialities as antitumor agents. Studies by Circular Dichroism indicated changes in the secondary structure of ct-DNA. Changes in the tertiary structure of pBR322 plasmid DNA were also observed in gel electrophoresis experiment and the images obtained by atomic force microscopy (AFM) suggest strong interaction with pBR322 plasmid DNA; the observed decreasing of the viscosity with time indicates that the complexes do not intercalate between DNA base pairs. Compounds1,2, and3showed much higher cytotoxicity than the cisplatin against human leukaemia cancer cells (HL-60 cells).

scholarly journals Magnetic Driven Two-Finger Micro-Hand with Soft Magnetic End-Effector for Force-Controlled Stable Manipulation in Microscale

Micromachines ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 410
Author(s):  
Dan Liu ◽  
Xiaoming Liu ◽  
Pengyun Li ◽  
Xiaoqing Tang ◽  
Masaru Kojima ◽  
...  
Keyword(s):  
Magnetic Force ◽  
Force Feedback ◽  
Soft Magnetic ◽  
End Effector ◽  
Force Microscopy ◽  
System A ◽  
Atomic Force ◽  
Afm Probe ◽  
End Effectors ◽  
Fixed End

In recent years, micromanipulators have provided the ability to interact with micro-objects in industrial and biomedical fields. However, traditional manipulators still encounter challenges in gaining the force feedback at the micro-scale. In this paper, we present a micronewton force-controlled two-finger microhand with a soft magnetic end-effector for stable grasping. In this system, a homemade electromagnet was used as the driving device to execute micro-objects manipulation. There were two soft end-effectors with diameters of 300 μm. One was a fixed end-effector that was only made of hydrogel, and the other one was a magnetic end-effector that contained a uniform mixture of polydimethylsiloxane (PDMS) and paramagnetic particles. The magnetic force on the soft magnetic end-effector was calibrated using an atomic force microscopy (AFM) probe. The performance tests demonstrated that the magnetically driven soft microhand had a grasping range of 0–260 μm, which allowed a clamping force with a resolution of 0.48 μN. The stable grasping capability of the magnetically driven soft microhand was validated by grasping different sized microbeads, transport under different velocities, and assembly of microbeads. The proposed system enables force-controlled manipulation, and we believe it has great potential in biological and industrial micromanipulation.

scholarly journals Visualization of circular DNA molecules labeled with colloidal gold spheres using atomic force microscopy

1993 ◽  
Vol 11 (4) ◽  
pp. 820-823 ◽  
Author(s):  
Wen‐Ling Shaiu ◽  
James Vesenka ◽  
Daniel Jondle ◽  
Eric Henderson ◽  
Drena D. Larson
Keyword(s):  
Atomic Force Microscopy ◽  
Colloidal Gold ◽  
Dna Molecules ◽  
Circular Dna ◽  
Force Microscopy ◽  
Atomic Force

Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches

Nanoscale ◽  
2019 ◽  
Vol 11 (37) ◽  
pp. 17206-17210 ◽  
Author(s):  
Wenjing Liu ◽  
Yourong Guo ◽  
Kaizhe Wang ◽  
Xingfei Zhou ◽  
Ying Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Dna Origami ◽  
Single Molecule Force Spectroscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Base Pair Mismatch ◽  
Dna Base ◽  
Single Base Pair ◽  
Target Molecules

AFM-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules at once. Target DNAs differing by only a single-base pair mismatch are clearly differentiated.

AFM and Ellipsometry Studies of Ultra Thin Ti Film Deposited on a Silicon Wafer

2013 ◽  
Vol 773-774 ◽  
pp. 616-625 ◽  
Author(s):  
Bing Jing Lin ◽  
Hong Tao Zhu ◽  
A. Kiet Tieu ◽  
Gerry Triani
Keyword(s):  
Silicon Wafer ◽  
Smooth Structure ◽  
Force Microscopy ◽  
System A ◽  
Atomic Force ◽  
Combined Use ◽  
Height Step ◽  
Deposited Film ◽  
Arc Deposition ◽  
Coated Area

An ultra- thin Ti film with a thickness of less than 30 nm was deposited on the surface of a silicon wafer by the filtered arc deposition system. A novel technique was adopted to create a height step between the coated area and non-coated area (silicon wafer) during deposition. The surface morphology and thickness of the film was detected by atomic force microscopy (AFM). The AFM results showed that the deposited film formed a smooth structure on the silicon wafer and the height step between the coating and silicon wafer was clear enough to give the thickness of the deposited film. The composition of the deposited film was detected by a combined use of Ellipsometry and AFM. Natural oxidisation of Ti (TiO2) was found on the top of the Ti film after deposition, and the thickness of TiO2 was determined by ellipsometry to be about 0.6 nm.

scholarly journals Revealing the planar chemistry of two-dimensional heterostructures at the atomic level

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Harry Chou ◽  
Ariel Ismach ◽  
Rudresh Ghosh ◽  
Rodney S. Ruoff ◽  
Andrei Dolocan
Keyword(s):  
Secondary Ion Mass Spectrometry ◽  
Structural Information ◽  
Layer Structure ◽  
Atomic Level ◽  
Chemical Information ◽  
Two Dimensional ◽  
Force Microscopy ◽  
System A ◽  
Atomic Force

Abstract Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devices.

Challenges and Results for Quantitative Piezoelectric Hysteresis Measurements by Piezo Force Microscopy

2005 ◽  
Vol 11 (S03) ◽  
pp. 6-9 ◽  
Author(s):  
B. D. Huey ◽  
R. Nath ◽  
R. E. Garcia ◽  
J. E. Blendell
Keyword(s):  
Electromechanical Properties ◽  
Materials Properties ◽  
Force Microscopy ◽  
Atomic Force ◽  
Measuring Surface ◽  
Contrast Mechanisms ◽  
Quantitative Results ◽  
Properties Of Materials ◽  
Piezo Force Microscopy ◽  
Nanoscale Features

Atomic Force Microscopy (AFM) has become a ubiquitous tool for analyzing the topography of a wide variety of materials, especially as nanoscale features become more significant for both understanding as well as determining materials properties [1]. Many AFM variations have also been developed for measuring surface properties beyond straightforward cartography. In many of these cases, the contrast mechanisms are often either extremely complex, or not well understood, even though the principles are simple. For example, Piezo-Force Microscopy (PFM) is relatively easy to understand and use in a standard lab for measuring electromechanical properties of materials, but care must be taken in order to obtain quantitative results as described below.

scholarly journals Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction

2016 ◽  
Vol 113 (5) ◽  
pp. 1208-1213 ◽  
Author(s):  
Jochen P. Müller ◽  
Salomé Mielke ◽  
Achim Löf ◽  
Tobias Obser ◽  
Christof Beer ◽  
...  
Keyword(s):  
Von Willebrand Factor ◽  
Single Molecule ◽  
Effective Length ◽  
Force Sensing ◽  
Force Microscopy ◽  
Atomic Force ◽  
Increased Risk ◽  
Afm Imaging ◽  
Von Willebrand ◽  
Willebrand Factor

The large plasma glycoprotein von Willebrand factor (VWF) senses hydrodynamic forces in the bloodstream and responds to elevated forces with abrupt elongation, thereby increasing its adhesiveness to platelets and collagen. Remarkably, forces on VWF are elevated at sites of vascular injury, where VWF’s hemostatic potential is important to mediate platelet aggregation and to recruit platelets to the subendothelial layer. Adversely, elevated forces in stenosed vessels lead to an increased risk of VWF-mediated thrombosis. To dissect the remarkable force-sensing ability of VWF, we have performed atomic force microscopy (AFM)-based single-molecule force measurements on dimers, the smallest repeating subunits of VWF multimers. We have identified a strong intermonomer interaction that involves the D4 domain and critically depends on the presence of divalent ions, consistent with results from small-angle X-ray scattering (SAXS). Dissociation of this strong interaction occurred at forces above ∼50 pN and provided ∼80 nm of additional length to the elongation of dimers. Corroborated by the static conformation of VWF, visualized by AFM imaging, we estimate that in VWF multimers approximately one-half of the constituent dimers are firmly closed via the strong intermonomer interaction. As firmly closed dimers markedly shorten VWF’s effective length contributing to force sensing, they can be expected to tune VWF’s sensitivity to hydrodynamic flow in the blood and to thereby significantly affect VWF’s function in hemostasis and thrombosis.

scholarly journals CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy

2018 ◽  
Vol 430 (6) ◽  
pp. 759-776 ◽  
Author(s):  
Matthew T. Mawhinney ◽  
Runcong Liu ◽  
Fang Lu ◽  
Jasna Maksimoska ◽  
Kevin Damico ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Dna Complexes ◽  
Circular Dna ◽  
Force Microscopy ◽  
Atomic Force
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