Time-Lapse Imaging of Conformational Changes in Supercoiled DNA by Scanning Force Microscopy

2002 ◽  
Vol 300 (2) ◽  
pp. 170-176 ◽  
Author(s):  
Fuji Nagami ◽  
Giampaolo Zuccheri ◽  
Bruno Samorí ◽  
Reiko Kuroda
Keyword(s):  
Conformational Changes ◽  
Scanning Force Microscopy ◽  
Time Lapse ◽  
Supercoiled Dna ◽  
Force Microscopy ◽  
Scanning Force ◽  
Time Lapse Imaging

Scanning Force Microscopy and Nanomangulation: Studies of Dna and Proteins Involved in Dna Repair

1999 ◽  
Vol 5 (S2) ◽  
pp. 1004-1005
Author(s):  
Dorothy Erie ◽  
Glenn Ratcliff ◽  
Martin Guthold ◽  
Valerie Bullock ◽  
Michelle Pliske ◽  
...  
Keyword(s):  
Dna Repair ◽  
Physical Properties ◽  
Conformational Changes ◽  
Excision Repair ◽  
Protein Complexes ◽  
Scanning Force Microscopy ◽  
Force Microscopy ◽  
Scanning Force ◽  
Base Excision ◽  
User Friendly

Repair of damaged or incorrectly matched DNA is essential to the survival of all organisms. Consequently cells have devised a plentitude of pathways for repair. We have been investigating the mechanisms of mismatch repair and base excision repair. Both of these repair processes involve a large number of proteins that interact with one another as well as with DNA. Our long-term goal is to assemble complexes that are fully functional for DNA repair and to image the process of DNA repair. In addition, we wish to i) determine the stoicheometry of binding of the protein complexes to each other and to DNA, ii) monitor conformational changes due to substrate binding, iii) measure physical properties of DNA and the complexes. To accomplish this end, we have endeavored to improve techniques for solution imaging as well as those for data analysis. In this presentation I will discuss data on the stoicheometry of binding in several protein complexes and data on the physical properties of DNA.To measure the physical properties of DNA, we utilize a nanoManipulator, a modified Scanning Force Microscope with a novel, user-friendly interface that allows easy and controlled manipulation of nanometer-sized samples.

scholarly journals Conformational changes in CLIP-170 regulate its binding to microtubules and dynactin localization

2004 ◽  
Vol 166 (7) ◽  
pp. 1003-1014 ◽  
Author(s):  
Gideon Lansbergen ◽  
Yulia Komarova ◽  
Mauro Modesti ◽  
Claire Wyman ◽  
Casper C. Hoogenraad ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Metal Binding ◽  
Intramolecular Interaction ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Scanning Force Microscopy ◽  
Binding Motif ◽  
Force Microscopy ◽  
Scanning Force ◽  
Metal Binding Motif

Cytoplasmic linker protein (CLIP)-170, CLIP-115, and the dynactin subunit p150Glued are structurally related proteins, which associate specifically with the ends of growing microtubules (MTs). Here, we show that down-regulation of CLIP-170 by RNA interference results in a strongly reduced accumulation of dynactin at the MT tips. The NH2 terminus of p150Glued binds directly to the COOH terminus of CLIP-170 through its second metal-binding motif. p150Glued and LIS1, a dynein-associating protein, compete for the interaction with the CLIP-170 COOH terminus, suggesting that LIS1 can act to release dynactin from the MT tips. We also show that the NH2-terminal part of CLIP-170 itself associates with the CLIP-170 COOH terminus through its first metal-binding motif. By using scanning force microscopy and fluorescence resonance energy transfer-based experiments we provide evidence for an intramolecular interaction between the NH2 and COOH termini of CLIP-170. This interaction interferes with the binding of the CLIP-170 to MTs. We propose that conformational changes in CLIP-170 are important for binding to dynactin, LIS1, and the MT tips.

DNA-loop Formation on Nucleosomes Shown by in situ Scanning Force Microscopy of Supercoiled DNA

2005 ◽  
Vol 345 (4) ◽  
pp. 695-706 ◽  
Author(s):  
Malte Bussiek ◽  
Katalin Tóth ◽  
Nathalie Brun ◽  
Jörg Langowski
Keyword(s):  
Scanning Force Microscopy ◽  
Loop Formation ◽  
Supercoiled Dna ◽  
Force Microscopy ◽  
Dna Loop ◽  
Scanning Force

Scanning force microscopy of the complexes of p53 core domain with supercoiled DNA 1 1Edited by M. Yaniv

2000 ◽  
Vol 299 (3) ◽  
pp. 585-592 ◽  
Author(s):  
Stephen D Jett ◽  
Dmitry I Cherny ◽  
Vinod Subramaniam ◽  
Thomas M Jovin
Keyword(s):  
Scanning Force Microscopy ◽  
Supercoiled Dna ◽  
Core Domain ◽  
Force Microscopy ◽  
Scanning Force

Scanned tip measurement of deep vertical facets on a flat surface: Measuring roughness on gaas laser waveguide mirrors

1993 ◽  
Vol 51 ◽  
pp. 532-533
Author(s):  
Chang Shen ◽  
Phil Fraundorf ◽  
Robert W. Harrick
Keyword(s):  
Integrated Circuits ◽  
Flat Surface ◽  
Scanning Force Microscopy ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Force Microscopy ◽  
Optoelectronic Integrated Circuits ◽  
Laser Waveguide ◽  
Scanning Force ◽  
Gaas Laser

Monolithic integration of optoelectronic integrated circuits (OEIC) requires high quantity etched laser facets which prevent the developing of more-highly-integrated OEIC's. The causes of facet roughness are not well understood, and improvement of facet quality is hampered by the difficulty in measuring the surface roughness. There are several approaches to examining facet roughness qualitatively, such as scanning force microscopy (SFM), scanning tunneling microscopy (STM) and scanning electron microscopy (SEM). The challenge here is to allow more straightforward monitoring of deep vertical etched facets, without the need to cleave out test samples. In this presentation, we show air based STM and SFM images of vertical dry-etched laser facets, and discuss the image acquisition and roughness measurement processes. Our technique does not require precision cleaving. We use a traditional tip instead of the T shape tip used elsewhere to preventing “shower curtain” profiling of the sidewall. We tilt the sample about 30 to 50 degrees to avoid the curtain effect.

Log-log scale roughness spectroscopy of surfaces

1993 ◽  
Vol 51 ◽  
pp. 224-225
Author(s):  
P. Fraundorf ◽  
B. Armbruster
Keyword(s):  
Power Spectrum ◽  
Autocorrelation Function ◽  
Power Spectra ◽  
Scanning Force Microscopy ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Force Microscopy ◽  
Scanning Force ◽  
Lateral Structure ◽  
Scale Roughness

Optical interferometry, confocal light microscopy, stereopair scanning electron microscopy, scanning tunneling microscopy, and scanning force microscopy, can produce topographic images of surfaces on size scales reaching from centimeters to Angstroms. Second moment (height variance) statistics of surface topography can be very helpful in quantifying “visually suggested” differences from one surface to the next. The two most common methods for displaying this information are the Fourier power spectrum and its direct space transform, the autocorrelation function or interferogram. Unfortunately, for a surface exhibiting lateral structure over several orders of magnitude in size, both the power spectrum and the autocorrelation function will find most of the information they contain pressed into the plot’s origin. This suggests that we plot power in units of LOG(frequency)≡-LOG(period), but rather than add this logarithmic constraint as another element of abstraction to the analysis of power spectra, we further recommend a shift in paradigm.

Anisotropy of Nanoindentation – a tool for the determination of nanocrystal orientation ?

2003 ◽  
Vol 779 ◽  
Author(s):  
David Christopher ◽  
Steven Kenny ◽  
Roger Smith ◽  
Asta Richter ◽  
Bodo Wolf ◽  
...  
Keyword(s):  
Crystal Surface ◽  
Scanning Force Microscopy ◽  
Depth Range ◽  
Dislocation Loops ◽  
Force Microscopy ◽  
Pile Up ◽  
Out Of Plane ◽  
Scanning Force ◽  
Dynamics Simulations

AbstractThe pile up patterns arising in nanoindentation are shown to be indicative of the sample crystal symmetry. To explain and interpret these patterns, complementary molecular dynamics simulations and experiments have been performed to determine the atomistic mechanisms of the nanoindentation process in single crystal Fe{110}. The simulations show that dislocation loops start from the tip and end on the crystal surface propagating outwards along the four in-plane <111> directions. These loops carry material away from the indenter and form bumps on the surface along these directions separated from the piled-up material around the indenter hole. Atoms also move in the two out-of-plane <111> directions causing propagation of subsurface defects and pile-up around the hole. This finding is confirmed by scanning force microscopy mapping of the imprint, the piling-up pattern proving a suitable indicator of the surface crystallography. Experimental force-depth curves over the depth range of a few nanometers do not appear smooth and show distinct pop-ins. On the sub-nanometer scale these pop-ins are also visible in the simulation curves and occur as a result of the initiation of the dislocation loops from the tip.

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