scholarly journals Three-dimensional Structure of G-banded Human Metaphase Chromosomes Observed by Atomic Force Microscopy.

2001 ◽  
Vol 64 (5) ◽  
pp. 475-482 ◽  
Author(s):  
Osamu HOSHI ◽  
Tatsuo USHIKI
Keyword(s):  
Atomic Force Microscopy ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Metaphase Chromosomes ◽  
Three Dimensional Structure ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays

Acta Naturae ◽  
2015 ◽  
Vol 7 (2) ◽  
pp. 108-114 ◽  
Author(s):  
E. V. Dubrovin ◽  
G. V. Presnova ◽  
M. Yu. Rubtsova ◽  
A. M. Egorov ◽  
V. G Grigorenko ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acids ◽  
Detection Threshold ◽  
Three Dimensional ◽  
Quantitative Measure ◽  
Nucleic Acid Hybridization ◽  
Dimensional Structure ◽  
3D Analysis ◽  
Force Microscopy ◽  
Atomic Force

Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

Three Dimensional Structure of Human Fibrinogen under Aqueous Conditions Visualized by Atomic Force Microscopy

1997 ◽  
Vol 77 (06) ◽  
pp. 1048-1051 ◽  
Author(s):  
Roger E Marchant ◽  
Matthew D Barb ◽  
John R Shainoff ◽  
Steven J Eppell ◽  
David L Wilson ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Three Dimensional ◽  
Hydrophobic Surface ◽  
Dimensional Structure ◽  
Structure And Properties ◽  
Human Fibrinogen ◽  
Force Microscopy ◽  
Atomic Force ◽  
Molecular Scale ◽  
Aqueous Conditions

SummaryFibrinogen plays a central role in surface-induced thrombosis. However, the interactions of fibrinogen with different substrata remain poorly understood because of the difficulties involved in imaging globular proteins under aqueous conditions. We present detailed three dimensional molecular scale images of fibrinogen molecules on a hydrophobic surface under aqueous conditions obtained by atomic force microscopy. Hydrated fibrinogen monomers are visualized as overlapping ellipsoids; dimers and trimers have linear conformations predominantly, and increased affinity for the hydrophobic surface compared with monomeric fibrinogen. The results demonstrate the importance of hydration on protein structure and properties that affect surface-dependent interactions.

scholarly journals Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

2019 ◽  
Author(s):  
Toru Niina ◽  
Sotaro Fuchigami ◽  
Shoji Takada
Keyword(s):  
Atomic Force Microscopy ◽  
Rigid Body ◽  
Protein Structures ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Surface Shape ◽  
Dimensional Structure ◽  
Force Microscopy ◽  
Atomic Force ◽  
Afm Image

AbstractAtomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here we developed a method to fit flexibly a three-dimensional biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given three-dimensional structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method, by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin-experiment; for a synthetic AFM image produced from a protein structure different from its native conformation, the flexible fitting MD simulations sampled those that fit well the AFM image. Then, parameter dependence in the protocol is discussed. Finally, we applied the method to a real experimental AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a fixed structure to the AFM image. Our method will be a general tool for structure modeling based on AFM images and is publicly available through CafeMol software.

scholarly journals Acoustic subsurface-atomic force microscopy: Three-dimensional imaging at the nanoscale

2021 ◽  
Vol 129 (3) ◽  
pp. 030901
Author(s):  
Hossein J. Sharahi ◽  
Mohsen Janmaleki ◽  
Laurene Tetard ◽  
Seonghwan Kim ◽  
Hamed Sadeghian ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Three Dimensional ◽  
Three Dimensional Imaging ◽  
Force Microscopy ◽  
Atomic Force

Three-dimensional imaging of undercut and sidewall structures by atomic force microscopy

2011 ◽  
Vol 82 (2) ◽  
pp. 023707 ◽  
Author(s):  
Sang-Joon Cho ◽  
Byung-Woon Ahn ◽  
Joonhui Kim ◽  
Jung-Min Lee ◽  
Yueming Hua ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Three Dimensional ◽  
Three Dimensional Imaging ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Development and AFM study of porous scaffolds for wound healing applications

2004 ◽  
Vol 18 (4) ◽  
pp. 587-596 ◽  
Author(s):  
T. A. Doneva ◽  
H. B. Yin ◽  
P. Stephens ◽  
W. R. Bowen ◽  
D. W. Thomas
Keyword(s):  
Atomic Force Microscopy ◽  
Wound Healing ◽  
Human Fibroblasts ◽  
Three Dimensional ◽  
Positive Influence ◽  
Porous Scaffolds ◽  
Force Microscopy ◽  
Cellular Assays ◽  
Atomic Force

An engineering approach to the development of biomaterials for promotion of wound healing emphasises the importance of a well‒controlled architecture and concentrates on optimisation of morphology and surface chemistry to stimulate guidance of the cells within the wound environment. A series of three‒dimensional porous scaffolds with 80–90% bulk porosity and fully interconnected macropores were prepared from two biodegradable materials – cellulose acetate (CA) and poly (lactic‒co‒glycolic acid) (PLGA) through the phase inversion mechanism of formation. Surface morphology of obtained scaffolds was determined using atomic force microscopy (AFM) in conjunction with optical microscopy. Scanning Electron Microscopy (SEM) was applied to characterise scaffolds bulk morphology. Biocompatibility and biofunctionality of the prepared materials were assessed through a systematic study of cell/material interactions using atomic force microscopy (AFM) methodologies together within vitrocellular assays. Preliminary data with human fibroblasts demonstrated a positive influence of both scaffolds on cellular attachment and growth. The adhesion of cells on both biomaterials were quantified by AFM force measurements in conjunction with a cell probe technique since, for the first time, a fibroblast probe has been successfully developed and optimal conditions of immobilisation of the cells on the AFM cantilever have been experimentally determined.

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