Atomic force microscopy on chromosomes, chromatin and DNA: A review

Kalle, Wouter; Strappe, Pádraig

doi:10.1016/j.micron.2012.04.004

Cited by 26 publications

(12 citation statements)

References 85 publications

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“…In general, compared to other techniques such as standard Scanning (SEM) and Transmission Electron (TEM) microscopy, the AFM not only offers the capacity to visualize nanometric features in two and three dimensions (for significantly smaller areas though, when compared to SEM) and to map the physicochemical characteristics of surfaces, but it also advantageously permits to do so in air, vacuum and especially in liquid environments. These characteristics have been fundamental to image static and dynamic events, such as the adsorption of proteins and DNA, [32][33][34][35][36] as well as the structural and molecular components of living cells and bacteria (Fig. 2), [37][38][39][40][41][42][43][44] while providing minimal perturbation of the native characteristics of biological samples and avoiding artifacts associated with drying, including the creation of artefactual structures (e.g.…”

Section: Afm and Other Imaging Techniquesmentioning

confidence: 99%

Atomic force microscopy in biomaterials surface science

Variola

2015

Phys. Chem. Chem. Phys.

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Recent progress in surface science, nanotechnology and biophysics has cast new light on the correlation between the physicochemical properties of biomaterials and the resulting biological response. One experimental tool that promises to generate an increasingly more sophisticated knowledge of how proteins, cells and bacteria interact with nanostructured surfaces is the atomic force microscope (AFM). This unique instrument permits to close in on interfacial events at the scale at which they occur, the nanoscale. This perspective covers recent developments in the exploitation of the AFM, and suggests insights on future opportunities that can arise from the exploitation of this powerful technique.

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Section: Afm and Other Imaging Techniquesmentioning

confidence: 99%

Atomic force microscopy in biomaterials surface science

Variola

2015

Phys. Chem. Chem. Phys.

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“…Results show that DNA breathing at the replication fork is enhanced upon binding of the processive bacteriophage T4-coded helicase-primase to the DNA compared to naked replication fork constructs, suggesting that DNA breathing is involved in the initial binding and function of the helicase-primase (Phelps et al, 2013). Additionally, atomic force microscopy (AFM) has been extensively used to characterize chromatin structure, ranging from entire chromosomes down to dinucleosomes (reviewed by Kalle and Strappe, 2012). For example, high-speed time-lapse AFM was used to demonstrate that nucleosomes undergo transient and spontaneous unfolding and sliding events (Miyagi et al, 2011).…”

Section: Methods For Probing the Biological Relevance Of Identified Hmentioning

confidence: 99%

Identification and interrogation of combinatorial histone modifications

et al. 2013

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Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs). Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.

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“…AFM studies of chromatin have been reviewed recently by Kalle et al 101 and Strappe et al 102 Below, we review studies that were focused on chromatin dynamics by time-lapse AFM. 86,103–105 Mononucleosomes are typicaly used in experimental systems to study chromatin dynamics.…”

Section: Time-lapse Afm Operationmentioning

confidence: 99%

Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy

Lyubchenko

Shlyakhtenko

2016

Crit Rev Eukaryot Gene Expr

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This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein–DNA complexes, including recent advances in the visualization of protein–DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein–DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein–DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.

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Atomic force microscopy on chromosomes, chromatin and DNA: A review

Cited by 26 publications

References 85 publications

Atomic force microscopy in biomaterials surface science

Atomic force microscopy in biomaterials surface science

Identification and interrogation of combinatorial histone modifications

Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy

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