Name: probing the structure and dynamics of nucleosomes using atomic force microscopy imaging
Uploaded: 2019-01-31T14:00:00.000+00:00
Duration: 9 min 52 s
Description: Watch this Scientific Journal Video about Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging at JoVE.com

Author contributions: YLL and MSD designed the project; MSD assembled nucleosomes. MSD and ZS performed AFM experiments and data analyses. All authors wrote and edited the manuscript.

The authors declare that they have no competing financial interests.

The protocol described above is rather straightforward and provide highly reproducible results, although a few important issues can be emphasized. Functionalized APS-mica is a key substrate for getting reliable and reproducible results. A high stability of APS-mica is one of the important features of this substrate that allows one to prepare the imaging substrate in advance for use that can be used at least two weeks after being prepared.59,61 However, the surfac...

In eukaryotic cells, DNA is highly condensed and organized into chromosomes.1 The first level of DNA organization within a chromosome is the assembly of nucleosomes in which 147 bp of DNA is tightly wrapped around a histone octamer core.2,3 Nucleosome particles assemble on a long DNA molecule forming a chromatin array which is then organized until a highly compact chromosome unit is formed.4 The disassembly of chromatin provides the access to free DNA required by critical cellular processes such as gene transcription and genome replication, suggesting that chromatin is a highly dynamic system.5,6,7 Understanding the dynamic properties of DNA at various chromatin levels is critically important for elucidating genetic processes at the molecular level where mistakes can lead to cell death or the development of diseases such as cancer.8 A chromatin property of great importance is the dynamics of nucleosomes.9,10,11,12 The high stability of these particles has allowed for the structural characterization by crystallographic techniques.2 What these studies lack are the dynamic details of nucleosomes such as the mechanism of DNA unwrapping from the histone core; the dynamic pathway of which is required for transcription and replication processes.7,9,13,14,15,16 Furthermore, special proteins termed remodeling factors have been shown to facilitate the disassembly of nucleosomal particles17; however, the intrinsic dynamics of nucleosomes is the critical factor in this process that contributes to the entire disassembly process.14,16,18,19
Single-molecule techniques such as single-molecule fluorescence19,20,21, optical trapping (tweezers)13,18,22,23 and AFM10,14,15,16,24,25,26 have been instrumental in understanding the dynamics of nucleosomes. Among these methods, AFM benefits from several unique and attractive features. AFM allows one to visualize and characterize individual nucleosomes as well as the longer arrays27. From AFM images, important characteristics of nucleosome structure such as the length of DNA wrapped around the histone core can be measured 10,14,26,28; a parameter that is central to the characterization of nucleosome unwrapping dynamics. Past AFM studies have revealed nucleosomes to be highly dynamic systems and that DNA can spontaneously unwrap from the histone core14. The spontaneous unwrapping of DNA from nucleosomes was directly visualized by AFM operating in the time-lapse mode when the imaging is done in aqueous solutions 14,26,29.
The advent of the high-speed time-lapse AFM (HS-AFM) instrumentation made it possible to visualize the nucleosome unwrapping process at the millisecond time-scale 14,15,24. Recent HS-AFM 16,30 studies of centromere specific nucleosomes revealed several novel features of the nucleosomes compared with the canonical type. Centromere nucleosomes constitute of a centromere, a small part of the chromosome critically important for chromosome segregation31. Unlike canonical nucleosomes in bulk chromatin, the histone core of centromere nucleosomes contains CENP-A histone instead of histone H332,33. As a result of this histone substitution, DNA wrapping in centromere nucleosomes is ~120 bp instead of the ~147 bp for canonical nucleosomes; a difference that can lead to distinct morphologies of the centromere and canonical nucleosomes arrays34, suggesting that centromere chromatin undergoes higher dynamics compared with the bulk one. The novel dynamics displayed by centromere nucleosomes in HS-AFM16,30 studies exemplify the unique opportunity provided by this single-molecule technique to directly visualize the structural and dynamic properties of nucleosomes. Examples of these features will be briefly discussed and illustrated at the end of the paper. This progress was made due to the development of novel protocols for AFM imaging of nucleosomes as well as the modifications of existing methods. The goal of the protocol described here is to make these exciting advances in single-molecule AFM nucleosome studies accessible to anyone who would like to utilize these techniques in their chromatin investigations. Many of the techniques described are applicable to problems beyond the study of nucleosomes and can be used for investigations of other protein and DNA systems of interest. A few examples of such applications can be found in publications35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 and prospects of AFM studies of various biomolecular systems are given in reviews29,50,51,53,54.

<table><tbody><tr><td>Plasmid pGEM3Z-601</td><td>Addgene, Cambridge, MA</td><td>26656</td><td></td></tr><tr><td>PCR Primers</td><td>IDT, Coralville, IA</td><td>Custom Order</td><td>(FP) 5&#039;- CAGTGAATTGTAATACGACTC-3&#039; (RP) 5&#039;-ACAGCTATGACCATGATTAC-3&#039;</td></tr><tr><td>DreamTaq polymerase</td><td>ThermoFischer Scientific, Waltham, MA</td><td>EP0701</td><td>Catalog number for 200 units</td></tr><tr><td>PCR purification kit</td><td>Qiagen, Hilden, Germany&amp;nbsp;</td><td>28104</td><td>Catalog number for 50 units</td></tr><tr><td>Tris base</td><td>Sigma-Aldrich, St. Louis, MO</td><td>10708976001</td><td>Catalog number for 250 g</td></tr><tr><td>EDTA</td><td>ThermoFischer Scientific, Waltham, MA</td><td>15576028</td><td>Catalog number for 500 g</td></tr><tr><td>(CENP-A/H4)2, recombinant human</td><td>EpiCypher, Durham, NC</td><td>16-0010</td><td>Catalog number for 50 ug</td></tr><tr><td>H2A/H2B, recombinant human</td><td>EpiCypher, Durham, NC</td><td>15-0311</td><td>Catalog number for 50 ug</td></tr><tr><td>H3 Octamer, recombinant human</td><td>EpiCypher, Durham, NC</td><td>16-0001</td><td>Catalog number for 50 ug</td></tr><tr><td>Slide-A-Lyzer MINI Dialysis Device Kit, 10K MWCO, 0.1 mL</td><td>ThermoFischer Scientific, Waltham, MA</td><td>69574</td><td>Catalog number for 10 devices</td></tr><tr><td>Sodium Chloride</td><td>Sigma-Aldrich, St. Louis, MO</td><td>S9888-500G</td><td>Catalog number for 500 mg</td></tr><tr><td>Amicon Ultra-0.5&amp;nbsp;mL Centrifugal Filters&amp;nbsp;</td><td>Millipore-sigma, Burlington, MO</td><td>UFC501008</td><td>Catalog number for 8 devices</td></tr><tr><td>HCl</td><td>Sigma-Aldrich, St. Louis, MO</td><td>258148-25ML</td><td>Catalog number for 25 mL</td></tr><tr><td>Tricine</td><td>Sigma-Aldrich, St. Louis, MO</td><td>T0377-25G</td><td>Catalog number for 25 g</td></tr><tr><td>SDS</td><td>Sigma-Aldrich, St. Louis, MO</td><td>11667289001</td><td>Catalog number for 1 kg</td></tr><tr><td>Ammonium Persulfate (AmmPS)&amp;nbsp;</td><td>Bio-Rad, Hercules, CA</td><td>1610700</td><td>Catalog number for 10 g</td></tr><tr><td>30% Acrylamide/Bis Solution, 37.5:1</td><td>Bio-Rad, Hercules, CA</td><td>1610158</td><td>Catalog number for 500 mL</td></tr><tr><td>TEMED</td><td>Bio-Rad, Hercules, CA</td><td>1610800</td><td>Catalog number for 5 mL</td></tr><tr><td>4x Laemmli protein sample buffer for SDS-PAGE</td><td>Bio-Rad, Hercules, CA</td><td>1610747</td><td>Catalog number for 10 mL</td></tr><tr><td>2-ME</td><td>Sigma-Aldrich, St. Louis, MO</td><td>M6250-10ML</td><td>Catalog number for 10 mL</td></tr><tr><td>ageRuler Prestained Protein Ladder&amp;nbsp;</td><td>ThermoFischer Scientific, Waltham, MA</td><td>26616</td><td>Catalog number for 500 uL</td></tr><tr><td>Bio-Safe&amp;trade; Coomassie Stain</td><td>Bio-Rad, Hercules, CA</td><td>1610786</td><td>Catalog number for 1 L</td></tr><tr><td>Nonwoven cleanroom wipes: TX604 TechniCloth&amp;nbsp;</td><td>TexWipe, Kernersvile, NC</td><td>TX604</td><td></td></tr><tr><td>Muscovite Block Mica</td><td>AshevilleMica, Newport News, VA</td><td>Grade-1</td><td></td></tr><tr><td>Aminopropyl silatrane (APS)</td><td>Synthesized as described in 22</td><td></td><td></td></tr><tr><td>HEPES</td><td>Sigma-Aldrich, St. Louis, MO</td><td>H4034-25G</td><td>Catalog number for 25 g</td></tr><tr><td>Scotch Tape</td><td>Scotch-3M, St. Paul, MN</td><td></td><td></td></tr><tr><td>TESPA-V2 afm probe (for static imaging)</td><td>Bruker AFM Probes, Camarillo, CA</td><td></td><td></td></tr><tr><td>MSNL-10 afm probe (for standard time-lapse imaing)</td><td>Bruker AFM Probes, Camarillo, CA</td><td></td><td></td></tr><tr><td>Aron Alpha Industrial Krazy Glue</td><td>Toagosei America, West Jefferson, OH</td><td>AA480</td><td>Catalog number for 2 g tube</td></tr><tr><td>MgCl2</td><td>Sigma-Aldrich, St. Louis, MO</td><td>M8266-100G</td><td>Catalog number for 100 g</td></tr><tr><td>Millex-GP Filter, 0.22&amp;nbsp;&amp;micro;m</td><td>Sigma-Aldrich, St. Louis, MO</td><td>SLGP05010</td><td>Catalog number for 10 devices</td></tr><tr><td>BL-AC10DS-A2 afm probe (for HS-AFM)</td><td>Olympus, Japan</td><td></td><td></td></tr><tr><td>Compound FG-3020C-20&amp;nbsp;</td><td>FluoroTechnology Co., Ltd., Kagiya, Kasugai, Aichi, Japan&amp;nbsp;</td><td></td><td></td></tr><tr><td>Compound FS-1010S135-0.5&amp;nbsp;</td><td>FluoroTechnology Co., Ltd., Kagiya, Kasugai, Aichi, Japan&amp;nbsp;</td><td></td><td></td></tr><tr><td>MultiMode Atomic Force Microscope</td><td>Bruker-Nano/Veeco, Santa Barbara, CA</td><td></td><td></td></tr><tr><td>High-Speed Time-Lapse Atomic Force Microsocopy</td><td>Toshio Ando, Nano-Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan</td><td></td><td></td></tr></tbody></table>

probing the structure and dynamics of nucleosomes using atomic force microscopy imaging

Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.

Mono-nucleosomes were first prepared for AFM imaging experiments using a continuous dilution assembly method (Figure 1). The prepared nucleosomes were then checked using discontinuous SDS-PAGE (Figure 2). A mica surface was next functionalized using APS, which captures nucleosomes at the surface while maintaining a smooth background for high-resolution imaging (Figure 3). Nucleosomes were deposited on APS-mica and were subsequently ...

Watch this Scientific Journal Video about Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging at JoVE.com

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Here, we present a protocol to characterize nucleosome particles at the single-molecule level using static and time-lapse atomic force microscopy (AFM) imaging techniques. The surface functionalization method described allows for the capture of the structure and dynamics of nucleosomes in high-resolution at the nanoscale.

Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription ...

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11.6K Views.  University of Nebraska Medical Center. Here, we present a protocol to characterize nucleosome particles at the single-molecule level using static and time-lapse atomic force microscopy (AFM) imaging techniques. The surface functionalization method described allows for the capture of the structure and dynamics of nucleosomes in high-resolution at the nanoscale.

Video: Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.

A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality ...

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. Atomic force microscopy (AFM) can address this problem by enabling stretching and relaxation of single protein molecules, which gives direct evidence of specific unfolding and refolding characteristics. AFM-based single-molecule force-spectroscopy (AFM-SMFS) provides a means to consistently measure high-energy conformations in proteins that are not possible in traditional bulk (biochemical) measurements. Although numerous papers were published to show principles of AFM-SMFS, it is not easy to conduct SMFS experiments due to a lack of an exhaustively complete protocol. In this study, we briefly illustrate the principles of AFM and extensively detail the protocols, procedures, and data analysis as a guideline to achieve good results from SMFS experiments. We demonstrate representative SMFS results of single protein mechanical unfolding measurements and we provide troubleshooting strategies for some commonly encountered problems.

We describe the detailed procedures and strategies to measure the mechanical properties and mechanical unfolding pathways of single protein molecules using an atomic force microscope. We also show representative results as a reference for selection and justification of good single protein molecule recordings.

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. ...

A Direct Force Probe for Measuring Mechanical Integration Between the Nucleus and the Cytoskeleton

The mechanical properties of the nucleus determine its response to mechanical forces generated in cells. Because the nucleus is molecularly continuous with the cytoskeleton, methods are needed to probe its mechanical behavior in adherent cells. Here, we discuss the direct force probe (DFP) as a tool to apply force directly to the nucleus in a living adherent cell. We attach a narrow micropipette to the nuclear surface with suction. The micropipette is translated away from the nucleus, which causes the nucleus to deform and translate. When the restoring force is equal to the suction force, the nucleus detaches and elastically relaxes. Because the suction pressure is precisely known, the force on the nuclear surface is known. This method has revealed that nano-scale forces are sufficient to deform and translate the nucleus in adherent cells, and identified cytoskeletal elements that enable the nucleus to resist forces. The DFP can be used to dissect the contributions of cellular and nuclear components to nuclear mechanical properties in living cells.

In this protocol, we describe a micropipette method to directly apply a controlled force to the nucleus in a living cell. This assay allows interrogation of nuclear mechanical properties in the living, adherent cell.

The mechanical properties of the nucleus determine its response to mechanical forces generated in cells. Because the nucleus is molecularly continuous ...

Analysis of &#946;-Amyloid-induced Abnormalities on Fibrin Clot Structure by Spectroscopy and Scanning Electron Microscopy

This article presents methods for generating in vitro fibrin clots and analyzing the effect of beta-amyloid (A&#946;) protein on clot formation and structure by spectrometry and scanning electron microscopy (SEM). A&#946;, which forms neurotoxic amyloid aggregates in Alzheimer&#39;s disease (AD), has been shown to interact with fibrinogen. This A&#946;-fibrinogen interaction makes the fibrin clot structurally abnormal and resistant to fibrinolysis. A&#946;-induced abnormalities in fibrin clotting may also contribute to cerebrovascular aspects of the AD pathology such as microinfarcts, inflammation, as well as, cerebral amyloid angiopathy (CAA). Given the potentially critical role of neurovascular deficits in AD pathology, developing compounds which can inhibit or lessen the A&#946;-fibrinogen interaction has promising therapeutic value. In vitro methods by which fibrin clot formation can be easily and systematically assessed are potentially useful tools for developing therapeutic compounds. Presented here is an optimized protocol for in vitro generation of the fibrin clot, as well as analysis of the effect of A&#946; and A&#946;-fibrinogen interaction inhibitors. The clot turbidity assay is rapid, highly reproducible and can be used to test multiple conditions simultaneously, allowing for the screening of large numbers of A&#946;-fibrinogen inhibitors. Hit compounds from this screening can be further evaluated for their ability to ameliorate A&#946;-induced structural abnormalities of the fibrin clot architecture using SEM. The effectiveness of these optimized protocols is demonstrated here using TDI-2760, a recently identified A&#946;-fibrinogen interaction inhibitor.

Presented here are two methods that can be used individually or in combination to analyze the effect of beta-amyloid on fibrin clot structure. Included is a protocol for creating an in vitro fibrin clot, followed by clot turbidity and scanning electron microscopy methods.

This article presents methods for generating in vitro fibrin clots and analyzing the effect of beta-amyloid (A&#946;) protein on clot formation and ...

In Situ Nucleosome Reconstitution for Single-Molecule Studies

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

Nucleosomes constitute the primary unit of eukaryotic chromatin and have been the focus of numerous informative single-molecule investigations regarding their biophysical properties and interactions with chromatin-binding proteins. Nucleosome reconstitution on DNA for these studies typically involves a salt dialysis procedure that provides precise control over the placement and number of nucleosomes formed along a DNA tether. However, this protocol is time-consuming and requires a substantial amount of DNA and histone octamers as inputs. To offer an alternative strategy, an in situ nucleosome reconstitution method for single-molecule force and fluorescence microscopy that utilizes the histone chaperone Nap1 is described. This method enables users to assemble nucleosomes on any DNA template without the need for strong nucleosome positioning sequences, adjust nucleosome density on demand, and use fewer reagents. In situ nucleosome formation occurs within seconds, offering a simpler experimental workflow and a convenient transition into single-molecule measurements. Examples of two downstream assays for probing nucleosome mechanics and visualizing the behavior of individual proteins on chromatin are further described.

Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques

This article presents a detailed experimental procedure for reconstituting nucleosome-containing DNA tethers for single-molecule correlative force and fluorescence microscopy. It further describes several downstream experiments that can be conducted to visualize the binding behavior of chromatin-interacting proteins and analyze changes in the physical properties of nucleosomes.

Nucleosomes constitute the primary unit of eukaryotic chromatin and have been the focus of numerous informative single-molecule investigations regarding ...

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Core histone octamers that are repetitively spaced along a DNA molecule are called nucleosomal arrays. Nucleosomal arrays are obtained in one of two ways: purification from in vivo sources, or reconstitution in vitro from recombinant core histones and tandemly repeated nucleosome positioning DNA. The latter method has the benefit of allowing for the assembly of a more compositionally uniform and precisely positioned nucleosomal array. Sedimentation velocity experiments in the analytical ultracentrifuge yield information about the size and shape of macromolecules by analyzing the rate at which they migrate through solution under centrifugal force. This technique, along with atomic force microscopy, can be used for quality control, ensuring that the majority of DNA templates are saturated with nucleosomes after reconstitution. Here we describe the protocols necessary to reconstitute milligram quantities of length and compositionally defined nucleosomal arrays suitable for biochemical and biophysical studies of chromatin structure and function.

A method is presented for the reconstitution of model nucleosomal arrays from recombinant core histones and tandemly repeated nucleosome positioning DNA. We also describe how sedimentation velocity experiments in the analytical ultracentrifuge, and atomic force microscopy (AFM) are used to monitor the extent of nucleosomal array saturation after reconstitution.

Core histone octamers that are repetitively spaced along a DNA molecule  are called nucleosomal arrays. Nucleosomal arrays are obtained in one of two  ...

Biology

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

Principles of DNA folding in the cell nucleus and its dynamic transformations that occur during the fulfillment of basic genetic functions (transcription, replication, segregation, etc.) remain poorly understood, partially due to the lack of experimental approaches to high-resolution visualization of specific chromatin loci in structurally preserved nuclei. Here we present a protocol for the visualization of replicative domains in monolayer cell culture in situ,&#160;by combining EdU labeling of newly synthesized DNA with subsequent label detection with Ag-amplification of Nanogold particles and ChromEM staining of chromatin. This protocol allows for the high-contrast, high-efficiency pre-embedding labeling, compatible with traditional glutaraldehyde fixation that provides the best structural preservation of chromatin for room-temperature sample processing. Another advantage of pre-embedding labeling is the possibility to pre-select cells of interest for sectioning. This is especially important for the analysis of heterogeneous cell populations, as well as compatibility with electron tomography approaches to high-resolution 3D analysis of chromatin organization at sites of replication, and the analysis of post-replicative chromatin rearrangement and sister chromatid segregation in the interphase.

This protocol presents a technique for high-resolution mapping of replication sites in structurally preserved chromatin in situ that employs a combination of pre-embedding EdU-streptavidin-Nanogold labeling and ChromEMT.

Principles of DNA folding in the cell nucleus and its dynamic transformations that occur during the fulfillment of basic genetic functions (transcription, ...

Static Atomic Force Microscopy to Visualize and Characterize Assembled Nucleosomes

Source: Stormberg, T., et al. <a href="https://app.jove.com/v/58820">Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging.</a> J. Vis. Exp.(2019)
In this video, we demonstrate static atomic force microscopy to visualize assembled nucleosomes. This high-resolution imaging technique allows the study of the nucleosome structure.

Source: Stormberg, T., et al. Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging. J. Vis. Exp.(2019)
In this video, ...

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High-Speed Time-Lapse Atomic Force Microscopy to Capture Nucleosome Dynamics

Source: Stumme-Diers, M. P., et al., <a href="https://app.jove.com/v/58820">Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging.</a>&#160;J. Vis. Exp.&#160;(2019)
In this video, we demonstrate high-speed time-lapse atomic force microscopy, AFM, imaging techniques to study the dynamics of nucleosome complexes. As the AFM tip scans across the surface of the nucleosome, it detects alterations in the nucleosome height and records the DNA unwrapping over time.