Name: preparation of nucleosome core particles complexed with dna repair factors for cryo-electron microscopy structural determination
Uploaded: 2022-08-17T13:30:00
Description: Watch this Scientific Journal Video about Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination at JoVE.com

We thank Dr. Mario Borgnia from the cryo-EM core at the National Institute of Environmental Health Sciences and Dr. Joshua Strauss from the University of North Carolina at Chapel Hill for their mentorship and training in the cryo-EM grid preparation. We also thank Dr. Juliana Mello Da Fonseca Rezende for technical assistance in the initial stages of this project. We appreciate the key contribution and support of the late Dr. Samuel H. Wilson and his lab members, especially Dr. Rajendra Prasad and Dr. Joonas Jamsen for the purification of the genetically fused APE1-Pol&#946; complex. Research has been supported by the Intramural Research Program of the National Institutes of Health, National Institute of Environmental Health Sciences [grant numbers Z01ES050158, Z01ES050159, and K99ES031662-01].

1. Assemble nucleosome core particles via salt-gardient dialysis
NOTE: The preparation of nucleosome core particles using recombinant histone proteins for structural studies has been extensively described in detail by others14,15,16. Follow the purification of recombinant X. laevis histones and histone octamer assembly described by others14,<s...

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A specific protocol for purifying the DNA repair factor will be dependent on the enzyme of interest. However, there are some general recommendations, including the use of recombinant methods for protein expression and purification18; if the protein of interest is too small (&#60;50 kDa), structure determination by cryo-EM had been nearly impossible until more recently through the use of fusion systems19, nanobody-binding scaffolds20, and optimizing i...

Eukaryotic DNA is organized and compacted by histone proteins, forming chromatin. The nucleosome core particle (NCP) constitutes the fundamental repeating unit of chromatin that regulates accessibility to DNA-binding proteins for DNA repair, transcription, and replication1. Although the first X-ray crystal structure of the NCP was first solved more than two decades ago2 and many more structures of the NCP have been published since3,4,5,6, DNA repair mechanisms in nucleosomal substrates have not yet been delineated. Uncovering the molecular details underlying DNA repair in chromatin will require structural characterization of the participating components to understand how local structural features of the NCP regulate DNA repair activities. This is particularly important in the context of base excision repair (BER) given that biochemical studies with BER enzymes suggest unique DNA repair mechanisms in nucleosomes that are dependent on enzyme-specific structural requirements for catalysis and the structural position of the DNA lesion within the nucleosome7,8,9,10,11,12,13. Given that BER is a vital DNA repair process, there is considerable interest to fill in these gaps while also establishing a starting point from which other technically feasible structural studies involving relevant nucleosomal complexes can be carried out.
Cryo-EM is rapidly becoming the method of choice for solving the three-dimensional (3D) structure of complexes whose large-scale preparation of homogeneous sample is challenging. Although, the design and purification of NCPs complexed with a DNA repair factor (NCP-DRF) will likely necessitate tailored optimization, the procedure presented here to generate and freeze a stable NCP-DRF complex provides details on how to optimize the sample and cryo-EM grid preparation. Two workflows (not mutually exclusive) shown in Figure 1, and the specific details in the protocol identify critical steps and provide strategies for optimizing these steps. This work will propel the chromatin and DNA repair field in a direction where complementing biochemical with structural studies becomes technically feasible to better understand the molecular mechanisms of nucleosomal DNA repair.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 M HEPES; pH 7.5</td>
			<td>Thermo Fisher Scientific</td>
			<td>15630080</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M MgCl2</td>
			<td>Thermo Fisher Scientific</td>
			<td>AM9530G</td>
			<td></td>
		</tr>
		<tr>
			<td>10x TBE</td>
			<td>Bio-rad</td>
			<td>1610733</td>
			<td></td>
		</tr>
		<tr>
			<td>25% glutaraldehyde</td>
			<td>Fisher Scientific</td>
			<td>50-262-23</td>
			<td></td>
		</tr>
		<tr>
			<td>3 M KCl</td>
			<td>Thermo Fisher Scientific</td>
			<td>043398.K2</td>
			<td></td>
		</tr>
		<tr>
			<td>491 prep cell</td>
			<td>Bio-rad</td>
			<td>1702926</td>
			<td></td>
		</tr>
		<tr>
			<td>Amicon Ultra 15 centrifugal filter (MW cutoff 30 kDa)</td>
			<td>Millipore Sigma</td>
			<td>Z717185</td>
			<td></td>
		</tr>
		<tr>
			<td>Amicon Ultra 4 centrifugal filter (MW cutoff 30 kDa)</td>
			<td>Millipore Sigma</td>
			<td>UFC8030</td>
			<td></td>
		</tr>
		<tr>
			<td>AutoGrid Tweezers</td>
			<td>Ted Pella</td>
			<td>47000-600</td>
			<td></td>
		</tr>
		<tr>
			<td>Automatic Plunge Freezer</td>
			<td>Leica</td>
			<td>Leica EM GP</td>
			<td></td>
		</tr>
		<tr>
			<td>C-1000 touch thermocycler</td>
			<td>Bio-rad</td>
			<td>1851148</td>
			<td></td>
		</tr>
		<tr>
			<td>C-clips and rings</td>
			<td>Thermo Fisher</td>
			<td>6640--6640</td>
			<td></td>
		</tr>
		<tr>
			<td>Clipping station</td>
			<td>SubAngostrom</td>
			<td>SCT08</td>
			<td></td>
		</tr>
		<tr>
			<td>Dialysis Membrane (MW cufoff 6-8 kDa)</td>
			<td>Fisher Scientific</td>
			<td>15370752</td>
			<td></td>
		</tr>
		<tr>
			<td>Diamond Tweezers</td>
			<td>Techni-Pro</td>
			<td>758TW0010</td>
			<td></td>
		</tr>
		<tr>
			<td>dsDNA</td>
			<td>Integrated DNA techonologies</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>FEI Titan Krios</td>
			<td>Thermo Fisher</td>
			<td>KRIOSG4TEM</td>
			<td></td>
		</tr>
		<tr>
			<td>FPLC purification system</td>
			<td>AKTA Pure</td>
			<td>29018224</td>
			<td></td>
		</tr>
		<tr>
			<td>Fraction collector Model 2110</td>
			<td>Bio-rad</td>
			<td>7318122</td>
			<td></td>
		</tr>
		<tr>
			<td>Glow Discharge Cleaning System</td>
			<td>Ted Pella</td>
			<td>91000S</td>
			<td></td>
		</tr>
		<tr>
			<td>Grid Boxes</td>
			<td>SubAngostrom</td>
			<td>PB-E</td>
			<td></td>
		</tr>
		<tr>
			<td>Grid Storage Accessory Pack</td>
			<td>SubAngostrom</td>
			<td>GSAX</td>
			<td></td>
		</tr>
		<tr>
			<td>Liquid Ethane</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Liquid Nitrogen</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Minipuls 3 peristaltic two-head pump</td>
			<td>Gilson</td>
			<td>F155008</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanodrop</td>
			<td>Thermo Fisher Scientific</td>
			<td>ND-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Novex 16%, Tricine, 1.0 mm, Mini Protein Gels</td>
			<td>Thermo Fisher Scientific</td>
			<td>EC6695BOX</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipetman</td>
			<td>Gilson</td>
			<td>FA10002M</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette tips (VWR) Low Retention</td>
			<td>VWR</td>
			<td>76322-528</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyacrylamide gel solution (37.5:1)</td>
			<td>Bio-rad</td>
			<td>1610158</td>
			<td></td>
		</tr>
		<tr>
			<td>polyethylene glycol (PEG)</td>
			<td>Millipore Sigma</td>
			<td>P4338-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Pur-A-lyzer Maxi 3500</td>
			<td>Millipore Sigma</td>
			<td>PURX35050</td>
			<td></td>
		</tr>
		<tr>
			<td>Purified recombinant DNA repair factor</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>R 1.2/1.3 Cu 300 mesh Grids</td>
			<td>Quantifoil</td>
			<td>N1-C14nCu30-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant histone octamer</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Spring clipping tools</td>
			<td>SubAngostrom</td>
			<td>CSA-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Superdex 200 column 10/300</td>
			<td>Millipore Sigma</td>
			<td>GE28-9909-44</td>
			<td></td>
		</tr>
		<tr>
			<td>Transmission Electron Microscope</td>
			<td>Thermo Fisher</td>
			<td>Talos Arctica 200 kV</td>
			<td></td>
		</tr>
		<tr>
			<td>Tweezers Assembly for FEI Vitrobot Mark IV-I</td>
			<td>Ted Pella</td>
			<td>47000-500</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure Glycerol</td>
			<td>Thermo Fisher Scientific</td>
			<td>15514011</td>
			<td></td>
		</tr>
		<tr>
			<td>Vitrobot</td>
			<td>Thermo Fisher</td>
			<td>Mark IV System</td>
			<td></td>
		</tr>
		<tr>
			<td>Whatman Filter paper (55 mM)</td>
			<td>Cytiva</td>
			<td>1005-055</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene cyanol</td>
			<td>Thermo Fisher Scientific</td>
			<td>440700500</td>
			<td></td>
		</tr>
		<tr>
			<td>Zeba Micro Spin Desalting Columns, 7K MWCO, 75 &#181;L</td>
			<td>Thermo Fisher Scientific</td>
			<td>89877</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of nucleosome core particles complexed with dna repair factors for cryo-electron microscopy structural determination

DNA repair in the context of chromatin is poorly understood. Biochemical studies using nucleosome core particles, the fundamental repeating unit of chromatin, show most DNA repair enzymes remove DNA damage at reduced rates as compared to free DNA. The molecular details on how base excision repair (BER) enzymes recognize and remove DNA damage in nucleosomes have not been elucidated. However, biochemical BER data of nucleosomal substrates suggest the nucleosome presents different structural barriers dependent on the location of the DNA lesion and the enzyme. This indicates the mechanisms employed by these enzymes to remove DNA damage in free DNA may be different than those employed in nucleosomes. Given that the majority of genomic DNA is assembled into nucleosomes, structural information of these complexes is needed. To date, the scientific community lacks detailed protocols to perform technically feasible structural studies of these complexes. Here, we provide two methods to prepare a complex of two genetically fused BER enzymes (Polymerase &#946; and AP Endonuclease1) bound to a single-nucleotide gap near the entry-exit of the nucleosome for cryo-electron microscopy (cryo-EM) structural determination. Both methods of sample preparation are compatible for vitrifying quality grids via plunge freezing. This protocol can be used as a starting point to prepare other nucleosomal complexes with different BER factors, pioneer transcription factors, and chromatin-modifying enzymes.

Properly assembled NCPs (Figure 2) were used to make a complex with a recombinant fusion protein of MBP-Pol&#946;-APE1 (Figure 3). To determine the ratio of NCP to MBP-Pol&#946;-APE1 to form a stable complex, we performed electrophoretic mobility shift assays (EMSA) (Figure 4), which showed a singly shifted band of the NCP with 5-fold molar excess of MBP-Pol&#946;-APE1. During the optimization of making this complex, crosslinking wi...

Watch this Scientific Journal Video about Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination at JoVE.com

Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination

This protocol outlines in detail the preparation of nucleosomal complexes using two methods of sample preparation for freezing TEM grids.

DNA repair in the context of chromatin is poorly understood. Biochemical studies using nucleosome core particles, the fundamental repeating unit of ...

Structural information on how base excision repair enzymes remove DNA lesions in the context of chromatin has been scarce. This constitutes a significant gap in our understanding of the mechanisms involved in etiology of human diseases. The main advantage of our protocol is that we have optimized sample preparation using standard laboratory equipment.This will allow other biochemists in the field to complement their biochemical work with technically feasible cryo-EM studies. Our protocol can additionally be used to investigate how other factors, including pioneer transcription factors, engage the nucleosome. This is an area where structural information has also been limited.Optimizing the sample preparation before moving onto the freezing conditions was key to moving our project forward, and this is best done with standard biochemical assays in substrate design, binding, and cross-linking conditions. To begin, incubate the NCP and the DNA repair factor of interest on ice for 15 minutes using an optimal buffer for the specific complex. Then, add glutaraldehyde to a final concentration of 0.005%After mixing it well, incubate at room temperature for 13 minutes.Quench with one molar Tris-CL to a final concentration of 20 millimolar Tris-CL with pH 7.5. Then, concentrate to approximately 50 microliters and exchange the buffer with freezing buffer using a desalting column. Next, determine the absorbances at optical density 280 and 260 nanometers and concentrate further if needed to reach 1.3 to 3 milligrams per milliliters based on optical density 280 nanometers.After preparing the dialysis button, place the button containing the sample on top of a polyethylene glycol bed with the membrane facing down. To perform the purification by size exclusion chromatography, wash and equilibrate a size exclusion column with 60 milliliters of distilled water, followed by 80 milliliters of freezing buffer overnight at a rate of 0.4 milliliters per minute. Then, immediately analyze the peak fractions and concentrate those fractions containing the histone's infusion protein MBP-PolBeta-APE1.Demonstrating the following procedures will be Elizabeth Viverette, a post-baccalaureate trainee from the cryo-EM core here in NIH. After turning on the plunge freezer and filling the humidifier with 50 milliliters of distilled water, set the chamber temperature to 22 degrees Celsius and humidity to 98%Then place the ethane cup and liquid nitrogen cup in the respective space holders. Afterward, cover the ethane cup with the ethane lid dispenser and carefully pour liquid nitrogen over it while also filling the nitrogen cup with liquid nitrogen.When the liquid nitrogen level has stabilized and reaches 100%and the temperature reaches minus 180 degrees Celsius, carefully open the ethane valve and fill the ethane cup until it forms a bubble on the clear lid. Then remove the ethane dispenser. Place two filter papers onto the blotting device and secure them with a metal ring.Go to the setup and set the blotting parameters as described in the manuscript, then select A-Plunge and click on OK.On the main screen, click on Load Forceps and load them with a grid with the carbon application side facing toward the left. Calibrate the forceps, adjusting the Z-axis to ensure a solid blot. Click on Lower Chamber and apply three microliters of the complex.Then click on Blot A-Plunge, which will rotate the grid to blot from the front and will plunge-freeze it. After transferring, store the grid in the grid box in the liquid nitrogen chamber. When all four grids have been frozen and placed in the grid box, rotate the lid to neutral position where all the grids are covered by the lid and tighten the screw.Before loading the samples in the microscope, place the vitrified grids on a ring and secure it using a C-clip under liquid nitrogen in a humidity-controlled room to avoid ice contamination. When loading the microscope, insert the grids in a 12-slot cassette. Shuffle the cassette into a nanocab capsule and load it into the autoloader.Then, transfer the grid from the cassette to the microscope stage. Adjust the stage to eucentric height by wobbling the stage 10 degrees and simultaneously moving the Z-height until minimal planar shift is observed in the images. Once the eucentric height is reached, start imaging by taking a 3-by-3 montage image of the grid in which each montage is taken at 62x magnification to obtain the atlas.After picking three squares of varying sizes and taking the eucentric height, image at 210x magnification. Once a square is imaged, pick one hole each from the edge, center, and in between within the squares. Then, image each hole at 2, 600x magnification.Take the high magnification image from the center of the hole at 36, 000x magnification and at 7.1 seconds exposure time, 60 frames, 1.18 pixel size, and three-micrometer defocus. See representative images of screening. To determine the ratio of NCP to MBP-PolBeta-APE1 to form stable complex, electrophoretic mobility shift assays were performed, which showed a singly-shifted band of the NCP with five-fold molar excess of MBP-PolBeta-APE1.In smaller volume, assembly of the complex of NCP-PolBeta-APE1 demonstrated that the sample was overly cross-linked and resulted in aggregates without discernible individual complexes. However, ten-fold dilution in NCPs resulted in significantly reduced aggregation and improved particle stability. The preparative gel and size exclusion methods can be combined where preparative gel improves the quality of the NCPs when they contain a significant amount of high molecular weight aggregates, followed by the purification of the complex via size exclusion.The results show that both methods can be used independently to generate stable complexes. Further, the data collected from both grids show almost identical two-dimensional classes and three dimensional maps at approximately 3.2-angstrom resolution. An optimal ratio of NCP to DNA repair factor should be determined first, then cross-linking of the complex with glutaraldehyde the should be performed at at least 10 times more dilute than the concentration needed for freezing.After obtaining a cryo-EM 3D map of the complex, further structural refinement will be needed to determine how the DNA repair factor is found and identify what regions are important for these interactions.

Research

JoVE Journal

Biochemistry

Expression and Purification of the Human Lipid-sensitive Cation Channel TRPC3 for Structural Determination by Single-particle Cryo-electron Microscopy

Transient receptor potential channels (TRPCs) of the canonical TRP subfamily are nonselective cation channels that play an essential role in calcium ...

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Measurements of the specificity and affinity of antigen-antibody interactions are critically important for medical and research applications. In this ...

Fast Grid Preparation for Time-Resolved Cryo-Electron Microscopy

The field of cryo-electron microscopy (cryo-EM) is rapidly developing with new hardware and processing algorithms, producing higher resolution structures ...

Preparation of Sample Support Films in Transmission Electron Microscopy using a Support Floatation Block

Structure determination by cryo-electron microscopy (cryo-EM) has rapidly grown in the last decade; however, sample preparation remains a significant ...

Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography

Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography

Today, cryo-electron tomography (cryo-ET) is the only technique that can provide near-atomic resolution structural data on macromolecular complexes in ...

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Cryo-electron microscopy (cryoEM) is a powerful technique for structure determination of macromolecular complexes, via single particle analysis (SPA). The ...

Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows

Whole-cell cryo-electron tomography (cryo-ET) is a powerful technology that is used to produce nanometer-level resolution structures of macromolecules ...

A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Recent advances in both instrumentation and image processing software have made single-particle cryo-electron microscopy (cryo-EM) the preferred method ...

Extracting Modified Microtubules from Mammalian Cells to Study Microtubule-Protein Complexes by Cryo-Electron Microscopy

Microtubules are an important part of the cytoskeleton and are involved in intracellular organization, cell division, and migration. Depending on the ...

Coating CryoEM Grids with Monolayer Graphene to Improve Cryo-Sample Preparation

Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination

Author Spotlight: Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids 

In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to ...