Waiting
Login processing...

Trial ends in Request Full Access Tell Your Colleague About Jove

Biology

Demonstration of the DNA Fiber Assay for Investigating DNA Damage and Repair Dynamics Induced by Nanoparticles

Published: March 3, 2023 doi: 10.3791/64903

Summary

The methodology assists in the analysis of variation in DNA replication dynamics in the presence of nanoparticles. Different methodologies can be adopted based on the cytotoxicity level of the material of interest. In addition, a description of the image analysis is provided to help in DNA fiber analysis.

Abstract

Nanomaterial exposure can cause replication stress and genomic instability in cells. The degree of instability depends on the chemistry, size, and concentration of the nanomaterials, the time of exposure, and the exposed cell type. Several established methods have been used to elucidate how endogenous/exogenous agents impact global replication. However, replicon-level assays, such as the DNA fiber assay, are imperative to understand how these agents influence replication initiation, terminations, and replication fork progression. Knowing this allows one to understand better how nanomaterials increase the chances of mutation fixation and genomic instability. We used RAW 264.7 macrophages as model cells to study the replication dynamics under graphene oxide nanoparticle exposure. Here, we demonstrate the basic protocol for the DNA fiber assay, which includes pulse labeling with nucleotide analogs, cell lysis, spreading the pulse-labeled DNA fibers onto slides, fluorescent immunostaining of the nucleotide analogs within the DNA fibers, imaging of the replication intermediates within the DNA fibers using confocal microscopy, and replication intermediate analysis utilizing a computer-assisted scoring and analysis (CASA) software.

Introduction

During each cell cycle, DNA replication ensures accurate genome duplication1. Eukaryotic chromosomal replication essentially depends on three factors: the timing of the firing of multiple replication origins, the speed of the forks that emerge from the fired origins, and the termination of the replication process when two replication forks from adjacent origins meet2. For the high-fidelity transmission of genetic information to daughter cells, as well as the preservation of genetic integrity, accurate DNA replication is crucial. Agents that develop from regular metabolism or are due to artificial or natural environmental materials are constantly attacking the genome. These endogenous and exogenous agents cause replication forks to slow down or stop due to encountering DNA damage caused by these agents, and the forks temporarily slowing down or stopping in response to these difficulties is termed replication stress3. In response to replication stress, cells have developed several molecular pathways that maintain the stability of the disturbed replication forks and allow them to restart4. In terms of genetic stability, cell survival, and human disease, these replication stress response mechanisms have emerged as the key factors for maintaining a healthy genome, ensuring cell survival, and decreasing the likelihood of disease formation5.

One of the exogenous agents capable of producing replication stress is nanoparticles. Nanoparticles are particles that range in size from 1 nm to 100 nm6. Due to their high surface areas, distinctive shapes, and unique chemical properties, nanoparticles are utilized in various medical, pharmaceutical, environmental, and industrial applications7,8. While nanoparticles have a lot of potential benefits, some of them (due to their inherited nature or longevity) can become toxic. Nanoparticles can also form due to the natural wear and tear of medical implants and be released into the peri-prosthetic region9,10.

Due to the exposure of humans to a myriad of nanoparticles produced for various applications, research in the field of nanoparticle toxicity has increased tremendously over the past 10 years11. While these research efforts have revealed information in abundance about the potential threat that nanoparticles pose to human health, knowledge about the potential for nanoparticles to cause genotoxicity is still limited. What has been discovered so far is that these nanoparticles can physically interact with the DNA, promote DNA damage, and damage or interfere with the proteins responsible for repairing or replicating DNA12. To detect how they interfere with DNA replication, DNA fiber combing, radioresistant DNA synthesis (RDS), and DNA fiber analysis are typically used13,14,15,16.

The DNA fiber combing method is flexible and gives information about replication fork dynamics at the single-molecule level17. In essence, a salinized coverslip is gently withdrawn from the DNA solution once the DNA ends bind to it. The DNA molecules are straightened and aligned by the solution's meniscus. The homogeneity, spacing, and alignment of the DNA fibers support accurate and dependable fiber tract length measurements. By adjusting the length and sequence of the treatments and the drugs used to cause stress or damage, many aspects of fork advancement can be monitored using this application. In this method, a dual labeling system is used, through which the speed and progression of the replication fork are assessed17,18. On the other hand, 2D gel electrophoresis takes advantage of the fact that, in agarose gel electrophoresis, branching DNA structures travel more slowly than linear DNA molecules of the same mass, allowing for the clean separation of the two in a 2D run. In fact, this method is investigated to segregate DNA molecules based on their mass in the first run and based on their shape in the second orthogonal run. After genomic DNA fragmentation, the uncommon replication and recombination intermediates develop a branching form, and they may be distinguished from the more common linear molecules in the 2D gel19.

The RDS method is used for determining how global DNA synthesis is impacted. In this method, the degree of inhibition of global replication is determined by comparing the amount of incorporated radioactively labeled nucleotides, such as [14C] thymidine, in untreated versus treated cells14,20. The percentage difference in radiolabeling between the untreated and treated cells represents the degree to which the DNA-damaging agent impacts DNA synthesis. Similar to this, another method uses the ability of cells to integrate nucleotide analogs like BrdU (5-bromo-2′-deoxyuridine) for flow cytometry to measure the overall rates of DNA synthesis21,22. While these methods demonstrate how DNA-damaging agents impact global DNA synthesis, they do not show how individual replicons are affected. Indeed, replicon-level assays are imperative to better understand the initiation and extent of genomic instability in the event of toxic particle (nanomaterial) exposure. DNA fiber autoradiography and electron microscopy are some methods used to determine this23,24,25,26.

The concepts of replication bubbles and bidirectional replication from unevenly spaced sources were first developed using single-molecule tests like electron microscopy and DNA fiber autoradiography27,28. The direct observation of branching replication intermediates on specific molecules dispersed across a carbon-coated grid is greatly facilitated by electron microscopy. This method, which is still in use today to track pathological shifts at replication forks, was utilized to locate the first eukaryotic origin of DNA replication28. Fiber autoradiography is centered around the concept of the autoradiographic identification of newly replicated areas and the pulse tagging of chromosomes with tritiated thymidine. The first quantitative evaluation of origin densities and replication fork rates in metazoan genomic sequences was made possible by DNA fiber autoradiography29.

Currently, fiber fluorography methods have taken the place of autoradiography, mainly because fiber fluorography is much faster than autoradiography. In fiber fluorography, two halogenated nucleotide derivatives, such as bromo- (Br), chloro- (Cl), or iododeoxyuridine (IdU), are sequentially incorporated into freshly replicated DNA and then identified by indirect immunofluorescence using antibodies30. Microscopic viewing of the nascent DNA that has incorporated one or both analogs is made possible by immunostaining one of the analogs in one color and the other analog in a different color (e.g., immunostaining nascent DNA with incorporated IdU red and incorporated CldU green) (Figure 1)21. Many different types of replication intermediates can be identified by DNA fiber analysis. The most commonly studied are individual elongating forks, initiations, and terminations. Individual elongating forks have a replication pattern of red followed by green (red-green; Figure 2A).13 The lengths of these intermediates are frequently used to gauge the fork speed (i.e., fork length/pulse time) or the exonucleolytic degradation of nascent DNA through track shortening (Figure 2E)30,31,32. In a study by Mimitou et al., it was found that upon long-term exposure to hydroxyurea, a replication poison that causes double-strand breaks in the DNA, RE11 was recruited33. MRE11 is an exonuclease known for its 3'-5' exonuclease activity, and it is capable of cutting the ends of DNA for repair. Therefore, when exposed to toxic agents, one may observe exonucleolytic degradation of nascent DNA, which is the shortening of the DNA strand due to exposure to a DNA-damaging agent34.

Replication fork breakages brought on by physical obstructions (DNA-protein complexes or DNA lesions), chemical impediments, or mutations may stop replication and necessitate homologous recombination to restart it. This is known as impaired fork progression. Numerous in vitro and in vivo investigations have indicated that transcription may, on occasion, prevent replication fork advancement in this manner35.

Initiations are replication origins that initiate and fire during the first or second pulse. Origins that fire during the first pulse and have replication forks that continue to be active have a green-red-green pattern (Figure 2B, lower). Origins that initiate during the second pulse have a green-only pattern (Figure 2B, upper) and are sometimes called newly initiated origins, so those origins can be differentiated from those that initiate during the first pulse. The comparison of the relative percentages of newly fired origins between two experimental conditions allows one to understand how a cell responds to a DNA-damaging agent or the presence or absence of a protein. Terminations are created when two replication forks from adjacent replicons merge, and they have a red-green-red pattern (Figure 2D)30.

Based on the facts described above, DNA fiber analysis is currently considered a preferred method to study the variation in DNA replication dynamics caused by toxic agents such as nanomaterials. Researchers now have a good understanding and knowledge of the dynamics of genome-wide DNA replication in eukaryotes, both quantitatively and qualitatively, owing to the discovery of this technology36. Based on the outcome variables, several methodologies can be adopted. Some examples of methods to study the variations in DNA damage induced by external agents/nanoparticles are shown in Figure 3. The overall goal of the DNA fiber analysis method described in this study is to determine how nanoparticles impact the replication process in vitro and how they differentially affect various tissues.

Subscription Required. Please recommend JoVE to your librarian.

Protocol

1. Preparation of antibodies and buffer

  1. Prepare the primary antibody solution, mouse anti-BrdU at a 1:300 dilution in 5% BSA and rat anti-BrdU at a 1:500 dilution in 5% BSA.
  2. Prepare the secondary antibody solution, alexafluor 594 rabbit anti-mouse at a 1:300 dilution in 5% BSA and alexafluor 488 chicken anti-rat at a 1:500 dilution in 5% BSA.
  3. Prepare the tertiary antibody solution, alexafluor 594 goat anti-rabbit at a 1:1,000 dilution in 5% BSA and alexafluor 488 goat anti-chicken at a 1:1,000 dilution in 5% BSA.
  4. Prepare 10 mL of lysis buffer in ddH2O with 2 mL of 1M Tris (pH 7.4), 1 mL of 0.5 M EDTA, and 0.5 mL of 10% SDS.

2. Preparation for the fiber assay

  1. Day 1: Cell culture and nanomaterial treatment for the fiber assay
    1. Plate RAW 264.5 macrophage cells or the cells of interest, so that the cells are in the log phase of their growth on the day of the experiment. For RAW cells, add 5 x 104 cells/well to 24-well plates for each condition. Maintain the cells in a 37 °C incubator with 5% CO2 and 98% humidity. Table 1 describes the constituents of the media used. Allow the cells to grow to 75%-80% confluency17,37.
    2. After the cells reach the level of 75%-80%confluency, remove the medium from the plates, take half of the medium and reserve it for the CldU pulse (CldU reserve), and add 5 µL IdU to the other half at a final concentration of 50 µM. Mix and add the IdU-containing medium back to the plates. Place the cells with IdU in the incubator for 20 min.
    3. Place the CldU reserve medium at 37 °C to keep it pre-warmed. Add CldU to this medium just before the CldU pulse.
    4. After 20 min, aspirate the IdU-medium mixture, and gently wash the cells with 500 µL of phosphate-buffered saline (PBS, pH 7.4) by gently rotating the plate. Discard the PBS.
    5. Treat the cells with various concentrations of nanoparticles in 500 µL of the medium, and incubate for another 30 min. For this study, use treated graphene oxide nanoparticles at a 25 µg/mL concentration.
    6. Aspirate the treatment-medium mixture, and gently wash the cells with 500 µL of PBS by gently rotating the plate. Discard the PBS.Add 5 µL of CldU (100 µM final
    7. concentration) to the CldU reserve medium, and cover the cells with the CldU reserve medium. Place cells in the incubator for the duration of the CldU pulse for 20 min.
    8. Wash the cells with PBS, scrape off or trypsinize for 3-4 min, and then add 5 mL of medium to the plate, and collect the cells.
    9. Spin at 264 x g for 4 min. Remove the medium, and resuspend the cells in 1 mL of ice-cold PBS. Determine the cell numbers using a trypan blue assay (hemocytometer counting), and then dilute the cells to ~200-400 cells/µL. Keep the cell suspension on ice during the cell counting.
      NOTE: If possible, limit the time the cells sit on the ice. This may help obtain a bead of cell solution along the top of the slide. If they are kept on ice, keep them on for less than 30 min.
  2. Day 1: Preparation of the DNA fibers
    1. Using a pencil, label the slides (glass slide, 75 mm x 25 mm) with the experimental condition and date.
    2. Take 2 µL of cells in a pipette, hold the pipette at a ~45° angle, place the pipette about 1 cm below the slide label, and move the pipette horizontally to the slide label. As the pipette moves across the slide, release a little of the cell solution at a time. Make multiple lines of cells on each slide (critical step).
      NOTE: There should be a horizontal line of cell suspension across the slide. If the cell suspension beads up, then add 5-10 µL of cell medium to the container that has the cell suspension, as this may help the solution to adhere to the slide when being applied again.
    3. Let the solution with the cells evaporate until the solution looks sticky and tacky. At this point, some liquid is associated with the cells, but not much. This step takes from 8-20 min and varies depending on how much humidity is in the air.
      NOTE: Ensure that all the solution has not evaporated, since this makes it very hard to obtain straight and aligned DNA fibers as most, if not all, of the DNA will be stuck together and unable to separate.
    4. When the solution is tacky, overlay the cells with 15 µL of spreading (lysis) buffer per each line of cells, taking care not to let the pipette tip touch the slide. Wait for 10 min. Tilt the slide at a 25° angle, and place the label of the slide horizontally against the edge of a tube rack (the bottom part of the label should line up with the edge of the tube rack).
    5. Allow the DNA spreads to air dry for a minimum of 4 h from the time the last slides were made.
      NOTE: A period of 4 h to 12 h is good for drying. However, do not let them dry overnight. If allowed to dry overnight, there will be a lot of relaxed DNA but very few straight and aligned DNA fibers.
  3. Day 1: Fixing the DNA fibers and freezing
    1. Once the slides have dried, fix the slides with methanol:acetic acid (3:1) by immersing the slides for 2 min. Perform this step under a hood, and let the slides dry overnight in an area with limited light exposure, or cover the slides with a tin foil tent.
  4. Day 2
    1. Place the slides in a glass slide carrier. Place the slides at −20 °C for a minimum of 24 h. This step improves the resolution or crispness of the image.

3. Performing the DNA fiber assay

  1. Denaturation of the DNA
    1. Prepare a humidified chamber using small pipette tip boxes with lids. Half-fill the containers with water, and place them in a 37 °C water bath for at least 1 h.
    2. Take the slides out from −20 °C, and defrost them for a few seconds. Place the slides carefully into a Coplin jar containing deionized (DI) water so that the coated surfaces do not touch the walls of the jar. Incubate the slide for 20 s, and then carefully pour out the water.
    3. Add 2.5 M HCL to the Coplin jar such that it covers all the slides. Wait for 80 min. This is a critical step in the protocol. A change in the time can change the outcome of the image.
    4. Wash the slides 1x with PBS plus Tween (PBS + 0.1% Tween [final concentration]) and then 2x with PBS for 3 min each at room temperature (RT).
  2. Immunostaining
    1. Keep the slides in the humidified chamber for the following steps. Block the slides in 5% BSA in PBS for 30 min at RT, and cover them with coverslips, coverslips made from a Western blot bag, or transparent plastic sheets.
    2. After blocking, carefully remove the coverslip, remove the blocking solution, and blot the slide on a paper towel (tap the slide on the towel) to remove the excess blocking solution.
    3. Add 100 µL of the primary antibody solution along the length of the slide. Add a new plastic coverslip, and wait for 2 h. When adding the coverslip, ensure that no bubbles form.
    4. After 2 h, knock off the antibody solution, and rinse the slides in a PBS-filled Coplin jar 2x at RT. Use fresh PBS each time to wash the slides.
    5. Block the slides again by adding 200 µL (three to four drops) of 5% BSA along each slide, and add a plastic coverslip. Wait for 15 min.
    6. Take off the coverslip, knock off the excess BSA on a paper towel, and add 100 µL of the secondary antibody solution along the length of the slide. Add a new plastic coverslip, and wait for 1 h.
    7. Take off the coverslip, knock off the excess BSA on a paper towel, and wash the slides 2x in PBS at RT.
    8. Block the slides again by adding 200 µL (three to four drops) of 5% BSA along each slide, and add a plastic coverslip. Wait for 15 min.
    9. If needed, remove the coverslip, remove the excess BSA on a paper towel, and add 100 µL of tertiary antibody solution along the length of the slide. Add new plastic coverslips, and wait for 30 min.
    10. Wash the slides with PBS 3x. Remove the excess PBS, and allow them to dry off completely.
    11. Once dry, add the mounting medium, and carefully place glass coverslips (24 mm x 60 mm) over the mounting medium so that bubbles are avoided. Re-label the slides, and leave them in the dark overnight.

4. Image acquisition

  1. Visualize the immunostained DNA fibers using an immunofluorescent microscope equipped with a camera, a 60x objective, and appropriate filter sets to detect alexafluor 488 and 594 dyes.
  2. Take images for the analysis in regions where the fibers are well separated and not entangled. It is important to capture images in different areas along the slide, as taking images in only one part of the slide may not provide representative data regarding all the replication intermediates found on the slide.
  3. If possible, obtain fiber images from 20 different regions on a slide. Use only one channel to select the areas for taking images to avoid bias.

Subscription Required. Please recommend JoVE to your librarian.

Representative Results

After obtaining enough images (from 20-100 images per condition), the replication intermediates need to be identified, measured, and counted. Whether analyzing the fibers manually or automatically via a program38, it is necessary to clearly define what characteristics a fiber must have for it to be counted or scored (or not counted or measured)39. For instance, the following questions can be considered. (1) Should one measure and count only fibers with 100% immunofluorescence throughout the fiber, or can they contain some regions without immunofluorescence (e.g., should all the intermediates in Figure 4Ai,ii,iii be analyzed or just a subset of them?)? If analyzing fibers with signal loss, what is the maximum signal loss acceptable within a fiber, and what is the maximum number of continuous pixels in the fiber that can be devoid of any signal (e.g., would the Figure 3Aiv be considered a red-green or red-only intermediate?)? (2) What should the minimum and maximum fiber widths/lengths be? (3) What should the signal-to-noise (S:N) ratio be when deciding if one should measure a fiber or not (e.g., how many fibers should be chosen in Figure 4B to analyze?)? (4) How close to the image edge does a fiber have to be before it is not counted or measured? (5) If a fluorescent signal is yellow, does one count that as red or green (e.g., should the yellow portion of the replication intermediate in Figure 4C be counted as red or green?)? (6) How long does a color segment have to be to be counted a true signal (e.g., is the replication intermediate in Figure 4D a green only track, a green-red-green track, or a green-red track?)? (7) If using an automated fiber analysis program, how confident is the program in the measurement/count that it has just performed? (8) If the fibers are being analyzed manually, how consistent should the analysis be over time and between individuals?

Typically, the parameters used for DNA fiber analysis are the following:
Signal-to-noise ratio: 3 (fiber intensity is three times greater than the background intensity)
Fiber thickness: ≤8 pixels in width
Minimal size: red or green only and 10 pixels; red-green tracks with each segment ≥10 pixels; red-green-red or green-red-green tracks with each segment ≥10 pixels.
Continuity of the fluorescent signal: at least 80% and no gaps in the signal greater than 6 pixels.
Confidence in assessment: confidence values should be similar to each other in an image and between images.

In addition to the parameters mentioned above, another important criterion is the selection of a clear fiber that does not overlap with other fibers during the imaging and analysis.

Figure 5A shows representative images of control (Figure 5Ai) and graphene oxide nanoparticle-treated macrophage DNA (Figure 5Aii,iii). The image shows an increase in the read-only tracks (terminations) and a decrease in newly fired origins in the graphene oxide-treated cells compared to the control (Figure 5C). It is also important to consider the number of images and the position of the slide from where the images are taken. As shown in Figure 5Aiii,C, a variation in the pattern of replication intermediates (an increase in new origins compared to control) was observed on a different region of the same condition. Even though a few of such observations might not affect the overall outcome, care must be taken to image the slide by including all the representative areas. It would be ideal to divide the total area of the slide into five to six regions and take multiple images from each region (example: 10 images) to find conclusive fiber data for each slide. It is ideal to select around 500 intermediates (Figure 5B) from multiple slides/conditions. With these variations in replication, intermediate quantification from DNA fiber analysis can be used to investigate the variation in DNA replication dynamics caused by graphene oxide nanoparticles or the genotoxicity of other nanomaterials. Hence, both a qualitative and quantitative understanding of the dynamics of genome-wide DNA replication can be obtained through this new methodology compared to other analyses mentioned in the introduction.

Figure 1
Figure 1: DNA fiber assay. Schematic representation of the assay with an overview of the major steps in the DNA fiber analysis. Scale: 10 µm. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Immunostaining of the DNA replication intermediates. Schematic representation of different replication intermediates identified by sequential pulse labeling with IdU (red) and CldU (green). Scale: 5 µm. Please click here to view a larger version of this figure.

Figure 3
Figure 3: Nanoparticle exposure. Different methodologies to study variations in nanoparticle-induced DNA damage. Please click here to view a larger version of this figure.

Figure 4
Figure 4: Characteristics of DNA fibers to be scored. Examples of replication intermediates in an image. (A) Gaps in immunofluorescence; (i) 0% immunofluorescence signal loss across the replication intermediate; (ii) ~7% signal loss; (iii) 50% signal loss; and (iv) >90% signal loss. (B) A region with many overlapping replication intermediates (the arrow indicates the region with clear fiber overlap). (C) A DNA fiber with a yellow region. (D) A replication intermediate open to interpretation (the arrow indicates the gaps in the fiber). Scale: 5 µm. Please click here to view a larger version of this figure.

Figure 5
Figure 5: DNA fiber analysis and interpretation. (A) Representative DNA fiber images from (i) control macrophage cells and (ii,iii) macrophage cells treated with nanoparticles for 20 min at a 25 µg/mL concentration. Images ii and iii were taken from different regions of the slide. (B) Representative automated software analysis of the control and nanoparticle-treated conditions. For this analysis, we used the automated DNA fiber tracking and measurement program developed by Wang et al.38. The numbers in the figure show the number of DNA tracks analyzed. (C) Graphical representation of the software analysis of the control and nanoparticle-treated conditions. NP represents nanoparticles. The relative percentage of the intermediate population (for example, for red only) is calculated from the total intermediates analyzed. Comparing NP-treated image 1 to image 2, there are big differences between the two images. Thus, it is important to obtain many images throughout the slide to understand how an experimental condition impacts the replication process. Abbreviations: R = red; G = green. Scale: 10 µm. Please click here to view a larger version of this figure.

Media composition
10% Fetal Bovine Serum
1% Penicillin-Streptomycin solution (10000 units/ml)
1% L Glutamine (200 mM)
Dulbecco’s Modified Eagle’s Medium-high Glucose

Table 1: Media composition used for the macrophage cell culture.

Subscription Required. Please recommend JoVE to your librarian.

Discussion

We discuss here a method to assist in the analysis of the variation in DNA replication dynamics in the presence of nanoparticles through the DNA fiber assay. Major critical steps involved in the standard assay are described in the protocol (step 2.2.2 and step 3.1.3). It is always recommended to use an area with limited overhead light exposure and constant airflow to prevent light-induced DNA breaks in the slides as well as to enhance reproducibility. Careful attention is required on the time duration for the drying of the cell lysate on the slides. Overdrying will negatively impact the fiber spread. The second critical step is fiber denaturation using an acid solution. The duration of the acid wash should be kept equal for all the slides in the same experiment. Troubleshooting for these two steps to find optimal conditions (lysis time, volume of lysate on the slide, drying time, and acid wash time) is recommended for different cell types and lab environments.

As discussed in Figure 3, the exposure duration of nanoparticles can be varied for the quantitative determination of alteration in DNA replication dynamics induced by the nanoparticles. To determine the initial impact of replication dynamics, a short-term exposure such as 1 min, 20 min, or 30 min with different dosages would be appropriate. The difference in replication patterns (as shown in Figure 2) after long-term exposure of the cells to the nanomaterials can be determined by comparing the patterns of IdU and CIdU exposure (20 min each) before and after the nanoparticle treatment. This approach can be used to determine the fork stalling, fork slowing, and difference in origin firing at different times of exposure, which can be interpreted as the effects of acute and chronic exposure to nanomaterials39,40.

There are several promising techniques available to detect the variation in DNA replication, such as DNA combing and the RDS method; however, in comparison to those methods, the DNA fiber assay is convenient and cost-effective without the need for expensive instruments for analysis41. The limitations of this method are the experimental duration, the time required to take enough images for quantification, as well as the software analysis. However, certainly, this approach will support nanotoxicology research in determining the genomic instability caused by particles in cell lines, as well as in different tissue samples and between different species.

Subscription Required. Please recommend JoVE to your librarian.

Disclosures

The authors have no conflicts of interest to disclose.

Acknowledgments

The authors acknowledge financial support from the Blazer foundation, the Medical Biotechnology Program at Biomedical Sciences, UIC Rockford, and the Department of Health Science Education, UIC Rockford. The authors thank Ananya Sangineni and James Bradley for their contributions to the project.

Materials

Name Company Catalog Number Comments
24 well plate Fisher brand FB012929
Acetic Acid  Sigma Aldrich 695092
Alexa flour 594 goat anti-rabbit  Invitrogen A11037
Alexa fluor 488 chicken anti-rat   Invitrogen A21470
Alexa fluor 488 goat anti-chicken  Invitrogen A11039
Alexa fluor 594 rabbit anti-mouse  Invitrogen A11062
BSA Sigma Aldrich A2153
CldU Sigma Aldrich 50-90-8
Coverslips (22 x 50 mm) Fisher brand 12-545-EP
EDTA Fisher Scientific 15575020
Frosted Microscope Slides Fisher brand 12-550-11
Hydrochloric Acid Sigma Aldrich 320331
IdU  Sigma Aldrich 54-42-2
Methanol Fisher Scientific A454-4
Mouse Anti-BrdU  BD Biosciences 347580
Phosphate Buffer Saline Gibco 10010072
Rat anti-BrdU  Abcam BU1--75(ICR1)
Raw 264.5 macrophage cells  ATCC TIB-71
SDS Sigma Aldrich L3771
Silane-Prep slides Sigma Aldrich S4651-72EA 
Superfrost gold plus slides Fischer scientific 22-035813
Tris pH 7.4 Sigma Aldrich 77861
Tween 20 Sigma Aldrich P9416

DOWNLOAD MATERIALS LIST

References

  1. Waga, S., Stillman, B. The DNA replication fork in eukaryotic cells. Annual Review of Biochemistry. 67 (1), 721-751 (1998).
  2. Gambus, A. Termination of eukaryotic replication forks. DNA Replication. 1042, 163-187 (2017).
  3. Berti, M., Cortez, D., Lopes, M. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress. Nature Reviews Molecular Cell Biology. 21 (10), 633-651 (2020).
  4. Carr, A. M., Lambert, S. Replication stress-induced genome instability: The dark side of replication maintenance by homologous recombination. Journal of Molecular Biology. 425 (23), 4733-4744 (2013).
  5. Berti, M., Vindigni, A. Replication stress: Getting back on track. Nature Structural and Molecular Biology. 23 (2), 103-109 (2016).
  6. Montes-Burgos, I., et al. Characterisation of nanoparticle size and state prior to nanotoxicological studies. Journal of Nanoparticle Research. 12 (1), 47-53 (2010).
  7. Khan, I., Saeed, K., Khan, I. Nanoparticles: Properties, applications and toxicities. Arabian Journal of Chemistry. 12 (7), 908-931 (2019).
  8. Ealia, S. A. M., Saravanakumar, M. P. A review on the classification, characterisation, synthesis of nanoparticles and their application. IOP Conference Series: Materials Science and Engineering. 263 (3), 032019 (2017).
  9. Bijukumar, D. R., et al. Differential toxicity of processed and non-processed states of CoCrMo degradation products generated from a hip simulator on neural cells. Nanotoxicology. 12 (9), 941-956 (2018).
  10. Bijukumar, D., Segu, A., Chastain, P., Mathew, M. T. Implant-derived CoCrMo alloy nanoparticle disrupts DNA replication dynamics in neuronal cells. Cell Biology and Toxicology. 37 (6), 833-847 (2021).
  11. Shekhar, S., et al. Deciphering the pathways for evaluation of nanotoxicity: Stumbling block in nanotechnology. Cleaner Engineering and Technology. 5, 100311 (2021).
  12. Bhabra, G., et al. Nanoparticles can cause DNA damage across a cellular barrier. Nature Nanotechnology. 4 (12), 876-883 (2009).
  13. Técher, H., et al. Replication dynamics: Biases and robustness of DNA fiber analysis. Journal of Molecular Biology. 425 (23), 4845-4855 (2013).
  14. Chastain, P. D., et al. DNA damage checkpoint responses in the S phase of synchronized diploid human fibroblasts. Photochemistry and Photobiology. 91 (1), 109-116 (2015).
  15. Frum, R. A., Deb, S., Deb, S. P. Use of the DNA fiber spreading technique to detect the effects of mutant p53 on DNA replication. p53 Protocols. , Humana Press. Totowa, NJ. 147-155 (2013).
  16. Ord, M. G., Stocken, L. A. Studies in synthesis of deoxyribonucleic acid: Radiobiochemical lesion in animal cells. Nature. 182 (4652), 1787-1788 (1958).
  17. Moore, G., Sainz, J. J., Jensen, R. B. DNA fiber combing protocol using in-house reagents and coverslips to analyze replication fork dynamics in mammalian cells. STAR Protocols. 3 (2), 101371 (2022).
  18. Blin, M., et al. Transcription-dependent regulation of replication dynamics modulates genome stability. Nature Structural and Molecular Biology. 26 (1), 58-66 (2019).
  19. Zardoni, L., Nardini, E., Liberi, G. 2D gel electrophoresis to detect DNA replication and recombination intermediates in budding yeast. DNA Electrophoresis. , Humana. New York, NY. 43-59 (2020).
  20. Painter, R. B. Radioresistant DNA synthesis: An intrinsic feature of ataxia telangiectasia. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 84 (1), 183-190 (1981).
  21. Aten, J. A., Bakker, P. J. M., Stap, J., Boschman, G. A., Veenhof, C. H. N. DNA double labelling with IdUrd and CldUrd for spatial and temporal analysis of cell proliferation and DNA replication. The Histochemical Journal. 24 (5), 251-259 (1992).
  22. Gratzner, H. G. Monoclonal antibody to 5-bromo-and 5-iododeoxyuridine: A new reagent for detection of DNA replication. Science. 218 (4571), 474-475 (1982).
  23. Huberman, J. A., Riggs, A. D. Autoradiography of chromosomal DNA fibers from Chinese hamster cells. Proceedings of the National Academy of Sciences of the United States of America. 55 (3), 599-606 (1966).
  24. Ockey, C. H. Differences in replicon behavior between X-irradiation-sensitive L5178Y mouse lymphoma cells and AT fibroblasts using DNA fiber autoradiography. Radiation Research. 94 (2), 427-438 (1983).
  25. Brayner, R. The toxicological impact of nanoparticles. Nano Today. 3 (1-2), 48-55 (2008).
  26. Mendez-Bermudez, A., et al. Genome-wide control of heterochromatin replication by the telomere capping protein TRF2. Molecular Cell. 70 (3), 449-461 (2018).
  27. Vindigni, A., Lopes, M. Combining electron microscopy with single molecule DNA fiber approaches to study DNA replication dynamics. Biophysical Chemistry. 225, 3-9 (2017).
  28. Herrick, J., Bensimon, A. Single molecule analysis of DNA replication. Biochimie. 81 (8-9), 859-871 (1999).
  29. Taylor, J. H., Miner, P. Units of DNA replication in mammalian chromosomes. Cancer Research. 28 (9), 1810-1814 (1968).
  30. Nieminuszczy, J., Schwab, R. A., Niedzwiedz, W. The DNA fibre technique-tracking helicases at work. Methods. 108, 92-98 (2016).
  31. Lemaçon, D., et al. MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells. Nature Communications. 8, 860 (2017).
  32. Vindigni Lab. Replication Fork Protection. Washington University School of Medicine. , https://vindignilab.wustl.edu/research/replication-fork-protection (2020).
  33. Mimitou, E. P., Symington, L. S. DNA end resection: Many nucleases make light work. DNA Repair. 8 (9), 983-995 (2009).
  34. Schlacher, K., et al. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell. 145 (4), 529-542 (2011).
  35. Prado, F., Aguilera, A. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. The EMBO Journal. 24 (6), 1267-1276 (2005).
  36. Jackson, D. A., Pombo, A. Replicon clusters are stable units of chromosome structure: Evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. The Journal of Cell Biology. 140 (6), 1285-1295 (1998).
  37. Halliwell, J. A., Gravells, P., Bryant, H. E. DNA fiber assay for the analysis of DNA replication progression in human pluripotent stem cells. Current Protocols in Stem Cell Biology. 54 (1), 115 (2020).
  38. Wang, Y., et al. Automated DNA fiber tracking and measurement. 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. , 1349-1352 (2011).
  39. Quinet, A., Carvajal-Maldonado, D., Lemacon, D., Vindigni, A. DNA fiber analysis: Mind the gap. Methods in Enzymology. 591, 55-82 (2017).
  40. Técher, H., et al. Replication dynamics: Biases and robustness of DNA fiber analysis. Journal of Molecular Biology. 425 (23), 4845-4855 (2013).
  41. Martins, D. J., Tirman, S., Quinet, A., Menck, C. F. Detection of post-replicative gaps accumulation and repair in human cells using the DNA fiber assay. Journal of Visualized Experiments. (180), e63448 (2022).

Tags

Keywords: DNA Fiber Assay DNA Damage DNA Repair Nanoparticles DNA Replication Dynamics Chromatin Dynamics Therapeutic Agents Nanomedicine RAW 264.5 Macrophage Cells Iododeoxyuridine Chloro-iododeoxyuridine
Demonstration of the DNA Fiber Assay for Investigating DNA Damage and Repair Dynamics Induced by Nanoparticles
Play Video
PDF DOI DOWNLOAD MATERIALS LIST

Cite this Article

Patel, S., Chastain, P., Bijukumar,More

Patel, S., Chastain, P., Bijukumar, D. Demonstration of the DNA Fiber Assay for Investigating DNA Damage and Repair Dynamics Induced by Nanoparticles. J. Vis. Exp. (193), e64903, doi:10.3791/64903 (2023).

Less
Copy Citation Download Citation Reprints and Permissions
View Video

Get cutting-edge science videos from JoVE sent straight to your inbox every month.

Waiting X
Simple Hit Counter