A subscription to JoVE is required to view this content. Sign in or start your free trial.
The D-loop capture (DLC) and D-loop extension (DLE) assays utilize the principle of proximity ligation together with quantitative PCR to quantify D-loop formation, D-loop extension, and product formation at the site of an inducible double-stranded break in Saccharomyces cerevisiae.
DNA damage, including DNA double-stranded breaks and inter-strand cross-links, incurred during the S and G2 phases of the cell cycle can be repaired by homologous recombination (HR). In addition, HR represents an important mechanism of replication fork rescue following stalling or collapse. The regulation of the many reversible and irreversible steps of this complex pathway promotes its fidelity. The physical analysis of the recombination intermediates formed during HR enables the characterization of these controls by various nucleoprotein factors and their interactors. Though there are well-established methods to assay specific events and intermediates in the recombination pathway, the detection of D-loop formation and extension, two critical steps in this pathway, has proved challenging until recently. Here, efficient methods for detecting key events in the HR pathway, namely DNA double-stranded break formation, D-loop formation, D-loop extension, and the formation of products via break-induced replication (BIR) in Saccharomyces cerevisiae are described. These assays detect their relevant recombination intermediates and products with high sensitivity and are independent of cellular viability. The detection of D-loops, D-loop extension, and the BIR product is based on proximity ligation. Together, these assays allow for the study of the kinetics of HR at the population level to finely address the functions of HR proteins and regulators at significant steps in the pathway.
Homologous recombination (HR) is a high-fidelity mechanism of repair of DNA double-stranded breaks (DSBs), inter-strand cross-links, and ssDNA gaps, as well as a pathway for DNA damage tolerance. HR differs from error-prone pathways for DNA damage repair/tolerance, such as non-homologous end-joining (NHEJ) and translesion synthesis, in that it utilizes an intact, homologous duplex DNA as a donor to template the repair event. Moreover, many of the key intermediates in the HR pathway are reversible, allowing for exquisite regulation of the individual pathway steps. During the S, G2, and M phases of the cell cycle, HR competes with NHEJ for the repair of the two-ended DSBs1. In addition, HR is essential to DNA replication for the repair of replication-associated DNA damage, including ssDNA gaps and one-sided DSBs, and as a mechanism of DNA lesion bypass2.
A critical intermediate in the HR pathway is the displacement loop, or D-loop (Figure 1). Following end resection, the central recombinase in the reaction, Rad51, loads onto the newly resected ssDNA of the broken molecule, forming a helical filament2. Rad51 then carries out a homology search to identify a suitable homologous donor, typically the sister chromatid in somatic cells. The D-loop is formed when the Rad51-ssDNA filament invades a homologous duplex DNA, which leads to the Watson-Crick base pairing of the broken strand with the complementary strand of the donor, displacing the opposite donor strand. Extension of the 3' end of the broken strand by a DNA polymerase replaces the bases that were lost during the DNA damage event and promotes resolution of the extended D-loop intermediate into a dsDNA product through the synthesis-dependent strand annealing (SDSA), the double-Holliday junction (dHJ), or the break-induced replication (BIR) HR sub-pathways.
Assays that physically monitor the intermediates in the HR pathway permit the analysis of the genetic requirements for each step (i.e., pathway analysis). DSB formation, end resection, dHJs, BIR replication bubbles, and HR products are readily observed by Southern blotting3,4,5,6,7. Yet, Southern blotting fails to report on nascent and extended D-loops, and, thus, an alternative method to reliably measure these joint molecules is required4,8,9. One widely used strategy to analyze nascent D-loop formation is chromatin-immunoprecipitation (ChIP) of Rad51 coupled with quantitative PCR (qPCR)10,11. However, Rad51 association with dsDNA as measured by ChIP-qPCR is independent of sequence homology and the Rad51 accessory factor Rad5410,11. In contrast, an appreciable signal using the method of D-loop analysis presented here, called the D-loop capture (DLC) assay, depends on DSB formation, sequence homology, Rad51, and the Rad51 accessory proteins Rad52 and Rad548. The finding that Saccharomyces cerevisiae Rad51-promoted D-loop formation depends on Rad54 in vivo is in agreement with numerous in vitro reconstitution experiments indicating that Rad54 is required for homology search and D-loop formation by budding yeast Rad518,12,13,14,15.
Current approaches to measuring D-loop extension, primarily through semi-quantitative PCR, are similarly problematic. A typical PCR-based assay to detect D-loop extension amplifies a unique sequence, resulting from recombination between a break site and an ectopic donor and the subsequent recombination-associated DNA synthesis, via a primer upstream of the region of homology on the broken strand and another primer downstream of the region of homology on the donor strand. Using this method, the detection of recombination-associated DNA synthesis requires the non-essential Pol δ processivity factor Pol3216. This finding conflicts with the observation that POL32 deletion has only a mild effect on gene conversion in vivo17. Moreover, these PCR-based assays fail to temporally resolve D-loop extension and BIR product formation, suggesting that the signal results from dsDNA products rather than ssDNA intermediates17,18,19. The D-loop extension (DLE) assay was recently developed to address these discrepancies. The DLE assay quantifies recombination-associated DNA synthesis at a site ~400 base pairs (bp) downstream of the initial 3' invading end9. By this method, D-loop extension is independent of Pol32 and is detectable within 4 h post-DSB induction, whereas BIR products are first observed at 6 h. Indeed, a recent publication from the Haber and Malkova laboratories noted that using this method of preparation of genomic DNA singularly results in ssDNA preservation9,20.
Here, the DLC and DLE assays are described in detail. These assays rely on proximity ligation to detect nascent and extended D-loops in S. cerevisiae (Figure 2)8,9. BIR products can be quantified using this same assay system. For both assays, DSB formation at an HO endonuclease cut site located at the URA3 locus on chromosome (Chr.) V is induced by the expression of the HO endonuclease under the control of a galactose-inducible promoter. Rad51-mediated DNA strand invasion leads to nascent D-loop formation at the site of an ectopic donor located at the LYS2 locus on Chr. II. As the right side of the DSB lacks homology to the donor, repair via SDSA and dHJ formation is not feasible. Initial repair of the DSB by BIR is possible, but the formation of viable products is inhibited by the presence of the centromere21. This deliberate design prevents productive DSB repair, thereby avoiding the resumption of growth by cells with repaired DBSs, which could otherwise overtake the culture during the time course analysis.
In the DLC assay, psoralen crosslinking of the two strands of the heteroduplex DNA within the D-loop preserves the recombination intermediate. Following restriction enzyme site restoration on the broken (resected) strand and digestion, the crosslinking allows for ligation of the unique sequences upstream of the homologous broken and donor DNAs. Using qPCR, the level of chimeric DNA molecule present in each sample is quantified. In the DLE assay, crosslinking is not required, and restriction enzyme site restoration and digestion followed by intramolecular ligation instead link the 5' end of the broken molecule to the newly extended 3' end. Again, qPCR is used to quantify the relative amounts of this chimeric product in each sample. In the absence of restriction enzyme site restoration, the DLE assay reports on the relative levels of the BIR (dsDNA) product that is formed following D-loop extension.
Representative results for each assay using a wild type strain are shown, and readers are referred to Piazza et al.8 and Piazza et al.9 for the use of these assays for the analysis of recombination mutants8,9. The intent of this contribution is to enable other laboratories to adopt the DLC and DLE assays, and support for them is available upon request.
1. Pre-growth, DSB induction, and sample collection
NOTE: Supplementation of all media with 0.01% adenine is recommended for Ade- strains.
2. Cell spheroplasting, lysis, and restriction site restoration
3. Restriction enzyme digest and intramolecular ligation
4. DNA purification
5. Psoralen crosslink reversal (for DLC assay only)
6. Quantitative PCR, controls, and analysis
DLC assay
The DLC assay detects both nascent and extended D-loops formed by the invasion of a site-specific DSB into a single donor (Figure 2). Psoralen crosslinking physically links the broken strand and the donor via the heteroduplex DNA within the D-loop. Restriction enzyme site restoration with a long, hybridizing oligo on the resected strand of the break allows for restriction enzyme cleavage, followed by ligation of the broken strand to the proximal dono...
The assays presented allow for the detection of nascent and extended D-loops (DLC assay), D-loop extension (DLE assay), and BIR product formation (DLE assay with no hybridizing oligonucleotides) using proximity ligation and qPCR. ChIP-qPCR of Rad51 to sites distant from the DSB has previously been used as a proxy for Rad51-mediated homology search and D-loop formation. However, this ChIP-qPCR signal is independent of the sequence homology between the break site and a potential donor, as well as the Rad51-associated facto...
The authors have nothing to disclose.
The work in the Heyer laboratory is supported by grants GM58015 and GM137751 to W.-D.H. Research in the Piazza laboratory is supported by the European Research Council (ERC-StG 3D-loop, grand agreement 851006). D.R. is supported by T32CA108459 and the A.P. Giannini Foundation. We thank Shih-Hsun Hung (Heyer Lab) for sharing his DLC/DLE assay results and for additionally validating the changes to the assays that are detailed in this protocol.
Name | Company | Catalog Number | Comments |
1. Pre-growth, DSB induction, and sample collection | |||
Equipment | |||
15 and 50 mL conical tubes | |||
15 mL glass culture tubes | |||
250 mL, 500 mL, or 1 L flasks | |||
60 mm x 15 mm optically clear petri dishes with flat bottom | Suggested: Corning, Catalog Number 430166; or Genesee Scientific, Catalog Number 32-150G | ||
Benchtop centrifuge with 15 and 50 mL conical tube adapters | |||
Benchtop orbital shaker or tube rotator/revolver | |||
Rotator | |||
UV crosslinker or light box with 365 nm UV bulbs set atop an orbital shaker | Suggested: Spectrolinker XL-1500 UV Crosslinker (Spectronics Corporation) or Vilbert Lourmat BLX-365 BIO-LINK, Catalog Number 611110831 | ||
Materials | |||
60% w/w sodium DL-lactate syrup | Sigma-Aldrich | L1375 | For media preparation |
Agar | Fisher | BP1423500 | For media preparation |
Bacto peptone | BD Difco | 211840 | For media preparation |
Bacto yeast extract | BD Difco | 212750 | For media preparation |
D-(+)-glucose | BD Difco | 0155-17-4 | For media preparation |
Trioxsalen | Sigma-Aldrich | T6137 | For psoralen cross-linking |
2. Spheroplasting, lysis, and restriction enzyme site restoration | |||
Supplies | |||
1.5 mL microcentrifuge tubes | |||
Dry bath | |||
Liquid nitrogen or dry ice/ethanol | |||
Refrigerated microcentrifuge or microcentrifuge | |||
Materials | |||
10X restriction enzyme (CutSmart) buffer (500 mM potassium acetate, 200 mM Tris-acetate, 100 mM magnesium acetate, 1 mg/mL BSA, pH 7.8-8.0) | |||
Zymolyase 100T | US Biological | Z1004 | For spheroplasting |
3. Restriction enzyme digest and intramolecular ligation | |||
Supplies | |||
Water bath | |||
Materials | |||
EcoRI-HF | New England Biolabs | R3101 | Restriction enzyme digest for DLC assay |
HindIII-HF | New England Biolabs | R3104 | Restriction enzyme digest for DLE assay |
T4 DNA ligase | New England Biolabs | M0202 | Intramolecular ligation |
4. DNA purification | |||
Supplies | |||
1.5 and 2 mL microcentrifuge tubes | |||
Materials | |||
Phenol/chloroform/isoamyl alcohol (P/C/IA) at 25:24:1 | Sigma-Aldrich | P2069 | DNA purification |
5. Psoralen cross-link reversal | |||
Supplies | |||
Thermocycler/PCR machine | |||
6. qPCR | |||
Supplies | |||
Lightcycler 480 | Roche | 5015278001 | qPCR machine used by the authors |
Lightcycler 96 | Roche | 5815916001 | qPCR machine used by the authors |
Materials | |||
LightCycler 480 96-Well Plate, white | Roche | 4729692001 | 96-well plates for qPCR |
SsoAdvanced Universal SYBR Green Super Mix | BioRad | 1725271 | qPCR kit used by the authors |
SYBR Green I Master Mix | Roche | 4707516001 | qPCR kit used by the authors |
Request permission to reuse the text or figures of this JoVE article
Request PermissionThis article has been published
Video Coming Soon
ISSN 2578-6326
Copyright © 2025 MyJoVE Corporation. All rights reserved
We use cookies to enhance your experience on our website.
By continuing to use our website or clicking “Continue”, you are agreeing to accept our cookies.