Fluorescence resonance energy transfer-based real-time observation systems of the DNA strand exchange reaction mediated by Rad51 were developed. Using the protocols presented here, we are able to detect the formation of reaction intermediates and their conversion into products, while also analyzing the enzymatic kinetics of the reaction.
The DNA strand exchange reaction mediated by Rad51 is a critical step of homologous recombination. In this reaction, Rad51 forms a nucleoprotein filament on single-stranded DNA (ssDNA) and captures double-stranded DNA (dsDNA) non-specifically to interrogate it for a homologous sequence. After encountering homology, Rad51 catalyzes DNA strand exchange to mediate pairing of the ssDNA with the complementary strand of the dsDNA. This reaction is highly regulated by numerous accessary proteins in vivo. Although conventional biochemical assays have been successfully employed to examine the role of such accessory protein in vitro, kinetic analysis of intermediate formation and its progression into a final product has proven challenging due to the unstable and transient nature of the reaction intermediates. To observe these reaction steps directly in solution, fluorescence resonance energy transfer (FRET)-based real-time observation systems of this reaction were established. Kinetic analysis of real-time observations shows that the DNA strand exchange reaction mediated by Rad51 obeys a three-step reaction model involving the formation of a three-strand DNA intermediate, maturation of this intermediate, and the release of ssDNA from the mature intermediate. The Swi5-Sfr1 complex, an accessary protein conserved in eukaryotes, strongly enhances the second and third steps of this reaction. The FRET-based assays presented here enable us to uncover the molecular mechanisms through which recombination accessary proteins stimulate the DNA strand exchange activity of Rad51. The primary goal of this protocol is to enhance the repertoire of techniques available to researchers in the field of homologous recombination, particularly those working with proteins from species other than Schizosaccharomyces pombe, so that the evolutionary conservation of the findings presented herein can be determined.
Homologous recombination (HR) facilitates the shuffling of genetic information between two different DNA molecules. HR is essential for two fundamental biological phenomena: the generation of genetic diversity during gametogenesis1 and the repair of DNA double-strand breaks (DSBs)2 during mitosis. DSBs are the most severe form of DNA damage and constitute a breakage in the chromosome. Incorrect repair of DSBs can cause extensive chromosomal rearrangements and genomic instability, which are both hallmarks of cancer3.
The DNA strand exchange reaction is the central phase of HR. The Rad51 protein, which is a member of the highly conserved RecA-type family of recombinases, is the key protein that catalyzes this reaction in eukaryotes4,5. In this reaction, Rad51 binds to single-stranded DNA (ssDNA) generated by nucleolytic processing of the DSB end and forms a helical nucleoprotein complex termed the presynaptic filament. This filament catches intact double-stranded DNA (dsDNA) nonspecifically to search for a homologous sequence. When the filament finds a homologous sequence, a reaction intermediate containing three-stranded DNA is formed and the Rad51 filament mediates strand exchange within this structure6,7,8. To accomplish this reaction efficiently, Rad51 requires several kinds of accessory proteins such as BRCA1 and BRCA2, products of breast cancer susceptibility genes9,10.
Understanding how accessory factors regulate Rad51 is an integral step in uncovering the causes of genomic instability during tumorigenesis. Although much research is concerned with the effects of these factors on presynaptic filament formation and stability11,12,13,14,15,16, the contribution of these factors to formation of the three-strand intermediate and its processing into the final product is still unclear. Observing these reaction steps through conventional biochemical experiments is very difficult because the three-strand intermediate is unstable and prone to collapse by common experimental manipulations such as deproteinization of samples or electrophoresis.
To overcome this problem, we adapted two previously developed real-time observation systems of the DNA strand exchange reaction using fluorescence resonance energy transfer (FRET): the DNA strand pairing and DNA strand displacement assays17,18 (Figure 1). In the DNA strand pairing assay, Rad51 forms a presynaptic filament with fluorescein amidite (FAM)-labeled ssDNA and then homologous carboxy-x-rhodamine (ROX)-labeled dsDNA is added to initiate the strand exchange reaction. When the filament catches the ROX-labeled dsDNA and forms the three-strand intermediate, the two fluorophores come into close proximity and fluorescence emission of FAM is quenched by ROX (Figure 1A). In the DNA strand displacement assay, a presynaptic filament formed on unlabeled ssDNA is incubated with FAM and ROX double-labeled dsDNA. When strand exchange is completed and the FAM labeled ssDNA is released from the three-strand intermediate, the emission of FAM increases because FAM is no longer in close proximity to ROX (Figure 1B). These assays enable us to observe the formation of three-strand intermediates and their processing into final products in real-time without any disturbances to the reaction.
Using this real-time observation system, we found that the DNA strand exchange reaction mediated by Rad51 proceeds in three-steps including the formation of the first reaction intermediate (C1), transitioning of the first intermediate into a second intermediate (C2), and release of ssDNA from C219. We also found that fission yeast (S. pombe) Swi5-Sfr1, which is an evolutionarily conserved Rad51 accessory protein complex13,16,20,21,22, stimulates the C1-C2 transitioning and release of ssDNA from C2 in a manner that is dependent on ATP-hydrolysis by Rad5119.
Whether these findings are evolutionarily conserved remains unknown. This protocol is provided with the hope that researchers in the field of HR, especially those working with proteins from organisms other than S. pombe, may apply these techniques to determine the extent to which the molecular mechanism of Rad51-driven strand exchange is conserved. Furthermore, these techniques have proven highly successful in determining the role of S. pombe Swi5-Sfr1. Thus, it is a rational prediction that these techniques will be invaluable in uncovering the precise roles of other HR accessory factors.
Here, we have described a detailed protocol that utilizes FRET to measure Rad51-driven DNA strand exchange in real time. Importantly, these measurements allow for the determination of reaction kinetics. While the descriptions provided above are sufficient to reproduce our published results, there are several critical points that will be described in this section. Furthermore, the advantages and disadvantages of FRET-based methodologies for studying DNA strand exchange will be discussed, along with the application of such techniques to study other aspects of DNA metabolism.
As with all biochemical reconstitutions, ensuring that all reaction substrates are of high purity is essential. It is negligent to assume the absence of contaminating activities based solely on the apparent purity of a protein preparation judged by Coomassie staining. In particular, the presence of trace amounts of nucleases or helicases can drastically affect the results of the pairing and displacement assays. Thus, we strongly encourage testing for such activities each time a new batch of protein is purified. Furthermore, it is prudent to check the purity of synthesized DNA substrates by native polyacrylamide gel electrophoresis. Despite many companies guaranteeing the purity of oligonucleotides, we have often found through our own testing that purity of the synthesized DNA can vary between batches.
It is important to consider the following two points when conducting experiments with quartz cuvettes. Firstly, some proteins are prone to bind quartz cuvettes nonspecifically. To counter this, BSA and polyoxyethylenesorbitan monolaurate are included in the reaction buffers. Secondly, temperature has a drastic effect on the reaction speed and fluorescence intensity. To minimize this effect, the quartz cuvette should be pre-incubated at 37 °C prior to use.
Although conventional biochemical assays have been hugely useful in studying DNA strand exchange, they have several drawbacks. In a typical time-course experiment, a reaction is incubated at a certain temperature and aliquots are withdrawn at desired timepoints and deproteinized by treatment with detergent and protease to terminate the reaction. Upon completion of the time-course, samples are then subjected to electrophoresis to separate DNA substrates from products. The major advantage of the method described here is that it allows for the real-time observation of the reaction without any disturbance. Any timepoint during the reaction can be inspected without disruption to the reaction itself and there is no need to deproteinize samples or subject them to the potentially disruptive forces of electrophoresis. This is especially relevant when monitoring labile DNA structures.
Despite these strengths over conventional assays, the method described here does have some disadvantages. While the use of oligonucleotide DNA substrates for strand exchange simplifies interpretation of the results, it is important to remember that such substrates do not resemble the DNA substrates involved in HR in the cell. Some conventional assays utilize plasmid-sized DNA substrates, which are more likely to reflect the number of base-pairs that are exchanged in vivo. Furthermore, the use of topologically constrained circular dsDNA substrates in a subset of conventional assays can at least partially recreate the tensions in physiological DNA.
The application of the method described here has started to unravel the molecular mechanisms of Rad51-driven DNA strand exchange. Nonetheless, there are many interesting questions that remain to be answered. There is clear evidence that HR during meiosis requires both Rad51 and Dmc1, the meiosis-specific RecA-type recombinase in eukaryotes24. However, the lack of major biochemical differences between these two recombinases has baffled researchers in the field for years. Moreover, the roles of numerous distinct groups of recombination accessory factors has been a focal topic of research in the field of HR. In addition to elucidating the biochemical differences between Rad51 and Dmc1, we aim to investigate and compare the effects of different recombination accessory factors on the kinetics of DNA strand exchange in the immediate future. Finally, it is important to stress that the FRET-based methodology described here is not limited to the study of DNA strand exchange. With relatively minor modifications, we envision many kinds of applications for this technique in investigating functionally diverse proteins involved in DNA metabolism25,26,27,28. We hope the developments described here will provide further options to researchers belonging to many different disciplines.
The authors have nothing to disclose.
This work was funded by Grants-in-Aid for Scientific Research (A) (18H03985) and on Innovative Areas (15H05974) to HI, for Young Scientists (B) (17K15061) to BA, and for Scientific Research (B) (18H02371) to HT from the Japan Society for the Promotion of Science (JSPS).
0.2 x 1.0 cm quartz cuvette | Hellma Analytics | 105-250-15-40 | |
1.0 x 1.0 cm quartz cuvette | Hellma Analytics | 101-10-40 | |
adenosine triphosphate (ATP) | Sigma | A2383 | |
DynaFit | BioKin, Ldt. | DynaFit is a program to analyze kinetics of biochemical reactions. | |
Fluorescent labeled and non-labeled oligonucleotides | Eurofins Genomics | The sequences of oligos are listed in Table. 1. | |
Magnetic stirrer | Aisis (Japan) | CM1609 | |
PCR machine | TAKARA (Japan) | TP600 | TAKARA PCR Thermal Cycler Dice |
Spectrofluorometer | JASCO | FP8300 | Contains a peltier temperature controller and magnetic stirrer system |
Syringe | HAMILTON | 1702RN 25ul SYR (22s/2"/2) |