Strand Exchange Research Articles

Proximity hybridization induced DNA assembly for label-free surface-enhanced Raman spectroscopic detection of carcinoembryonic antigen

In our research, label-free and surface-enhanced Raman dyes-free Raman spectroscopy which was used to detect carcinoembryonic antigen (CEA) according to poly adenine (Poly A)-regulated self-assembly methods was developed and studied. CEA induced partial hybridization of Ab-H2 and Ab-H1, and Ab-H1-CEA-Ab-H2 (a sandwich proximity CEA-DNA complex) was formed, which unfolded molecular beacon 1 (MB1) and modified the substrate. Subsequently, MB2-AuNPs were hybridized with MB1, and Ab-H1-CEA-Ab-H2 was released via toehold regulated displacements of DNA strands. Therefore, hybridization processes of MB2 and MB1 were induced and promoted by CEA-DNA complexes which worked as catalysts. The misplaced target then induced a next round of strand exchange, and the signals for determination of CEA were amplified by AuNPs absorbed on the substrate. It was indicated that the spectral characteristics of adenine at 736 cm−1 were consistent with the SERS spectrum of DNA. Adenine acted as an internal marker for label-free SERS detection of CEA. Moreover, satisfactory stability and reproducibility were found. Meanwhile, the antibody could specifically recognize the corresponding antigen. Since adenine was dominant in SERS spectra, which was also proximal to Au surface, the sensitivity of the novel method was high without modifications. The analytical performance of this method in determining serum CEA was satisfactory.

Nucleic acid extraction without electrical equipment via magnetic nanoparticles in Pasteur pipettes for pathogen detection

The outbreak of COVID-19 makes epidemic prevention and control become a growing global concern. Nucleic acid amplification testing (NAAT) can realize early and rapid detection of targets, thus it is considered as an ideal approach for detecting pathogens of severe acute infectious diseases. Rapid acquisition of high-quality target nucleic acid is the prerequisite to ensure the efficiency and accuracy of NAAT. Herein, we proposed a simple system in which magnetic nanoparticles (MNPs) based nucleic acid extraction was carried out in a plastic Pasteur pipette. Different from traditional approaches, this proposed system could be finished in 15 min without the supports of any electrical instruments. Furthermore, this system was superior to traditional MNPs based extraction methods in the aspects of rapid extraction and enhancing the sensitivity of a NAAT method, accelerated denaturation bubbles mediated strand exchange amplification (ASEA), to the pathogens from various artificial samples. Finally, this Pasteur pipette system was utilized for pathogen detection in actual samples of throat swabs, cervical swabs and gastric mucosa, the diagnosis results of which were identical with that provided by hospital. This rapid, easy-performing and efficiency extraction method ensures the applications of the NAAT in pathogen detection in regions with restricted resources.

Design and comparative characterization of RecA variants

RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure–function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure–function relationship and on the monomer–monomer interactions that perturb the activity of the protein as a whole.

P-057: A helicase “ASCC3” is coupled to FEN1-mediated genomic instability and cancer cell proliferation

<h3>Background</h3> We have previously reported the identification of FEN1 a driver of genomic instability in myeloma (MM) as well as esophageal adenocarcinoma (EAC) cells. We demonstrated that FEN1 is overexpressed in MM cell lines and in clinical datasets of MM and several other cancers including EAC, and FEN1-knockdown inhibited spontaneous DNA breaks, homologous recombination (HR) activity as well as genomic instability in MM cells. We now show that FEN1-overexpression in non-cancerous (normal fibroblasts and bone marrow/stroma HS5) cells increases DNA breaks and genomic instability, as assessed by micronucleus assay. <h3>Methods</h3> In order to further evaluate the impact on genomic instability, control and FEN1-overexpressing cells were cultured for three weeks and new genomic changes acquired in cultured relative to "day 0" cells (representing baseline genome), were identified using single nucleotide polymorphism (SNP) arrays. <h3>Results</h3> Overall, the acquisition of amplification and deletion events were increased by ~ 3-fold in FEN1-overexpressing relative to control cells. Evaluation by RNA sequencing in two different non-cancerous cell types showed that FEN1-overexpression was associated with upregulation of several interconnected pathways including DNA double strand break repair, cell cycle, mitotic G2 M phases, TP53, homologous DNA pairing and strand exchange. Top downregulated pathways included several metabolic pathways and an apoptosis pathway. These data demonstrate a significant role and the impact of FEN1 on DNA repair and genome maintenance, especially HR. We next identified FEN1-interacting proteins from two different MM cell lines (MM1S, RPMI8226) by mass spectrometry. Forty-one proteins interacted with FEN1 in both MM cell lines including two helicases (ASCC3, RUVBL2) and several proteins involved in DNA damage response and recruitment. To investigate the functional relevance of FEN1-ASCC3 interaction, FEN1 was overexpressed in non-cancerous (stromal HS5) cells and ASCC3 was suppressed in control as well as FEN1-overexpressed cells, and impact on different parameters of genome stability (HR activity, micronuclei) and growth (cell viability and DNA replication) monitored. FEN1-overexpression increased HR activity, whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced HR activity. Consistent with these data, FEN1-overexpression also increased genomic instability, whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced genomic instability as assessed by micronucleus assay. Importantly, FEN1-overexpression also increased DNA replication (as assessed by BrdU-labelling), whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced DNA replication in these cells. <h3>Conclusion</h3> These data suggest that helicase activity of ASCC3 is coupled to endonuclease activity of FEN1 to cause genomic instability and cancer cell proliferation, and is currently being investigated in MM and other cancer models to develop translational application.

Non-Recombinogenic Functions of Rad51, BRCA2, and Rad52 in DNA Damage Tolerance.

The DNA damage tolerance (DDT) response is aimed to timely and safely complete DNA replication by facilitating the advance of replication forks through blocking lesions. This process is associated with an accumulation of single-strand DNA (ssDNA), both at the fork and behind the fork. Lesion bypass and ssDNA filling can be performed by translation synthesis (TLS) and template switching mechanisms. TLS uses low-fidelity polymerases to incorporate a dNTP opposite the blocking lesion, whereas template switching uses a Rad51/ssDNA nucleofilament and the sister chromatid to bypass the lesion. Rad51 is loaded at this nucleofilament by two mediator proteins, BRCA2 and Rad52, and these three factors are critical for homologous recombination (HR). Here, we review recent advances showing that Rad51, BRCA2, and Rad52 perform some of these functions through mechanisms that do not require the strand exchange activity of Rad51: the formation and protection of reversed fork structures aimed to bypass blocking lesions, and the promotion of TLS. These findings point to the central HR proteins as potential molecular switches in the choice of the mechanism of DDT.

Nucleotide proofreading functions by nematode RAD51 paralogs facilitate optimal RAD51 filament function

The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Here, we define unappreciated mechanisms by which the RAD51 paralog complex RFS-1/RIP-1 limits the accumulation of RAD-51-ssDNA complexes with unfavorable nucleotide content. We find RAD51 paralogs promote the turnover of ADP-bound RAD-51 from ssDNA, in striking contrast to their ability to stabilize productive ATP-bound RAD-51 nucleoprotein filaments. In addition, RFS-1/RIP-1 inhibits binding of nucleotide-free RAD-51 to ssDNA. We propose that ‘nucleotide proofreading’ activities of RAD51 paralogs co-operate to ensure the enrichment of active, ATP-bound RAD-51 filaments on ssDNA to promote HR.

Immobilization-free electrochemical DNA sensor based on signal cascade amplification strategy.

The development of convenient and efficient strategies without using complex nanomaterials or enzymes for signal amplification is very important for bioanalytical applications. Herein, a novel electrochemical DNA sensor was developed by harnessing the signal amplification efficiency of catalytic hairpin assembly (CHA) and a brand-new signal marker tetraferrocene. The prepared sensor had both ends of the probe H2 labeled with tetraferrocene; both ends have a large number of unhybridized T bases, which cause tetraferrocene to move closer to the electrode surface, generating a high-efficiency amplification signal. In the presence of target DNA, it induced strand exchange reactions promoting the formation of double-stranded DNA and recycling of target DNA. Under optimal conditions, the sensor showed a good linear correlation between the peak currents and logarithm of target DNA concentrations (ranging from 0.1 fM to 0.3125 pM) with a detection limit of 0.06 fM, which is obtained by a triple signal-to-noise ratio. Additionally, the prepared sensor possesses excellent selectivity, reproducibility, and stability, demonstrating efficient and stable DNA detection methodology.

Ultra-thin self-healing vitrimer coatings for durable hydrophobicity

Durable hydrophobic materials have attracted considerable interest in the last century. Currently, the most popular strategy to achieve hydrophobic coating durability is through the combination of a perfluoro-compound with a mechanically robust matrix to form a composite for coating protection. The matrix structure is typically large (thicker than 10 μm), difficult to scale to arbitrary materials, and incompatible with applications requiring nanoscale thickness such as heat transfer, water harvesting, and desalination. Here, we demonstrate durable hydrophobicity and superhydrophobicity with nanoscale-thick, perfluorinated compound-free polydimethylsiloxane vitrimers that are self-healing due to the exchange of network strands. The polydimethylsiloxane vitrimer thin film maintains excellent hydrophobicity and optical transparency after scratching, cutting, and indenting. We show that the polydimethylsiloxane vitrimer thin film can be deposited through scalable dip-coating on a variety of substrates. In contrast to previous work achieving thick durable hydrophobic coatings by passively stacking protective structures, this work presents a pathway to achieving ultra-thin (thinner than 100 nm) durable hydrophobic films.

SARS-CoV-2 Point-of-Care (POC) Diagnosis Based on Commercial Pregnancy Test Strips and a Palm-Size Microfluidic Device.

Coronavirus diseases such as the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), pose serious threats. Portable and accurate nucleic acid detection is still an urgent need to achieve on-site virus screening and timely infection control. Herein, we have developed an on-site, semiautomatic detection system, aiming at simultaneously overcoming the shortcomings suffered by various commercially available assays, such as low accuracy, poor portability, instrument dependency, and labor intensity. Ultrasensitive isothermal amplification [i.e., reverse transcription loop-mediated isothermal amplification (RT-LAMP)] was applied to generate intensified SARS-CoV-2 RNA signals, which were then transduced to portable commercial pregnancy test strips (PTSs) via ultraspecific human chorionic gonadotropin (hCG)-conjugated toehold-mediated strand exchange (TMSE) probes (hCG-P). The entire detection was integrated into a four-channel, palm-size microfluidic device, named the microfluidic point-of-care (POC) diagnosis system based on the PTS (MPSP) detection system. It provides rapid, cost-effective, and sensitive detection, of which the lowest concentration of detection was 0.5 copy/μL of SARS-CoV-2 RNA, regardless of the presence of other similar viruses, even highly similar severe acute respiratory syndrome coronavirus (SARS-CoV). The successful detection of the authentic samples from different resources evaluated the practical application. The commercial PTS provides a colorimetric visible signal, which is instrument- and optimization-free. Therefore, this MPSP system can be immediately used for SARS-CoV-2 emergency detection, and it is worthy of further optimization to achieve full automation and detection for other infectious diseases.

Glucometer‐based Ultra‐sensitive BRAF V600E Mutation Detection Facilitated by Magnetic Nanochains and a Self‐made Point‐of‐Care (POC) Device

AbstractWe realized the user‐friendly and field‐based point‐of‐care detection on a self‐made portable device with the aid of personal glucose meter (PGM) for single nucleotide polymorphisms (SNPs) of melanoma and colon cancer marker BRAF V600E with good sensitivity and selectivity by integrating the loop‐mediated isothermal amplification (LAMP) reaction and the strand exchange signal transduction. The device is equipped with a rotating magnetic field as well as a heating element, under which the pre‐added magnetic nanochains (MNCs) help to homogenize the reaction mixture and overcome the low diffusion efficacy of the reactant and the required temperature for different reactions can be met.

Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens.

Here, we report the development of methodologies that enable genetic modification of a Basidiomycota yeast, Naganishia liquifaciens. The gene targeting method employs electroporation with PCR products flanked by an 80bp sequence homologous to the target. The method, combined with a newly devised CRISPR-Cas9 system, routinely achieves 80% gene targeting efficiency. We further explored the genetic requirement for this homologous recombination (HR)-mediated gene targeting. The absence of Ku70, a major component of the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair, almost completely eliminated inaccurate integration of the marker. Gene targeting with short homology (80bp) was almost exclusively dependent on Rad52, an essential component of HR in the Ascomycota yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. By contrast, the RecA homolog Rad51, which performs homology search and strand exchange in HR, plays a relatively minor role in gene targeting, regardless of the homology length (80bp or 1kb). The absence of both Rad51 and Rad52, however, completely eliminated gene targeting. Unlike Ascomycota yeasts, the absence of Rad52 in N. liquefaciens conferred only mild sensitivity to ionizing radiation. These traits associated with the absence of Rad52 are reminiscent of findings in mice.

Fission yeast Rad8/HLTF facilitates Rad52-dependent chromosomal rearrangements through PCNA lysine 107 ubiquitination.

Gross chromosomal rearrangements (GCRs), including translocation, deletion, and inversion, can cause cell death and genetic diseases such as cancer in multicellular organisms. Rad51, a DNA strand exchange protein, suppresses GCRs by repairing spontaneous DNA damage through a conservative way of homologous recombination, gene conversion. On the other hand, Rad52 that catalyzes single-strand annealing (SSA) causes GCRs using homologous sequences. However, the detailed mechanism of Rad52-dependent GCRs remains unclear. Here, we provide genetic evidence that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. In rad51Δ cells, loss of Rad8 eliminated 75% of the isochromosomes resulting from centromere inverted repeat recombination, showing that Rad8 is essential for the formation of the majority of isochromosomes in rad51Δ cells. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3’ DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating enzymes were required for GCRs. Consistent with this, mutating PCNA K107 rather than the well-studied PCNA K164 reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. In contrast to GCRs, PCNA K107R did not significantly change gene conversion rates, suggesting a specific role of PCNA K107 ubiquitination in GCRs. PCNA K107R enhanced temperature-sensitive growth defects of DNA ligase I cdc17-K42 mutant, implying that PCNA K107 ubiquitination occurs when Okazaki fragment maturation fails. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 and Rad8 ubiquitin ligase for GCRs. These data suggest that Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs by changing the PCNA clamp structure.

Biochemical characterization of Recombinase A from Wolbachia endosymbiont of filarial nematode Brugia malayi (wBmRecA)

Lymphatic filariasis is a debilitating disease that affects over 890 million people in 49 countries. A lack of vaccines, non-availability of adulticidal drugs, the threat of emerging drug resistance against available chemotherapeutics and an incomplete understanding of the immunobiology of the disease have sustained the problem. Characterization of Wolbachia proteins, the bacterial endosymbiont which helps in the growth and development of filarial worms, regulates fecundity in female worms and mediates immunopathogenesis of Lymphatic Filariasis, is an important approach to gain insights into the immunopathogenesis of the disease. In this study, we carried out extensive biochemical characterization of Recombinase A from Wolbachia of the filarial nematode Brugia malayi (wBmRecA) using an Electrophoretic Mobility Shift Assay, an ATP binding and hydrolysis assay, DNA strand exchange reactions, DAPI displacement assay and confocal microscopy, and evaluated anti-filarial activity of RecA inhibitors. Confocal studies showed that wBmRecA was expressed and localised within B. malayi microfilariae (Mf) and uteri and lateral chord of adult females. Recombinant wBmRecA was biochemically active and showed intrinsic binding capacity towards both single-stranded DNA and double-stranded DNA that were enhanced by ATP, suggesting ATP-induced cooperativity. wBmRecA promoted ATP hydrolysis and DNA strand exchange reactions in a concentration-dependent manner, and its binding to DNA was sensitive to temperature, pH and salt concentration. Importantly, the anti-parasitic drug Suramin, and Phthalocyanine tetrasulfonate (PcTs)-based inhibitors Fe-PcTs and 3,4-Cu-PcTs, inhibited wBmRecA activity and affected the motility and viability of Mf. The addition of Doxycycline further enhanced microfilaricidal activity of wBmRecA, suggesting potential synergism. Taken together, the omnipresence of wBmRecA in B. malayi life stages and the potent microfilaricidal activity of RecA inhibitors suggest an important role of wBmRecA in filarial pathogenesis.

Expression of Rad51 and the histo-morphological evaluation of testis of the sterile male cattle-yak

Meiotic recombination is key to the repair of DNA double-strand break damage, provide a link between homologs for proper chromosome segregation as well as ensure genetic diversity in organisms. Defects in recombination often lead to sterility. The ubiquitously expressed Rad51 and the meiosis-specific DMC1 are two closely related recombinases that catalyze the key strand invasion and exchange step of meiotic recombination. This study cloned and sequenced the coding region of cattle-yak Rad51 and determined its mRNA and protein expression levels, evaluated its molecular and evolutionary relationship as well as evaluated the histo-morphological structure of testes in the yellow cattle, yak and the sterile cattle-yak hybrid. The Rad51 gene was amplified using PCR, cloned and sequenced using testicular cDNA from yak and cattle-yak. Real-time PCR was used to examine the expression levels of Rad51/DMC1 mRNA in the cattle, yak and cattle-yak testis while western blotting, immunofluorescence and immunohistochemistry were used to assess the protein expression and localization of Rad51/DMC1 protein in the testicular tissue sections. The results revealed that the mRNA and protein expression of Rad51 and DMC1 are extremely low in the male cattle-yak testis with a corresponding higher incidence of germ cell apoptosis. There was also thinning of the germinal epithelium possibly due to the depletion of the germ cells leading to the widening of the lumen area of the cattle-yak seminiferous tubule. Our findings provide support for the hypothesis that the low expression of Rad51 and DMC1 may contribute to the male hybrid sterility in the cattle-yak.

The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process

The C-terminus of Escherichia coli RecA protein can affect the DNA binding affinity, interact with accessory proteins, and regulate the RecA activity. A substantial upward shift in the pH-reaction profile of RecA-mediated DNA strand-exchange reactions was observed for C-terminal-truncated E. coli ΔC17 RecA, Deinococcus radiodurans RecA, and Deinococcus ficus RecA. Here, the process of RecA-mediated strand exchange from the beginning to the end was investigated with florescence resonance energy transfer and tethered particle motion experiments to determine the detailed regulation mechanism. RecA proteins with a shorter C-terminus possess more stable nuclei, higher DNA binding affinities, and lower protonation requirements for the formation of nucleoprotein filaments. Moreover, more stable synaptic complexes in the homologous sequence searching process were also observed for RecA proteins with a shorter C-terminus. Our results suggest that the C-terminus of RecA proteins regulates not only the formation of RecA nucleoprotein filaments but also the entrance of secondary DNA into RecA nucleoprotein filaments.

MCM2-7 and FANCD2 Are Required for RAD51 Function in Homologous Recombination and ICL Repair

MCM2-7 helicase is required for DNA replication and has been implicated in the maintenance of genomic instability, as more than 90% of MCM complexes are in dormant origins. Decreased levels of MCM2-7 complex on chromatin lead to genomic instability. The Fanconi anemia (FA) pathway, whose proteins are defective in the genetic disorder that entails bone marrow failure, congenital defects, and acute myeloid leukemia, is also important in maintaining genomic instability through the regulation of homologous recombinatorial repair (HRR) of interstrand cross links (ICL). FANCD2 is the central protein in the FA pathway, exhibiting monoubiquitination in response to DNA damage, and has been shown to interact with MCM2-7. Here we show that monoubiquitinated FANCD2 interacts with MCM2-7 and is required for maintenance of MCM2-7 on chromatin upon DNA interstrand crosslinking (ICL) drug mitomycin C treatment. FANCD2-MCM2-7 also interacts with RAD51, an interaction which is decreased in the absence of FANCD2 or with the expression of the ubiquitination mutant FANCD2(K561R). Also, RAD51 chromatin localization and homologous recombination (HR) function is impaired in MCM7 knockdown cells. MCM2, MCM5, or MCM7 knock down cells exhibit hypersensitive to ICL and G2/M accumulation as well, and the hypersensitivity of MCM7 knock down cells can be rescued by re-expressing MCM7. Importantly FANCD2 and MCM7 are epistatic for MMC hypersensitivity. At the levels of MCM7 knock down, we observe that cells are not defective for replication as measured by BrdU labeling and are not hypersensitive to replication inhibitor hydroxyurea (HU) but remain ICL sensitive. Using recombinant protein reconstitution in vitro, we observe MCM2-7 and FANCI-FANCD2 dependent RAD51 filament stabilization and strand exchange, which are key steps in HRR. MCM2-7 proteins defective for helicase activity and thus replication defective remain functional in these in vitro biochemical assays. On the other hand, a FANCI DNA binding mutant completely abrogates these activities, suggesting that the FANCD2-FANCI-MCM2-7-RAD51 complex requires a regulated interaction with DNA and is separable from MCM2-7 replication function. Taken together, the FA pathway, MCM2-7, and RAD51 work cooperatively in the biochemical and cell response to DNA damage ICL. DisclosuresNo relevant conflicts of interest to declare.

A Small Molecule RAD51 Inhibitor Preferentially Affects Cells Expressing High Cytidine Deaminase Activity

RAD51 is a homologous recombination factor critical for DNA replication, recombination, and DNA double strand break repair. RAD51 forms nucleoprotein filaments at damaged DNA sites or corrupted DNA replication forks to mediate DNA strand exchange, culminating in recombinational repair of breaks and replication fork restart. RAD51 is essential for the repair of DNA lesions induced by agents that stall or collapse DNA replication forks. In this context, RAD51 is an important factor in resistance to DNA replication stress induced by the cellular cytidine deaminase AICDA (also known as AID). AICDA is a DNA-directed cytidine deaminase that normally acts to initiate somatic hypermutation and immunoglobulin class switching in activated B-lymphocytes. However, AICDA is often constitutively overexpressed in tumor cells in a range of cancer types. In transformed cells the cytidine deamination activity of AICDA, and the resulting DNA base pair mismatches, cause tumor cell hypermutation. As a byproduct of its mutational activity, AICDA also destabilizes DNA replication, causing a high concentration of DNA double stranded breaks in AIDCA-expressing cells. This leads to an obligate dependency on RAD51 for DSB repair and cell survival. We previously demonstrated that RAD51 depletion induces acute sensitivity to AICDA activity in transformed cells. We now describe the mechanistic characterization of a small molecule RAD51 inhibitor - CYT01A- that is preferentially cytotoxic to AICDA expressing cells. CYT01A is a potent RAD51 inhibitor (EC50 ~150nM) that promotes DNA replication catastrophe selectively in cells expressing AICDA. Exposure to CYT01A in cell culture leads to the depletion of nuclear RAD51, resulting in diminished nuclear foci formation in response to DNA damage. We demonstrate a dose-dependent cytotoxic response to CYT01A that was reflected by RAD51 foci suppression. We further demonstrate compromised RAD51 nucleoprotein filament formation, evidenced by persistence of Replication Protein A (RPA) foci following CYT01A treatment. RAD51 depletion and reduced foci formation correlates with a reduction in homologous recombination activity. Finally, we show that CYT01A treated cells undergo replication catastrophe, associated with caspase3/7 activation. Collectively, these data indicate that CYT01A prevents RAD51 transport into the nucleus and thereby inhibits DNA repair activity. This demonstrates the feasibility of targeting RAD51 to induce cell death selectively in cells with high DNA replication stress, such as AICDA overexpressing tumor cells. These findings form the basis for a new synthetic lethal therapeutic approach, targeting the AICDA/RAD51 axis in cancers that exhibit high levels of AICDA activity DisclosuresMills:Cyteir Therapeutics: Employment, Equity Ownership. Cyr:Cyteir Therapeutics: Employment, Equity Ownership. Maclay:Cyteir Therapeutics: Employment, Equity Ownership. Day:Cyteir Therapeutics: Employment, Equity Ownership. Khalil:Cyteir Therapeutics: Consultancy, Equity Ownership.

Synergistic Action between PfHsp90 Inhibitor and PfRad51 Inhibitor Induces Elevated DNA Damage Sensitivity in the Malaria Parasite.

The DNA recombinase Rad51 from the human malaria parasite Plasmodium falciparum has emerged as a potential drug target due to its central role in the homologous recombination (HR)-mediated double-strand break (DSB) repair pathway. Inhibition of the ATPase and strand exchange activity of P. falciparum Rad51 (PfRad51) by a small-molecule inhibitor, B02 [3-(phenylmethyl)-2-[(1E)-2-(3-pyridinyl)ethenyl]-4(3H)-quinazolinone], renders the parasite more sensitive to genotoxic agents. Here, we investigated whether the inhibition of the molecular chaperone PfHsp90 potentiates the antimalarial action of B02. We found that the PfHsp90 inhibitor 17-AAG [17-(allylamino)-17-demethoxygeldanamycin] exhibits strong synergism with B02 in both drug-sensitive (strain 3D7) and multidrug-resistant (strain Dd2) P. falciparum parasites. 17-AAG causes a greater than 200-fold decrease in the half-maximal inhibitory concentration (IC50) of B02 in 3D7 parasites. Our results provide mechanistic insights into such profound synergism between 17-AAG and B02. We report that PfHsp90 physically interacts with PfRad51 and promotes the UV irradiation-induced DNA repair activity of PfRad51 by controlling its stability. We find that 17-AAG reduces PfRad51 protein levels by accelerating proteasomal degradation. Consequently, PfHsp90 inhibition renders the parasites more susceptible to the potent DNA-damaging agent methyl methanesulfonate (MMS) in a dose-dependent manner. Thus, our study provides a rationale for targeting PfHsp90 along with the recombinase PfRad51 for controlling malaria propagation.

Control of the Serine Integrase Reaction: Roles of the Coiled-Coil and Helix E Regions in DNA Site Synapsis and Recombination.

Bacteriophage serine integrases catalyze highly specific recombination reactions between defined DNA segments called att sites. These reactions are reversible depending upon the presence of a second phage-encoded directionality factor. The bipartite C-terminal DNA-binding region of integrases includes a recombinase domain (RD) connected to a zinc-binding domain (ZD), which contains a long flexible coiled-coil (CC) motif that extends away from the bound DNA. We directly show that the identities of the phage A118 integrase att sites are specified by the DNA spacing between the RD and ZD DNA recognition determinants, which in turn directs the relative trajectories of the CC motifs on each subunit of the att-bound integrase dimer. Recombination between compatible dimer-bound att sites requires minimal-length CC motifs and 14 residues surrounding the tip where the pairing of CC motifs between synapsing dimers occurs. Our alanine-scanning data suggest that molecular interactions between CC motif tips may differ in integrative (attP × attB) and excisive (attL × attR) recombination reactions. We identify mutations in 5 residues within the integrase oligomerization helix that control the remodeling of dimers into tetramers during synaptic complex formation. Whereas most of these gain-of-function mutants still require the CC motifs for synapsis, one mutant efficiently, but indiscriminately, forms synaptic complexes without the CC motifs. However, the CC motifs are still required for recombination, suggesting a function for the CC motifs after the initial assembly of the integrase synaptic tetramer. IMPORTANCE The robust and exquisitely regulated site-specific recombination reactions promoted by serine integrases are integral to the life cycle of temperate bacteriophage and, in the case of the A118 prophage, are an important virulence factor of Listeria monocytogenes. The properties of these recombinases have led to their repurposing into tools for genetic engineering and synthetic biology. In this report, we identify determinants regulating synaptic complex formation between correct DNA sites, including the DNA architecture responsible for specifying the identity of recombination sites, features of the unique coiled-coil structure on the integrase that are required to initiate synapsis, and amino acid residues on the integrase oligomerization helix that control the remodeling of synapsing dimers into a tetramer active for DNA strand exchange.

Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair

Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.