51
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Abstract
Human RAD51 promotes accurate DNA repair by homologous recombination and is involved in protection and repair of damaged DNA replication forks. The active species of RAD51 and related recombinases in all organisms is a nucleoprotein filament assembled on single-stranded DNA (ssDNA). The formation of a nucleoprotein filament competent for the recombination reaction, or for DNA replication support, is a delicate and strictly regulated process, which occurs through filament nucleation followed by filament extension. The rates of these two phases of filament formation define the capacity of RAD51 to compete with the ssDNA-binding protein RPA, as well as the lengths of the resulting filament segments. Single-molecule approaches can provide a wealth of quantitative information on the kinetics of RAD51 nucleoprotein filament assembly, internal dynamics, and disassembly. In this chapter, we describe how to set up a single-molecule total internal reflection fluorescence microscopy experiment to monitor the initial steps of RAD51 nucleoprotein filament formation in real-time and at single-monomer resolution. This approach is based on the unique, stretched-ssDNA conformation within the recombinase nucleoprotein filament and follows the efficiency of Förster resonance energy transfer (EFRET) between two DNA-conjugated fluorophores. We will discuss the practical aspects of the experimental setup, extraction of the FRET trajectories, and how to analyze and interpret the data to obtain information on RAD51 nucleation kinetics, the mechanism of nucleation, and the oligomeric species involved in filament formation.
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52
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Abstract
Many single-molecule experimental techniques exploit fluorescence as a tool to investigate conformational dynamics, molecular interactions, or track the movement of proteins in order to gain insight into their biological functions. A prerequisite to these experimental approaches is to graft one or more fluorophores on the protein of interest with the desired photophysical properties. Here, we describe procedures for efficient methods used to covalently attach fluorophores to proteins. Alternative direct and indirect labeling strategies are also described.
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Affiliation(s)
- Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, 27 boulevard Leï Roure CS30059, 13273, Marseille Cedex 9, France.
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53
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Human RAD52 Captures and Holds DNA Strands, Increases DNA Flexibility, and Prevents Melting of Duplex DNA: Implications for DNA Recombination. Cell Rep 2017; 18:2845-2853. [PMID: 28329678 PMCID: PMC5379009 DOI: 10.1016/j.celrep.2017.02.068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/20/2017] [Accepted: 02/21/2017] [Indexed: 11/30/2022] Open
Abstract
Human RAD52 promotes annealing of complementary single-stranded DNA (ssDNA). In-depth knowledge of RAD52-DNA interaction is required to understand how its activity is integrated in DNA repair processes. Here, we visualize individual fluorescent RAD52 complexes interacting with single DNA molecules. The interaction with ssDNA is rapid, static, and tight, where ssDNA appears to wrap around RAD52 complexes that promote intra-molecular bridging. With double-stranded DNA (dsDNA), interaction is slower, weaker, and often diffusive. Interestingly, force spectroscopy experiments show that RAD52 alters the mechanics dsDNA by enhancing DNA flexibility and increasing DNA contour length, suggesting intercalation. RAD52 binding changes the nature of the overstretching transition of dsDNA and prevents DNA melting, which is advantageous for strand clamping during or after annealing. DNA-bound RAD52 is efficient at capturing ssDNA in trans. Together, these effects may help key steps in DNA repair, such as second-end capture during homologous recombination or strand annealing during RAD51-independent recombination reactions. RAD52 binds ssDNA rapidly and tightly using wrapping and bridging modes RAD52 binding to dsDNA is slower, weaker, and often diffusive RAD52 changes dsDNA mechanics and intercalates into the double helix RAD52 prevents DNA melting by clamping DNA strands
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54
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Sánchez H, Paul MW, Grosbart M, van Rossum-Fikkert SE, Lebbink JHG, Kanaar R, Houtsmuller AB, Wyman C. Architectural plasticity of human BRCA2-RAD51 complexes in DNA break repair. Nucleic Acids Res 2017; 45:4507-4518. [PMID: 28168276 PMCID: PMC5416905 DOI: 10.1093/nar/gkx084] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/03/2017] [Indexed: 12/05/2022] Open
Abstract
The tumor suppressor BRCA2 is a large multifunctional protein mutated in 50–60% of familial breast cancers. BRCA2 interacts with many partners and includes multiple regions with potentially disordered structure. In homology directed DNA repair BRCA2 delivers RAD51 to DNA resulting in removal of RPA and assembly of a RAD51 nucleoprotein filament. Dynamic rearrangements of BRCA2 likely drive this molecular hand-off initiating DNA strand exchange. We show human BRCA2 forms oligomers which can have an extended shape. Scanning force microscopy and quantitative single molecule fluorescence define the variety of BRCA2 complexes, reveal dramatic rearrangements upon RAD51 binding and the loading of RAD51 patches on single strand DNA. At sites of repair in cell nuclei, super-resolution microscopy shows BRCA2 and RAD51 arranged in largely separate locations. We identified dynamic structural transitions in BRCA2 complexes suggested to facilitate loading of RAD51 onto RPA coated single strand DNA and subsequent release of BRCA2.
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Affiliation(s)
- Humberto Sánchez
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Maarten W Paul
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Malgorzata Grosbart
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sarah E van Rossum-Fikkert
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Pathology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Claire Wyman
- Department of Molecular Genetics, Cancer Genomics Center Netherlands, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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55
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Alligand B, Le Breton M, Marquis D, Vallette F, Fleury F. Functional effects of diphosphomimetic mutations at cAbl-mediated phosphorylation sites on Rad51 recombinase activity. Biochimie 2017; 139:115-124. [PMID: 28571978 DOI: 10.1016/j.biochi.2017.05.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/27/2017] [Indexed: 01/10/2023]
Abstract
Homologous Recombination enables faithful repair of the deleterious double strand breaks of DNA. This pathway relies on Rad51 to catalyze homologous DNA strand exchange. Rad51 is known to be phosphorylated in a sequential manner on Y315 and then on Y54, but the effect of such phosphorylation on Rad51 function remains poorly understood. We have developed a phosphomimetic model in order to study all the phosphorylation states. With the purified phosphomimetic proteins we performed in vitro assays to determine the activity of Rad51. Here we demonstrate the inhibitory effect of the double phosphomimetic mutant and suggest that it may be due to a defect in nucleofilament formation.
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Affiliation(s)
- Brendan Alligand
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France; Team 9 Apoptosis in Nervous Central System Tumours, CRCINA, INSERM U892, Nantes University, France
| | - Magali Le Breton
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France
| | - Damien Marquis
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France
| | - François Vallette
- Team 9 Apoptosis in Nervous Central System Tumours, CRCINA, INSERM U892, Nantes University, France
| | - Fabrice Fleury
- Team 3 Mechanism and Regulation of DNA Repair, UFIP, CNRS UMR 6286, Nantes University, France.
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56
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Syrjänen JL, Heller I, Candelli A, Davies OR, Peterman EJG, Wuite GJL, Pellegrini L. Single-molecule observation of DNA compaction by meiotic protein SYCP3. eLife 2017; 6. [PMID: 28287952 PMCID: PMC5348128 DOI: 10.7554/elife.22582] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/04/2017] [Indexed: 12/14/2022] Open
Abstract
In a previous paper (Syrjänen et al., 2014), we reported the first structural characterisation of a synaptonemal complex (SC) protein, SYCP3, which led us to propose a model for its role in chromosome compaction during meiosis. As a component of the SC lateral element, SYCP3 has a critical role in defining the specific chromosome architecture required for correct meiotic progression. In the model, the reported compaction of chromosomal DNA caused by SYCP3 would result from its ability to bridge distant sites on a DNA molecule with the DNA-binding domains located at each end of its strut-like structure. Here, we describe a single-molecule assay based on optical tweezers, fluorescence microscopy and microfluidics that, in combination with bulk biochemical data, provides direct visual evidence for our proposed mechanism of SYCP3-mediated chromosome organisation. DOI:http://dx.doi.org/10.7554/eLife.22582.001
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Affiliation(s)
- Johanna L Syrjänen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrea Candelli
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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57
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Hashemi Shabestari M, Meijering AEC, Roos WH, Wuite GJL, Peterman EJG. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy. Methods Enzymol 2016; 582:85-119. [PMID: 28062046 DOI: 10.1016/bs.mie.2016.09.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy. Thereby, it provides information on the local presence, identity, spatial dynamics, and conformational dynamics of single biomolecules. Together, these techniques allow comprehensive studies of, among others, molecular motors, protein-protein and protein-DNA interactions, biomolecular conformational changes, and mechanotransduction pathways. In this chapter, recent applications of fluorescence microscopy in combination with optical trapping are discussed. After an introductory section, we provide a description of instrumentation together with the current capabilities and limitations of the approaches. Next we summarize recent studies that applied this combination of techniques in biological systems and highlight some representative biological assays to mark the exquisite opportunities that optical tweezers combined with fluorescence microscopy provide.
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Affiliation(s)
| | | | - W H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - G J L Wuite
- Vrije Universiteit, Amsterdam, The Netherlands
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58
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Ma CJ, Gibb B, Kwon Y, Sung P, Greene EC. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 2016; 45:749-761. [PMID: 27903895 PMCID: PMC5314761 DOI: 10.1093/nar/gkw1125] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly.
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Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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59
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Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. Proc Natl Acad Sci U S A 2016; 113:E6045-E6054. [PMID: 27671650 DOI: 10.1073/pnas.1604807113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The DNA strand exchange protein RAD51 facilitates the central step in homologous recombination, a process fundamentally important for accurate repair of damaged chromosomes, restart of collapsed replication forks, and telomere maintenance. The active form of RAD51 is a nucleoprotein filament that assembles on single-stranded DNA (ssDNA) at the sites of DNA damage. The c-Abl tyrosine kinase and its oncogenic counterpart BCR-ABL fusion kinase phosphorylate human RAD51 on tyrosine residues 54 and 315. We combined biochemical reconstitutions of the DNA strand exchange reactions with total internal reflection fluorescence microscopy to determine how the two phosphorylation events affect the biochemical activities of human RAD51 and properties of the RAD51 nucleoprotein filament. By mimicking RAD51 tyrosine phosphorylation with a nonnatural amino acid, p-carboxymethyl-l-phenylalanine (pCMF), we demonstrated that Y54 phosphorylation enhances the RAD51 recombinase activity by at least two different mechanisms, modifies the RAD51 nucleoprotein filament formation, and allows RAD51 to compete efficiently with ssDNA binding protein RPA. In contrast, Y315 phosphorylation has little effect on the RAD51 activities. Based on our work and previous cellular studies, we propose a mechanism underlying RAD51 activation by c-Abl/BCR-ABL kinases.
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60
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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61
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Browning CL, Qin Q, Kelly DF, Prakash R, Vanoli F, Jasin M, Wise JP. Prolonged Particulate Hexavalent Chromium Exposure Suppresses Homologous Recombination Repair in Human Lung Cells. Toxicol Sci 2016; 153:70-8. [PMID: 27449664 DOI: 10.1093/toxsci/kfw103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genomic instability is one of the primary models of carcinogenesis and a feature of almost all cancers. Homologous recombination (HR) repair protects against genomic instability by maintaining high genomic fidelity during the repair of DNA double strand breaks. The defining step of HR repair is the formation of the Rad51 nucleofilament, which facilitates the search for a homologous sequence and invasion of the template DNA strand. Particulate hexavalent chromium (Cr(VI)), a human lung carcinogen, induces DNA double strand breaks and chromosome instability. Since the loss of HR repair increases Cr(VI)-induced chromosome instability, we investigated the effect of extended Cr(VI) exposure on HR repair. We show acute (24 h) Cr(VI) exposure induces a normal HR repair response. In contrast, prolonged (120 h) exposure to particulate Cr(VI) inhibited HR repair and Rad51 nucleofilament formation. Prolonged Cr(VI) exposure had a profound effect on Rad51, evidenced by reduced protein levels and Rad51 mislocalization to the cytoplasm. The response of proteins involved in Rad51 nuclear import and nucleofilament formation displayed varying responses to prolonged Cr(VI) exposure. BRCA2 formed nuclear foci after prolonged Cr(VI) exposure, while Rad51C foci formation was suppressed. These results suggest that particulate Cr(VI), a major chemical carcinogen, inhibits HR repair by targeting Rad51, causing DNA double strand breaks to be repaired by a low fidelity, Rad51-independent repair pathway. These results further enhance our understanding of the underlying mechanism of Cr(VI)-induced chromosome instability and thus, carcinogenesis.
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Affiliation(s)
- Cynthia L Browning
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| | - Qin Qin
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Rohit Prakash
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Fabio Vanoli
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Maria Jasin
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - John Pierce Wise
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
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62
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Chemla YR. High‐resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins. Biopolymers 2016; 105:704-14. [DOI: 10.1002/bip.22880] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Quantitative BiologyUniversity of IllinoisUrbana‐Champaign
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63
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Zhang L, Rajendram M, Weibel DB, Yethiraj A, Cui Q. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers. J Phys Chem B 2016; 120:8424-37. [PMID: 27095675 DOI: 10.1021/acs.jpcb.6b02164] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe a computational and experimental approach for probing the binding properties of the RecA protein at the surface of anionic membranes. Fluorescence measurements indicate that RecA behaves differently when bound to phosphatidylglycerol (PG)- and cardiolipin (CL)-containing liposomes. We use a multistage computational protocol that integrates an implicit membrane/solvent model, the highly mobile mimetic membrane model, and the full atomistic membrane model to study how different anionic lipids perturb RecA binding to the membrane. With anionic lipids studied here, the binding interface involves three key regions: the N-terminal helix, the DNA binding loop L2, and the M-M7 region. The nature of binding involves both electrostatic interactions between cationic protein residues and lipid polar/charged groups and insertion of hydrophobic residues. The L2 loop contributes more to membrane insertion than the N-terminal helix. More subtle aspects of RecA-membrane interaction are influenced by specific properties of anionic lipids. Ionic hydrogen bonds between the carboxylate group in phosphatidylserine and several lysine residues in the C-terminal region of RecA stabilize the parallel (∥) binding orientation, which is not locally stable on PG- and CL-containing membranes despite similarity in the overall charge density. Lipid packing defects, which are more prevalent in the presence of conical lipids, are observed to enhance the insertion depth of hydrophobic motifs. The computational finding that RecA binds in a similar orientation to PG- and CL-containing membranes is consistent with the fact that PG alone is sufficient to induce RecA polar localization, although CL might be more effective because of its tighter binding to RecA. The different fluorescence behaviors of RecA upon binding to PG- and CL-containing liposomes is likely due to the different structures and flexibility of the C-terminal region of RecA when it binds to different anionic phospholipids.
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Affiliation(s)
- Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Manohary Rajendram
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Douglas B Weibel
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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64
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Song D, Graham TGW, Loparo JJ. A general approach to visualize protein binding and DNA conformation without protein labelling. Nat Commun 2016; 7:10976. [PMID: 26952553 PMCID: PMC4786781 DOI: 10.1038/ncomms10976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/08/2016] [Indexed: 01/29/2023] Open
Abstract
Single-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein–DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein–DNA interactions. Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation.
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Affiliation(s)
- Dan Song
- Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
| | - Thomas G W Graham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
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65
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Friedrich SM, Zec HC, Wang TH. Analysis of single nucleic acid molecules in micro- and nano-fluidics. LAB ON A CHIP 2016; 16:790-811. [PMID: 26818700 PMCID: PMC4767527 DOI: 10.1039/c5lc01294e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.
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Affiliation(s)
- Sarah M Friedrich
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Helena C Zec
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA. and Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
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Schay G, Borka B, Kernya L, Bulyáki É, Kardos J, Fekete M, Fidy J. Without Binding ATP, Human Rad51 Does Not Form Helical Filaments on ssDNA. J Phys Chem B 2016; 120:2165-78. [PMID: 26890079 DOI: 10.1021/acs.jpcb.5b12220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Bálint Borka
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Linda Kernya
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Éva Bulyáki
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Pázmány P. sétány 1/C, Budapest H-1117, Hungary
| | - Melinda Fekete
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University , Tűzoltó utca 37-47, Budapest H-1094, Hungary
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Kowalczykowski SC. An Overview of the Molecular Mechanisms of Recombinational DNA Repair. Cold Spring Harb Perspect Biol 2015; 7:a016410. [PMID: 26525148 PMCID: PMC4632670 DOI: 10.1101/cshperspect.a016410] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for genomic integrity. It is a template-directed process that uses a second chromosomal copy (sister, daughter, or homolog) to ensure proper repair of broken chromosomes. The key steps of recombination are conserved from phage through human, and an overview of those steps is provided in this review. The first step is resection by helicases and nucleases to produce single-stranded DNA (ssDNA) that defines the homologous locus. The ssDNA is a scaffold for assembly of the RecA/RAD51 filament, which promotes the homology search. On finding homology, the nucleoprotein filament catalyzes exchange of DNA strands to form a joint molecule. Recombination is controlled by regulating the fate of both RecA/RAD51 filaments and DNA pairing intermediates. Finally, intermediates that mature into Holliday structures are disjoined by either nucleolytic resolution or topological dissolution.
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Affiliation(s)
- Stephen C Kowalczykowski
- Department of Microbiology & Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616
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