The Experts below are selected from a list of 306 Experts worldwide ranked by ideXlab platform
Stephen C. Kowalczykowski - One of the best experts on this subject based on the ideXlab platform.
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the reca binding locus of recbcd is a general domain for recruitment of DNA Strand exchange proteins
Molecular Cell, 2006Co-Authors: Maria Spies, Stephen C. KowalczykowskiAbstract:RecBCD enzyme facilitates loading of RecA protein onto ssDNA produced by its helicase/nuclease activity. This process is essential for RecBCD-mediated homologous recombination. Here, we establish that the C-terminal nuclease domain of the RecB subunit (RecBnuc) forms stable complexes with RecA. Interestingly, RecBnuc also interacts with and loads noncognate DNA Strand exchange proteins. Interaction is with a conserved element of the RecA-fold, but because the binding to noncognate proteins decreases in a phylogenetically consistent way, species-specific interactions are also present. RecBnuc does not impede activities of RecA that are important to DNA Strand exchange, consistent with its role in targeting of RecA. Modeling predicts the interaction interface for the RecA-RecBCD complex. Because a similar interface is involved in the binding of human Rad51 to the conserved BRC repeat of BRCA2 protein, the RecB-domain may be one of several structural domains that interact with and recruit DNA Strand exchange proteins to DNA.
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DNA Strand EXCHANGE PROTEINS: A BIOCHEMICAL AND PHYSICAL COMPARISON
Frontiers in Bioscience, 1998Co-Authors: Piero R. Bianco, Robert B. Tracy, Stephen C. KowalczykowskiAbstract:Homologous genetic recombination is an essential biological process that involves the pairing and exchange of DNA between two homologous chromosomes or DNA molecules. It is of fundamental importance to the preservation of genomic integrity, the production of genetic diversity, and the proper segregation of chromosomes. In Escherichia coli, the RecA protein is essential to recombination, and biochemical analysis demonstrates that it is responsible for the crucial steps of homologous pairing and DNA Strand exchange. The presence of RecA-like proteins, or their functional equivalents, in bacteriophage, other eubacteria, archaea, and eukaryotes, confirms that the mechanism of homologous pairing and DNA Strand exchange is conserved throughout all forms of life. This review focuses on the biochemical and physical characteristics of DNA Strand exchange proteins from three diverse organisms: RecA protein from E. coli, UvsX protein from Bacteriophage T4, and RAD51 protein from Saccharomyces cerevisiae.
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The function of the secondary DNA-binding site of RecA protein during DNA Strand exchange.
The EMBO Journal, 1998Co-Authors: Alexander V. Mazin, Stephen C. KowalczykowskiAbstract:RecA protein features two distinct DNA-binding sites. During DNA Strand exchange, the primary site binds to single-Stranded DNA (ssDNA), forming the helical RecA nucleoprotein filament. The weaker secondary site binds double-Stranded DNA (dsDNA) during the homology search process. Here we demonstrate that this site has a second important function. It binds the ssDNA Strand that is displaced from homologous duplex DNA during DNA Strand exchange, stabilizing the initial heteroduplex DNA product. Although the high affinity of the secondary site for ssDNA is essential for DNA Strand exchange, it renders DNA Strand exchange sensitive to an excess of ssDNA which competes with dsDNA for binding. We further demonstrate that single-Stranded DNA-binding protein can sequester ssDNA, preventing its binding to the secondary site and thereby assisting at two levels: it averts the inhibition caused by an excess of ssDNA and prevents the reversal of DNA Strand exchange by removing the displaced Strand from the secondary site.
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rad52 protein stimulates DNA Strand exchange by rad51 and replication protein a
Nature, 1998Co-Authors: Tomohiko Sugiyama, Elena Zaitseva, Stephen C. KowalczykowskiAbstract:The generation of a double-Strand break in the Saccharomyces cerevisiae genome is a potentially catastrophic event that can induce cell-cycle arrest or ultimately result in loss of cell viability.The repair of such lesions is strongly dependent on proteins encoded by the RAD52 epistasis group of genes (RAD50-55, RAD57, MRE11, XRS2)1,2, as well as the RFA13,4 and RAD59 genes5. rad52 mutants exhibit the most severe phenotypic defects in double-Strand break repair2, but almost nothing is known about the biochemical role of Rad52 protein. Rad51 protein promotes DNA Strand exchange6,7,8 and acts similarly to RecA protein9. Yeast Rad52 protein interacts with Rad51 protein10,11, binds single-Stranded DNA and stimulates annealing of complementary single-Stranded DNA12. We find that Rad52 protein stimulates DNA Strand exchange by targeting Rad51 protein to a complex of replication protein A (RPA) with single-Stranded DNA. Rad52 protein affects an early step in the reaction, presynaptic filament formation, by overcoming the inhibitory effects of the competitor, RPA. Furthermore, stimulation is dependent on the concerted action of both Rad51 protein and RPA, implying that specific protein–protein interactions between Rad52 protein, Rad51 protein and RPA are required.
Ilko Bald - One of the best experts on this subject based on the ideXlab platform.
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Vacuum-uv and low-energy electron-Induced DNA Strand breaks - influence of the DNA sequence and substrate
ChemPhysChem, 2019Co-Authors: Stefanie Vogel, Aleksandar R. Milosavljević, Alexandre Giuliani, Kenny Ebel, Robin M. Schuermann, Christian Heck, Till Meiling, Ilko BaldAbstract:DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA Strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA Strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA Strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance Strand break cross sections. Atomic force microscopy is used to visualize Strand breaks on DNA origami platforms and to determine absolute values for the Strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar Strand break cross sections in the range of 1.7-2.3x10(-16) cm(2). The Strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies
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Using DNA origami nanostructures to determine absolute cross sections for uv photon-induced DNA Strand breakage
Journal of Physical Chemistry Letters, 2015Co-Authors: Stefanie Vogel, Jenny Rackwitz, Robin Schuerman, Julia Prinz, Aleksandar R. Milosavljević, Matthieu Refregiers, Alexandre Giuliani, Ilko BaldAbstract:We have characterized ultraviolet (UV) photon-induced DNA Strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single Strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA Strand breaks. Oligonudeotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA Strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for Strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA Strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold Strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.
Stefanie Vogel - One of the best experts on this subject based on the ideXlab platform.
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Vacuum-uv and low-energy electron-Induced DNA Strand breaks - influence of the DNA sequence and substrate
ChemPhysChem, 2019Co-Authors: Stefanie Vogel, Aleksandar R. Milosavljević, Alexandre Giuliani, Kenny Ebel, Robin M. Schuermann, Christian Heck, Till Meiling, Ilko BaldAbstract:DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA Strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA Strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA Strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance Strand break cross sections. Atomic force microscopy is used to visualize Strand breaks on DNA origami platforms and to determine absolute values for the Strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar Strand break cross sections in the range of 1.7-2.3x10(-16) cm(2). The Strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies
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Using DNA origami nanostructures to determine absolute cross sections for uv photon-induced DNA Strand breakage
Journal of Physical Chemistry Letters, 2015Co-Authors: Stefanie Vogel, Jenny Rackwitz, Robin Schuerman, Julia Prinz, Aleksandar R. Milosavljević, Matthieu Refregiers, Alexandre Giuliani, Ilko BaldAbstract:We have characterized ultraviolet (UV) photon-induced DNA Strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single Strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA Strand breaks. Oligonudeotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA Strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for Strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA Strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold Strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.
Seo Eun-kyoung - One of the best experts on this subject based on the ideXlab platform.
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A DNA Strand-nicking principle of a higher plant,caesalpinia sappan
Archives of Pharmacal Research, 2003Co-Authors: Mar Woongchon, Lee Hyun-tai, Je Kang-hoon, Choi Hye-young, Seo Eun-kyoungAbstract:To find anticancer agents from higher plants, DNA Strand-scission assay method was employed for bioassay-guided fractionation as well as for screening the crude extracts. During the screening, an ethyl acetate extracts of the heartwood of Caesalpinia sappan L. (Leguminosae) exhibited potent DNA Strand-scission activity. Therefore, the ethyl acetate extracts of the dried heartwood of C. sappan was subjected to the bioassay-guided fractionation, which led to the isolation of a known compound, brazilin ( 1 ) as the active constituent. In addition, caesalpine J ( 2 ) was also isolated as an inactive constituent.
Maria Spies - One of the best experts on this subject based on the ideXlab platform.
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the reca binding locus of recbcd is a general domain for recruitment of DNA Strand exchange proteins
Molecular Cell, 2006Co-Authors: Maria Spies, Stephen C. KowalczykowskiAbstract:RecBCD enzyme facilitates loading of RecA protein onto ssDNA produced by its helicase/nuclease activity. This process is essential for RecBCD-mediated homologous recombination. Here, we establish that the C-terminal nuclease domain of the RecB subunit (RecBnuc) forms stable complexes with RecA. Interestingly, RecBnuc also interacts with and loads noncognate DNA Strand exchange proteins. Interaction is with a conserved element of the RecA-fold, but because the binding to noncognate proteins decreases in a phylogenetically consistent way, species-specific interactions are also present. RecBnuc does not impede activities of RecA that are important to DNA Strand exchange, consistent with its role in targeting of RecA. Modeling predicts the interaction interface for the RecA-RecBCD complex. Because a similar interface is involved in the binding of human Rad51 to the conserved BRC repeat of BRCA2 protein, the RecB-domain may be one of several structural domains that interact with and recruit DNA Strand exchange proteins to DNA.