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Holliday junction

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https://www.readbyqxmd.com/read/28731332/tuning-the-cavity-size-and-chirality-of-self-assembling-3d-dna-crystals
#1
Chad R Simmons, Fei Zhang, Tara MacCulloch, Nour Eddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C Seeman, Hao Yan
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals, and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28645372/analysis-of-structure-selective-endonuclease-activities-from-yeast-and-human-extracts
#2
Joao Matos, Stephen C West
The efficient separation of two equal DNA masses to the daughter cells is an essential step in mitosis. This process is dependent upon the removal of any remaining recombination or replication intermediates that link sister chromatids, and a failure to resolve these intermediates leads to genome instability. Similarly, a failure to resolve meiotic recombination intermediates that link homologous chromosomes can cause chromosome nondisjunction and aneuploidy. Cleavage of these potentially toxic replication/recombination intermediates requires the Mus81 endonuclease, which is active upon flaps, forks, and more complex secondary structures in DNA such as Holliday junctions...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28642366/saccharomyces-cerevisiae-red1-protein-exhibits-nonhomologous-dna-end-joining-activity-and-potentiates-hop1-promoted-pairing-of-double-stranded-dna
#3
Rucha Kshirsagar, Indrajeet Ghodke, Kalappa Muniyappa
Elucidation of the function of synaptonemal complex (SC) in <Saccharomyces cerevisiae> has mainly focused on in vivo analysis of recombination-defective meiotic mutants. Consequently, significant gaps remain in the mechanistic understanding of the activities of different SC proteins and the functional relationships among them. S. cerevisiae Hop1 and Red1 are essential structural components of the SC axial/lateral elements. Previous studies have demonstrated that Hop1 is a structure-specific DNA-binding protein that exhibits high affinity for the Holliday junction, promotes DNA bridging, condensation and pairing between duplex DNA molecules...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28640495/control-of-mus81-nuclease-during-the-cell-cycle
#4
REVIEW
Boris Pfander, Joao Matos
DNA replication and homologous recombination rely on the formation of branched DNA structures that physically link chromosomes. Such DNA-based connections, which arise during S phase, are typically disengaged prior to entry into mitosis, in order to ensure proper chromosome segregation. Exceptions can, however, occur: replication stress, or elevated levels of DNA damage, may cause cells to enter mitosis with unfinished replication as well as carrying recombination intermediates, such as Holliday junctions. Hence, cells are equipped with pathways that recognize and process branched DNA structures, and evolved mechanisms to enhance their function when on the verge of undergoing cell division...
June 22, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28611731/the-genomic-architecture-of-novel-simulium-damnosum-wolbachia-prophage-sequence-elements-and-implications-for-onchocerciasis-epidemiology
#5
James L Crainey, Jacob Hurst, Poppy H L Lamberton, Robert A Cheke, Claire E Griffin, Michael D Wilson, Cláudia P Mendes de Araújo, María-Gloria Basáñez, Rory J Post
Research interest in Wolbachia is growing as new discoveries and technical advancements reveal the public health importance of both naturally occurring and artificial infections. Improved understanding of the Wolbachia bacteriophages (WOs) WOcauB2 and WOcauB3 [belonging to a sub-group of four WOs encoding serine recombinases group 1 (sr1WOs)], has enhanced the prospect of novel tools for the genetic manipulation of Wolbachia. The basic biology of sr1WOs, including host range and mode of genomic integration is, however, still poorly understood...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28553125/holliday-junction-recognizing-protein-promotes-cell-proliferation-and-correlates-with-unfavorable-clinical-outcome-of-hepatocellular-carcinoma
#6
Baohong Hu, Qianli Wang, Yueju Wang, Jian Chen, Peng Li, Mingyong Han
AIM: To investigate the expression and clinical significance of Holliday junction-recognizing protein (HJURP) in hepatocellular carcinoma (HCC). METHODS: In this study, we detected the expression of HJURP protein in samples of 164 patients with HCC, and based on this, we divided the patients into two cohorts: high expression of HJURP and low expression of HJURP. We analyzed the correlation between HJURP expression and the clinicopathological factors using chi-square test...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28532385/erratum-to-the-holliday-junction-resolvase-recu-is-required-for-chromosome-segregation-and-dna-damage-repair-in-staphylococcus-aureus
#7
Ana R Pereira, Patricia Reed, Helena Veiga, Mariana G Pinho
No abstract text is available yet for this article.
May 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28527403/interplay-between-bacillus-subtilis-recd2-and-the-recg-or-ruvab-helicase-in-recombinational-repair
#8
Rubén Torres, Hector Romero, Violeta Rodríguez-Cerrato, Juan C Alonso
Bacillus subtilis AddAB, RecS, RecQ, PcrA, HelD, DinG, RecG, RuvAB, PriA and RecD2 are genuine recombinational repair enzymes, but the biological role of RecD2 is poorly defined. A ΔrecD2 mutation sensitizes cells to DNA-damaging agents that stall or collapse replication forks. We found that this ΔrecD2 mutation impaired growth, and that a mutation in the pcrA gene (pcrA596) relieved this phenotype. The ΔrecD2 mutation was not epistatic to ΔaddAB, ΔrecQ, ΔrecS, ΔhelD, pcrA596 and ΔdinG, but epistatic to recA...
May 12, 2017: DNA Repair
https://www.readbyqxmd.com/read/28511132/activity-and-in-vivo-dynamics-of-bacillus-subtilis-disa-are-affected-by-rada-sms-and-by-holliday-junction-processing-proteins
#9
Carolina Gándara, Daniella K C de Lucena, Rubén Torres, Ester Serrano, Stephan Altenburger, Peter L Graumann, Juan C Alonso
Bacillus subtilis c-di-AMP synthase DisA and RecA-related RadA/Sms are involved in the repair of DNA damage in exponentially growing cells. We provide genetic evidence that DisA or RadA/Sms is epistatic to the branch migration translocase (BMT) RecG and the Holliday junction (HJ) resolvase RecU in response to DNA damage. We provide genetic evidence damage. Functional DisA-YFP formed dynamic foci in exponentially growing cells, which moved through the nucleoids at a speed compatible with a DNA-scanning mode...
May 5, 2017: DNA Repair
https://www.readbyqxmd.com/read/28505149/distinct-dna-binding-surfaces-in-the-atpase-and-linker-domains-of-mutl%C3%AE-determine-its-substrate-specificities-and-exert-separable-functions-in-meiotic-recombination-and-mismatch-repair
#10
Corentin Claeys Bouuaert, Scott Keeney
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA-binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28495749/holliday-junction-resolvases-mediate-chloroplast-nucleoid-segregation
#11
Yusuke Kobayashi, Osami Misumi, Masaki Odahara, Kota Ishibashi, Masafumi Hirono, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hiroshi Iwasaki, Tsuneyoshi Kuroiwa, Toshiharu Shikanai, Yoshiki Nishimura
Holliday junctions, four-stranded DNA structures formed during homologous recombination, are disentangled by resolvases that have been found in prokaryotes and eukaryotes but not in plant organelles. Here, we identify monokaryotic chloroplast 1 (MOC1) as a Holliday junction resolvase in chloroplasts by analyzing a green alga Chlamydomonas reinhardtii mutant defective in chloroplast nucleoid (DNA-protein complex) segregation. MOC1 is structurally similar to a bacterial Holliday junction resolvase, resistance to ultraviolet (Ruv) C, and genetically conserved among green plants...
May 12, 2017: Science
https://www.readbyqxmd.com/read/28484802/tree-hierarchy-of-dna-and-distribution-of-holliday-junctions
#12
U A Rozikov
We define a DNA as a sequence of [Formula: see text]'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy has property that each vertex of the Cayley tree belongs only to one of DNA. Then we give a model (energy, Hamiltonian) of this set of DNAs by an analogue of Ising model with three spin values (considered as DNA base pairs) on a set of admissible configurations...
May 8, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28453523/the-mismatch-repair-and-meiotic-recombination-endonuclease-mlh1-mlh3-is-activated-by-polymer-formation-and-can-cleave-dna-substrates-in-trans
#13
Carol M Manhart, Xiaodan Ni, Martin A White, Joaquin Ortega, Jennifer A Surtees, Eric Alani
Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28400564/a-novel-4-arm-dna-rna-nanoconstruct-triggering-rapid-apoptosis-of-triple-negative-breast-cancer-cells-within-24%C3%A2-hours
#14
Joline Tung, Lih Shin Tew, Yuan-Man Hsu, Yit Lung Khung
Measuring at ~30 nm, a fully customizable holliday junction DNA nanoconstruct, was designed to simultaneously carry three unmodified SiRNA strands for apoptosis gene knockout in cancer cells without any assistance from commercial transfection kits. In brief, a holliday junction structure was intelligently designed to present one arm with a cell targeting aptamer (AS1411) while the remaining three arms to carry different SiRNA strands by means of DNA/RNA duplex for inducing apoptosis in cancer cells. By carrying the three SiRNA strands (AKT, MDM2 and Survivin) into triple negative breast MDA-MB-231 cancer cells, cell number had reduced by up to ~82% within 24 hours solely from one single administration of 32 picomoles...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393832/structural-insights-into-pot1-tpp1-interaction-and-pot1-c-terminal-mutations-in-human-cancer
#15
Cong Chen, Peili Gu, Jian Wu, Xianyun Chen, Shuangshuang Niu, Hong Sun, Lijie Wu, Na Li, Junhui Peng, Shaohua Shi, Cuiying Fan, Min Huang, Catherine C L Wong, Qingguo Gong, Chandan Kumar-Sinha, Rongguang Zhang, Lajos Pusztai, Rekha Rai, Sandy Chang, Ming Lei
Mammalian shelterin proteins POT1 and TPP1 form a stable heterodimer that protects chromosome ends and regulates telomerase-mediated telomere extension. However, how POT1 interacts with TPP1 remains unknown. Here we present the crystal structure of the C-terminal portion of human POT1 (POT1C) complexed with the POT1-binding motif of TPP1. The structure shows that POT1C contains two domains, a third OB fold and a Holliday junction resolvase-like domain. Both domains are essential for binding to TPP1. Notably, unlike the heart-shaped structure of ciliated protozoan Oxytricha nova TEBPα-β complex, POT1-TPP1 adopts an elongated V-shaped conformation...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28386965/perioperative-chemotherapy-versus-postoperative-chemoradiotherapy-in-patients-with-resectable-gastric-gastroesophageal-junction-adenocarcinomas-a-survival-analysis-of-5058-patients
#16
Timothy L Fitzgerald, Jimmy T Efird, Nelly Bellamy, Suzanne M Russo, Charulata Jindal, Catalina Mosquera, Elizabeth G Holliday, Tithi Biswas
BACKGROUND: Both perioperative chemotherapy (PECT) and postoperative chemoradiotherapy (POCRT) have a significant survival advantage over surgery alone for the treatment of patients with gastric cancer. However, to the best of our knowledge, these regimens have not been compared in a randomized clinical trial. The purpose of the current observational study was to compare overall survival among patients receiving PECT versus POCRT for the treatment of gastric/gastroesophageal junction (GEJ) adenocarcinomas...
April 6, 2017: Cancer
https://www.readbyqxmd.com/read/28369583/substrate-preference-of-gen-endonucleases-highlights-the-importance-of-branched-structures-as-dna-damage-repair-intermediates
#17
Stephanie P Bellendir, Danielle J Rognstad, Lydia P Morris, Grzegorz Zapotoczny, William G Walton, Matthew R Redinbo, Dale A Ramsden, Jeff Sekelsky, Dorothy A Erie
Human GEN1 and yeast Yen1 are endonucleases with the ability to cleave Holliday junctions (HJs), which are proposed intermediates in recombination. In vivo, GEN1 and Yen1 function secondarily to Mus81, which has weak activity on intact HJs. We show that the genetic relationship is reversed in Drosophila, with Gen mutants having more severe defects than mus81 mutants. In vitro, DmGen, like HsGEN1, efficiently cleaves HJs, 5΄ flaps, splayed arms, and replication fork structures. We find that the cleavage rates for 5΄ flaps are significantly higher than those for HJs for both DmGen and HsGEN1, even in vast excess of enzyme over substrate...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28357386/a-new-role-for-holliday-junction-resolvase-yen1-in-processing-dna-replication-intermediates-exposes-dna2-as-an-accessory-replicative-helicase
#18
COMMENT
Benoît Falquet, Ulrich Rass
DNA replication is mediated by a multi-protein complex known as the replisome. With the hexameric MCM (minichromosome maintenance) replicative helicase at its core, the replisome splits the parental DNA strands, forming replication forks (RFs), where it catalyses coupled leading and lagging strand DNA synthesis. While replication is a highly effective process, intrinsic and oncogene-induced replication stress impedes the progression of replisomes along chromosomes. As a consequence, RFs stall, arrest, and collapse, jeopardizing genome stability...
January 2, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28356341/essential-role-for-centromeric-factors-following-p53-loss-and-oncogenic-transformation
#19
Dan Filipescu, Monica Naughtin, Katrina Podsypanina, Vincent Lejour, Laurence Wilson, Zachary A Gurard-Levin, Guillermo A Orsi, Iva Simeonova, Eleonore Toufektchan, Laura D Attardi, Franck Toledo, Geneviève Almouzni
In mammals, centromere definition involves the histone variant CENP-A (centromere protein A), deposited by its chaperone, HJURP (Holliday junction recognition protein). Alterations in this process impair chromosome segregation and genome stability, which are also compromised by p53 inactivation in cancer. Here we found that CENP-A and HJURP are transcriptionally up-regulated in p53-null human tumors. Using an established mouse embryonic fibroblast (MEF) model combining p53 inactivation with E1A or HRas-V12 oncogene expression, we reproduced a similar up-regulation of HJURP and CENP-A...
March 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28327556/control-of-structure-specific-endonucleases-to-maintain-genome-stability
#20
REVIEW
Pierre-Marie Dehé, Pierre-Henri L Gaillard
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress...
May 2017: Nature Reviews. Molecular Cell Biology
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