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Holliday junction

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https://www.readbyqxmd.com/read/29767969/single-molecule-imaging-reveals-conformational-manipulation-of-holliday-junction-dna-by-the-junction-processing-protein-ruva
#1
Dalton Gibbs, Soma Dhakal
Interactions between DNA and motor proteins regulate nearly all biological functions of DNA such as gene expression, DNA replication and repair, and transcription. During the late stages of homologous recombination (HR), the Escherichia coli recombination machinery, RuvABC, resolves the four-way DNA motifs called Holliday junctions (HJs) that are formed during exchange of nucleotide sequences between two homologous duplex DNA. Although the formation of RuvA-HJ complex is known to be the first critical step in the RuvABC pathway, the mechanism for the binding interaction between RuvA and HJ has remained elusive...
May 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29743473/increased-expression-of-holliday-junction-recognizing-protein-hjurp-as-an-independent-prognostic-biomarker-in-advanced-stage-serous-ovarian-carcinoma
#2
Lin Li, Xiaoli Li, Qin Meng, Abdul Qadir Khan, Xiaomei Chen
BACKGROUND Advanced-stage serous ovarian carcinoma results in the majority of deaths from ovarian carcinoma. The histone chaperone, Holliday junction-recognizing protein (HJURP), binds with centromere protein-A (CENP-A) and its expression has been shown to be a prognostic biomarker in some cancers. The aim of this study was to investigate the role of HJURP expression in advanced-stage serous ovarian carcinoma. MATERIAL AND METHODS Ninety-eight patients with advanced-stage serous ovarian carcinoma, who had tumor tissue samples available, were studied...
May 10, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29742437/atp-binding-to-rad5-initiates-replication-fork-reversal-by-inducing-the-unwinding-of-the-leading-arm-and-the-formation-of-the-holliday-junction
#3
Soochul Shin, Kwangbeom Hyun, Jaehoon Kim, Sungchul Hohng
Replication fork reversal is one of the major pathways for reactivating stalled DNA replication. Many enzymes with replication fork reversal activity have DNA-unwinding activity as well, but none of the fork reversal enzymes in the SWI/SNF family shows a separate DNA-unwinding activity, raising the question of how they initiate the remodeling process. Here, we found ATP binding to Rad5 induces the unwinding of the leading arm of the replication fork and proximally positions the leading and lagging arms. This facilitates the spontaneous remodeling of the replication fork into a four-way junction...
May 8, 2018: Cell Reports
https://www.readbyqxmd.com/read/29644789/construction-of-holliday-junction-in-small-circular-dna-molecules-for-stable-motifs-and-two-dimensional-lattices
#4
Xin Guo, Xue-Mei Wang, Shuai Wei, Shou-Jun Xiao
Design rules for DNA nanotechnology have been mostly learnt from using linear single stranded (ss) DNAs as the source materials. For example, a typical DAO (Double crossover, Antiparallel, Odd half turns) tile for assembling two-dimensional (2D) lattices is built by only two linear ss-oligonucleotide scaffold strands, like two ropes making a square knot. We demonstrate here a new type of coupled DAO (cDAO) tiles and their 2D lattices using small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands...
April 12, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29625041/mechanistic-view-and-genetic-control-of-dna-recombination-during-meiosis
#5
Marie-Claude Marsolier-Kergoat, Md Muntaz Khan, Jonathan Schott, Xuan Zhu, Bertrand Llorente
Meiotic recombination is essential for fertility and allelic shuffling. Canonical recombination models fail to capture the observed complexity of meiotic recombinants. Here, by combining genome-wide meiotic heteroduplex DNA patterns with meiotic DNA double-strand break (DSB) sites, we show that part of this complexity results from frequent template switching during synthesis-dependent strand annealing that yields noncrossovers and from branch migration of double Holliday junction (dHJ)-containing intermediates that mainly yield crossovers...
April 5, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29604857/kinetic-analysis-of-single-molecule-fret-transitions-without-trajectories
#6
Lukas Schrangl, Janett Göhring, Gerhard J Schütz
Single molecule Förster resonance energy transfer (smFRET) is a popular tool to study biological systems that undergo topological transitions on the nanometer scale. smFRET experiments typically require recording of long smFRET trajectories and subsequent statistical analysis to extract parameters such as the states' lifetimes. Alternatively, analysis of probability distributions exploits the shapes of smFRET distributions at well chosen exposure times and hence works without the acquisition of time traces...
March 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29547221/new-tricks-for-old-dogs-improving-the-accuracy-of-biomolecular-force-fields-by-pair-specific-corrections-to-non-bonded-interactions
#7
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29483821/disruption-of-gen1-causes-congenital-anomalies-of-the-kidney-and-urinary-tract-in-mice
#8
Herui Wang, Chi Zhang, Xiaowen Wang, Yaru Lian, Bin Guo, Miao Han, Xiaoe Zhang, Xiaoting Zhu, Sixian Xu, Zengli Guo, Yunli Bi, Qian Shen, Xiang Wang, Jiaojiao Liu, Yuan Zhuang, Ting Ni, Hong Xu, Xiaohui Wu
Congenital anomalies of the kidney and urinary tract (CAKUT) are among the most common developmental defects in humans. Despite of several known CAKUT-related loci ( HNF1B , PAX2 , EYA1 , etc.), the genetic etiology of CAKUT remains to be elucidated for most patients. In this study, we report that disruption of the Holliday Junction resolvase gene Gen1 leads to renal agenesis, duplex kidney, hydronephrosis, and vesicoureteral reflux (VUR) in mice. GEN1 interacts with SIX1 and enhances the transcriptional activity of SIX1/EYA1, a key regulatory complex of the GDNF morphogen...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29471050/the-protein-protein-interactions-between-amsacta-moorei-entomopoxvirus-amev-protein-kinases-pks-and-all-viral-proteins
#9
Mehtap Danismazoglu, Remziye Nalcacioglu, Hacer Muratoglu, Zihni Demirbag
Entomopoxviruses are an important group of viruses infecting only insects. They belong to Poxviridae which infect both invertebrates and vertebrates, including humans. Protein kinases are known to have roles at virus morphogenesis, host selectivity, the regulation of cell division and apoptosis in some vertebrate poxviruses. In this study, 2 protein kinases (PKs) (AMV153 and AMV197) of Amsacta moorei entomopoxvirus (AMEV) were investigated for the interactions among 230 viral proteins using yeast two-hybrid system (Y2H)...
March 15, 2018: Virus Research
https://www.readbyqxmd.com/read/29458775/preparation-and-resolution-of-holliday-junction-dna-recombination-intermediates
#10
Rajvee Shah Punatar, Stephen C West
Holliday junctions provide a covalent link between recombining DNA molecules and need to be removed prior to chromosome segregation at mitosis. Defects in their resolution lead to mitotic catastrophe, characterized by the formation of DNA breaks and chromosome aberrations. Enzymes that resolve recombination intermediates have been identified in all forms of life, from bacteriophage, to bacteria, yeast, and humans. In higher eukaryotes, Holliday junctions are resolved by GEN1, a nuclease that is mechanistically similar to the prototypic resolvase Escherichia coli RuvC, and by the SMX trinuclease complex...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29458774/biochemical-and-structural-properties-of-fungal-holliday-junction-resolving-enzymes
#11
Yijin Liu, Alasdair Freeman, Anne-Cécile Déclais, Anton Gartner, David M J Lilley
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29458773/gen1-endonuclease-purification-and-nuclease-assays
#12
Ying Wai Chan, Stephen C West
Successful chromosome segregation depends on the timely removal of DNA recombination and replication intermediates that interlink sister chromatids. These intermediates are acted upon by structure-selective endonucleases that promote incisions close to the junction point. GEN1, a member of the Rad2/XPG endonuclease family, was identified on the basis of its ability to cleave Holliday junction recombination intermediates. Resolution occurs by a nick and counter-nick mechanism in strands that are symmetrically related across the junction point, leading to the formation of ligatable nicked duplex products...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29432282/phase-i-study-of-multiple-epitope-peptide-vaccination-in-patients-with-recurrent-or-persistent-cervical-cancer
#13
Kosei Hasegawa, Yuji Ikeda, Yuko Kunugi, Akira Kurosaki, Yuichi Imai, Shunsuke Kohyama, Shoji Nagao, Eito Kozawa, Koji Yoshida, Takuya Tsunoda, Yusuke Nakamura, Keiichi Fujiwara
Cancer immunotherapy has now been established as a leading standard therapeutic option in a subset of patients with cancer. In this study, we conducted a phase I dose-escalation trial using a mixture of 5 peptides to vaccinate cervical cancer patients with HLA-A*2402. The primary endpoints were safety and determination of a recommended vaccine dose, and the secondary endpoints were evaluations of immunologic responses and clinical efficacy. All patients had recurrent or persistent disease and had failed to respond to or were intolerant to prior standard chemotherapy...
May 2018: Journal of Immunotherapy
https://www.readbyqxmd.com/read/29420037/large-davydov-splitting-and-strong-fluorescence-suppression-an-investigation-of-exciton-delocalization-in-dna-templated-holliday-junction-dye-aggregates
#14
Brittany L Cannon, Lance K Patten, Donald L Kellis, Paul H Davis, Jeunghoon Lee, Elton Graugnard, Bernard Yurke, William B Knowlton
Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397...
March 1, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29389041/programmable-and-multifunctional-dna-based-materials-for-biomedical-applications
#15
REVIEW
Yuezhou Zhang, Jing Tu, Dongqing Wang, Haitao Zhu, Sajal Kumar Maity, Xiangmeng Qu, Bram Bogaert, Hao Pei, Hongbo Zhang
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures...
February 1, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29383368/direct-observation-of-the-external-force-mediated-conformational-dynamics-of-an-ihf-bound-holliday-junction
#16
Subhas C Bera, Tapas Paul, A N Sekar Iyengar, Padmaja P Mishra
We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0...
April 17, 2018: Faraday Discussions
https://www.readbyqxmd.com/read/29348327/genome-instability-as-a-consequence-of-defects-in-the-resolution-of-recombination-intermediates
#17
Stephen C West, Ying Wai Chan
The efficient processing of homologous recombination (HR) intermediates, which often contain four-way structures known as Holliday junctions (HJs), is required for proper chromosome segregation at mitosis. Eukaryotic cells possess three distinct pathways of resolution: (i) HJ dissolution mediated by BLM-topoisomerase IIIα-RMI1-RMI2 (BTR) complex, and HJ resolution catalyzed by either (ii) SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex) or (iii) GEN1. The BTR pathway acts at all times throughout the cell cycle, whereas the actions of SMX and GEN1 are restrained in S phase and become elevated late in the cell cycle to ensure the resolution of persistent recombination intermediates before mitotic division...
January 18, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29295984/rad54-n-terminal-domain-is-a-dna-sensor-that-couples-atp-hydrolysis-with-branch-migration-of-holliday-junctions
#18
Nadish Goyal, Matthew J Rossi, Olga M Mazina, Yong Chi, Robert L Moritz, Bruce E Clurman, Alexander V Mazin
In eukaryotes, RAD54 catalyzes branch migration (BM) of Holliday junctions, a basic process during DNA repair, replication, and recombination. RAD54 also stimulates RAD51 recombinase and has other activities. Here, we investigate the structural determinants for different RAD54 activities. We find that the RAD54 N-terminal domain (NTD) is responsible for initiation of BM through two coupled, but distinct steps; specific binding to Holliday junctions and RAD54 oligomerization. Furthermore, we find that the RAD54 oligomeric state can be controlled by NTD phosphorylation at S49, a CDK2 consensus site, which inhibits RAD54 oligomerization and, consequently, BM...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29290614/topoisomerase-3%C3%AE-is-required-for-decatenation-and-segregation-of-human-mtdna
#19
Thomas J Nicholls, Cristina A Nadalutti, Elisa Motori, Ewen W Sommerville, Gráinne S Gorman, Swaraj Basu, Emily Hoberg, Doug M Turnbull, Patrick F Chinnery, Nils-Göran Larsson, Erik Larsson, Maria Falkenberg, Robert W Taylor, Jack D Griffith, Claes M Gustafsson
How mtDNA replication is terminated and the newly formed genomes are separated remain unknown. We here demonstrate that the mitochondrial isoform of topoisomerase 3α (Top3α) fulfills this function, acting independently of its nuclear role as a component of the Holliday junction-resolving BLM-Top3α-RMI1-RMI2 (BTR) complex. Our data indicate that mtDNA replication termination occurs via a hemicatenane formed at the origin of H-strand replication and that Top3α is essential for resolving this structure. Decatenation is a prerequisite for separation of the segregating unit of mtDNA, the nucleoid, within the mitochondrial network...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29247687/genotypic-variations-between-wild-type-and-small-colony-variant-of-staphylococcus-aureus-in-prosthetic-valve-infectious-endocarditis-a-comparative-genomic-and-transcriptomic-analysis
#20
Hongbin Chen, Qi Wang, Yuyao Yin, Shuguang Li, Deng-Ke Niu, Hui Wang
Staphylococcus aureus small colony variants (SCVs) can cause persistent infections. However, the genomes and transcriptomes of S. aureus SCVs remain poorly understood. A pair of isogenic wild-type and SCV methicillin-resistant S. aureus (MRSA) strains (IE1 and IE2, respectively) were isolated from a patient with prosthetic valve infectious endocarditis. The SCV strain IE2 grew more slowly than the wild-type strain, and serum killing and mouse lethality assays revealed that the virulence of SCV strain IE2 was decreased...
December 13, 2017: International Journal of Antimicrobial Agents
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