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Protein sliding dna

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https://www.readbyqxmd.com/read/29764123/the-folding-pathways-and-thermodynamics-of-semiflexible-polymers
#1
Jing Wu, Chenqian Cheng, Gaoyuan Liu, Ping Zhang, Tao Chen
Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm...
May 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29712753/birth-evolution-and-transmission-of-satellite-free-mammalian-centromeric-domains
#2
Solomon G Nergadze, Francesca M Piras, Riccardo Gamba, Marco Corbo, Federico Cerutti, Joseph G W McCarter, Eleonora Cappelletti, Francesco Gozzo, Rebecca M Harman, Douglas F Antczak, Donald Miller, Maren Scharfe, Giulio Pavesi, Elena Raimondi, Kevin F Sullivan, Elena Giulotto
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Equus caballus Chromosome 11. Here, we investigated the satellite-free centromeres of Equus asinus by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31)...
April 30, 2018: Genome Research
https://www.readbyqxmd.com/read/29700825/synthetic-polymers-as-substrates-for-a-dna-sliding-clamp-protein
#3
S F M van Dongen, J Clerx, O I van den Boomen, M Pervaiz, M A Trakselis, T Ritschel, L Schoonen, D C Schoenmakers, R J M Nolte
The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Experiments aimed at verifying these interactions are presented and discussed...
April 26, 2018: Biopolymers
https://www.readbyqxmd.com/read/29643509/structural-basis-for-atp-dependent-chromatin-remodelling-by-the-ino80-complex
#4
Sebastian Eustermann, Kevin Schall, Dirk Kostrewa, Kristina Lakomek, Mike Strauss, Manuela Moldt, Karl-Peter Hopfner
In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers1-3 such as the 15-subunit INO80 complex 4 . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA5-8 . The structures and mechanisms of these remodelling reactions are currently unknown...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29643506/structure-and-regulation-of-the-human-ino80-nucleosome-complex
#5
Rafael Ayala, Oliver Willhoft, Ricardo J Aramayo, Martin Wilkinson, Elizabeth A McCormack, Lorraine Ocloo, Dale B Wigley, Xiaodong Zhang
Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines 1 . Biochemical studies2-4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes5-7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29584872/sliding-of-a-single-lac-repressor-protein-along-dna-is-tuned-by-dna-sequence-and-molecular-switching
#6
Alessia Tempestini, Carina Monico, Lucia Gardini, Francesco Vanzi, Francesco S Pavone, Marco Capitanio
In any living cell, genome maintenance is carried out by DNA-binding proteins that recognize specific sequences among a vast amount of DNA. This includes fundamental processes such as DNA replication, DNA repair, and gene expression and regulation. Here, we study the mechanism of DNA target search by a single lac repressor protein (LacI) with ultrafast force-clamp spectroscopy, a sub-millisecond and few base-pair resolution technique based on laser tweezers. We measure 1D-diffusion of proteins on DNA at physiological salt concentrations with 20 bp resolution and find that sliding of LacI along DNA is sequence dependent...
March 23, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29529386/cell-type-specific-quantification-of-telomere-length-and-dna-double-strand-breaks-in-individual-lung-cells-by-fluorescence-in-situ-hybridization-and-fluorescent-immunohistochemistry
#7
Aernoud A van Batenburg, Karin M Kazemier, Ton Peeters, Matthijs F M van Oosterhout, Joanne J van der Vis, Jan C Grutters, Roel Goldschmeding, Coline H M van Moorsel
Telomeres are small repetitive DNA sequences at the ends of chromosomes which act as a buffer in age-dependent DNA shortening. Insufficient telomere repeats will be recognized as double-strand breaks. Presently, it is becoming more evident that telomere attrition, whether or not caused by mutations in telomere maintenance genes, plays an important role in many inflammatory and age-associated diseases. In this report, a method to (semi)quantitatively assess telomere length and DNA double-strand breaks in formalin-fixed paraffin-embedded (FFPE) tissue is described...
March 1, 2018: Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society
https://www.readbyqxmd.com/read/29529283/investigation-of-sliding-dna-clamp-dynamics-by-single-molecule-fluorescence-mass-spectrometry-and-structure-based-modeling
#8
Varun V Gadkari, Sophie R Harvey, Austin T Raper, Wen-Ting Chu, Jin Wang, Vicki H Wysocki, Zucai Suo
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon...
February 26, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29501294/human-beta-defensin-1-is-involved-in-the-susceptibility-to-adeno-tonsillar-hypertrophy
#9
Luisa Zupin, Fulvio Celsi, Martina Bresciani, Eva Orzan, Domenico Leonardo Grasso, Sergio Crovella
INTRODUCTION: Innate immunity molecules are known to play a pivotal role in the homeostasis of the oral mucosa, permitting the presence of commensal microflora and, at the same time, providing a first line of defense against pathogens attempting to invade the oral cavity. Tonsils represent the local immune tissue in oral cavity, being able to provide a non-specific response to pathogens; however, in the presence of microbes or foreign materials present in the mouth tonsils could became infected and develop chronic inflammation, thus leading to hypertrophy...
April 2018: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/29499038/crystal-structures-of-pcna-mutant-proteins-defective-in-gene-silencing-suggest-a-novel-interaction-site-on-the-front-face-of-the-pcna-ring
#10
Christine M Kondratick, Jacob M Litman, Kurt V Shaffer, M Todd Washington, Lynne M Dieckman
Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro...
2018: PloS One
https://www.readbyqxmd.com/read/29339834/use-of-multicolor-fluorescence-in-situ-hybridization-to-detect-deletions-in-clinical-tissue-sections
#11
REVIEW
Maisa Yoshimoto, Olga Ludkovski, Jennifer Good, Ciro Pereira, Robert J Gooding, Jean McGowan-Jordan, Alexander Boag, Andrew Evans, Ming-Sound Tsao, Paulo Nuin, Jeremy A Squire
A variety of laboratory methods are available for the detection of deletions of tumor suppressor genes and losses of their proteins. The clinical utility of fluorescence in situ hybridization (FISH) for the identification of deletions of tumor suppressor genes has previously been limited by difficulties in the interpretation of FISH signal patterns. The first deletion FISH assays using formalin-fixed paraffin-embedded tissue sections had to deal with a significant background level of signal losses affecting nuclei that are truncated by the cutting process of slide preparation...
January 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29323271/cryo-em-structures-of-the-human-ino80-chromatin-remodeling-complex
#12
Ricardo J Aramayo, Oliver Willhoft, Rafael Ayala, Rohan Bythell-Douglas, Dale B Wigley, Xiaodong Zhang
Access to chromatin for processes such as transcription and DNA repair requires the sliding of nucleosomes along DNA. This process is aided by chromatin-remodeling complexes, such as the multisubunit INO80 chromatin-remodeling complex. Here we present cryo-EM structures of the active core complex of human INO80 at 9.6 Å, with portions at 4.1-Å resolution, and reconstructions of combinations of subunits. Together, these structures reveal the architecture of the INO80 complex, including Ino80 and actin-related proteins, which is assembled around a single RUVBL1 (Tip49a) and RUVBL2 (Tip49b) AAA+ heterohexamer...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29307468/high-free-energy-barrier-of-1d-diffusion-along-dna-by-architectural-dna-binding-proteins
#13
Kiyoto Kamagata, Eriko Mano, Kana Ouchi, Saori Kanbayashi, Reid C Johnson
Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis...
March 2, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29286440/preparation-of-meiotic-chromosome-spreads-from-mouse-spermatocytes
#14
Ferdusy Dia, Tierra Strange, Jenny Liang, Jacob Hamilton, Karen M Berkowitz
Mammalian meiosis is a dynamic developmental process that occurs in germ cells and can be studied and characterized. Using a method to spread nuclei on the surface of slides (rather than dropping them from a height), we demonstrate an optimized technique on mouse spermatocytes that was first described in 1997. This method is widely used in laboratories to study mammalian meiosis because it yields a plethora of high quality nuclei undergoing substages of prophase I. Seminiferous tubules are first placed in a hypotonic solution to swell spermatocytes...
November 22, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29278803/sorption-of-nucleic-acids-and-proteins-on-polyaniline-and-polyaramide-nano-coatings-as-studied-by-spectral-correlation-interferometry-in-a-real-time-mode
#15
Elena Yagudaeva, Dmitry Zybin, Alexander Vikhrov, Anna Prostyakova, Anatoly Ischenko, Vitaly Zubov, Dmitry Kapustin
Polyaniline (PANI) and polyaramides deposited on the surfaces of glass slides and particulate silica were studied as adsorbents of nucleic acids and proteins by flow-through spectral correlation interferometry and solid-state extraction using spin-cartridges. Double stranded DNA from E. coli as well as pepsin, bovine serum albumin and lysozyme were the analytes studied in contact with the polymer nanolayers in phosphate buffer solution, pH 7.2. None of the coated glass slides could bind the DNA, which passed them practically without adsorption...
March 1, 2018: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29202219/direct-single-molecule-observation-of-mode-and-geometry-of-reca-mediated-homology-search
#16
Andrew J Lee, Masayuki Endo, Jamie K Hobbs, Christoph Wälti
Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging...
January 23, 2018: ACS Nano
https://www.readbyqxmd.com/read/29118994/interval-mapping-for-red-green-skin-color-in-asian-pears-using-a-modified-qtl-seq-method
#17
Huabai Xue, Ting Shi, Fangfang Wang, Huangkai Zhou, Jian Yang, Long Wang, Suke Wang, Yanli Su, Zhen Zhang, Yushan Qiao, Xiugen Li
Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29095607/how-does-the-proliferating-cell-nuclear-antigen-modulate-binding-specificity-to-multiple-partner-proteins
#18
Hubert Li, Manbir Sandhu, Linda H Malkas, Robert J Hickey, Nagarajan Vaidehi
Proliferating cell nuclear antigen (PCNA) is a member of the family of sliding clamp proteins that serves as a clamp during DNA repair, DNA replication, cell cycle control, and multiple forms of chromatin modification. PCNA functions as a homotrimer and complexes with multiple proteins in order to carry out each of these varied functions. PCNA binds to different partner proteins in the same region of its structure, called the " interdomain connecting loop", but with different affinities. This interdomain connecting loop is an intrinsically disordered region that takes different conformations when binding to different partner proteins...
December 26, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29082290/-in-vitro-assays-for-eukaryotic-leading-lagging-strand-dna-replication
#19
Grant Schauer, Jeff Finkelstein, Mike O'Donnell
The eukaryotic replisome is a multiprotein complex that duplicates DNA. The replisome is sculpted to couple continuous leading strand synthesis with discontinuous lagging strand synthesis, primarily carried out by DNA polymerases ε and δ, respectively, along with helicases, polymerase α-primase, DNA sliding clamps, clamp loaders and many other proteins. We have previously established the mechanisms by which the polymerases ε and δ are targeted to their 'correct' strands, as well as quality control mechanisms that evict polymerases when they associate with an 'incorrect' strand...
September 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29081827/study-of-genetic-association-with-dcdc2-and-developmental-dyslexia-in-hong-kong-chinese-children
#20
Mary M Y Waye, Lim K Poo, Connie S-H Ho
BACKGROUND: Doublecortin domain-containing 2 (DCDC2) is a doublecortin domain-containing gene family member and the doublecortin domain has been demonstrated to bind to tubulin and enhance microtubule polymerization. It has been associated with developmental dyslexia and this protein family member is thought to function in neuronal migration where it may affect the signaling of primary cilia. OBJECTIVES: The objective of the study is to find out if there is any association of genetic variants of DCDC2 with developmental dyslexia in Chinese children from Hong Kong...
2017: Clinical Practice and Epidemiology in Mental Health: CP & EMH
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