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Protein sliding dna

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
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
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
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
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
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
Kiyoto Kamagata, Mano Eriko, 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...
January 4, 2018: Journal of Molecular Biology
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
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...
December 15, 2017: Colloids and Surfaces. B, Biointerfaces
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
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
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...
November 17, 2017: Journal of Chemical Information and Modeling
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
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
Joshua Lequieu, David C Schwartz, Juan J de Pablo
Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
Megan D Warner, Ishara F Azmi, Yanding Zhao, Sukhyun Kang, Stephen P Bell
In eukaryotes, DNA replication initiates from multiple origins of replication for timely genome duplication. These sites are selected by origin licensing, during which the core enzyme of the eukaryotic DNA replicative helicase, the Mcm2-7 (minichromosome maintenance) complex, is loaded at each origin. This origin licensing requires loading two Mcm2-7 helicases around origin DNA in a head-to-head orientation. Current models suggest that the origin recognition complex (ORC) and cell-division cycle 6 (Cdc6) proteins recognize and encircle origin DNA and assemble an Mcm2-7 double hexamer around adjacent double-stranded DNA...
October 26, 2017: Journal of Biological Chemistry
Heidi D Lehrke, Rondell P Graham, Robert R McWilliams, Dora M Lam-Himlin, Thomas C Smyrk, Sarah Jenkins, Haidong Dong, Lizhi Zhang
Objectives: Programmed death ligand 1 (PD-L1) expression in pancreatic ductal adenocarcinoma (PDA) has been described, but unselected PDAs have shown limited clinical responsiveness to anti-programmed death 1 (PD-1)/PD-L1 therapy. Methods: We studied 24 cases of undifferentiated pancreatic carcinoma (UPC) using immunohistochemistry for PD-L1 (E1L3N clone), CD3, CD20, CD68, and DNA mismatch repair proteins in this study. Slides were scored for extent of PD-L1 expression on tumor cells and tumor-infiltrating immune cells...
November 2, 2017: American Journal of Clinical Pathology
Manika Indrajit Singh, Vikas Jain
Protein folding process involves formation of transiently occurring intermediates that are difficult to isolate and characterize. It is both necessary and interesting to characterize the structural conformations adopted by these intermediates, also called molten globules (MG), to understand protein folding. Here, we investigated the equilibrium (un)folding intermediate state of T4 phage gene product 45 (gp45, also known as DNA polymerase processivity factor or sliding clamp) obtained during chemical denaturation...
October 17, 2017: Biophysical Journal
Xiakun Chu, Victor Muñoz
Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario...
November 1, 2017: Physical Chemistry Chemical Physics: PCCP
Tsu-Pei Chiu, Satyanarayan Rao, Richard S Mann, Barry Honig, Remo Rohs
Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data...
December 1, 2017: Nucleic Acids Research
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