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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28738244/dna-binding-and-unwinding-by-hel308-helicase-requires-dual-functions-of-a-winged-helix-domain
#1
Sarah J Northall, Ryan Buckley, Nathan Jones, J Carlos Penedo, Panos Soultanas, Edward L Bolt
Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities...
July 16, 2017: DNA Repair
https://www.readbyqxmd.com/read/28735897/radx-promotes-genome-stability-and-modulates-chemosensitivity-by-regulating-rad51-at-replication-forks
#2
Huzefa Dungrawala, Kamakoti P Bhat, Rémy Le Meur, Walter J Chazin, Xia Ding, Shyam K Sharan, Sarah R Wessel, Aditya A Sathe, Runxiang Zhao, David Cortez
RAD51 promotes homology-directed repair (HDR), replication fork reversal, and stalled fork protection. Defects in these functions cause genomic instability and tumorigenesis but also generate hypersensitivity to cancer therapeutics. Here we describe the identification of RADX as an RPA-like, single-strand DNA binding protein. RADX is recruited to replication forks, where it prevents fork collapse by regulating RAD51. When RADX is inactivated, excessive RAD51 activity slows replication elongation and causes double-strand breaks...
July 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28721653/comparison-of-flow-cytometry-and-elasa-for-screening-of-proper-candidate-aptamer-in-cell-selex-pool
#3
Maryam Sadat Nabavinia, Fahimeh Charbgoo, Mona Alibolandi, Fatemeh Mosaffa, Aida Gholoobi, Mohammad Ramezani, Khalil Abnous
Aptamers are single-stranded RNA or DNA, which bind to their target with high affinity and specificity. Method of isolating aptamers against cell surface protein is called cell-SELEX. Common approach for monitoring cell-SELEX developed aptamers is flow cytometry. Since flow cytometry is costly and requires sophisticated equipments, we suggested implementing easy access, high throughput enzyme-link apta-sorbent assay test (ELASA) to confirm the specificity of aptamers selected through cell-SELEX process. In this regard, we compared ELASA and flow cytometry techniques in order to screen potent candidate aptamers against A2780 Rcis cell line, which were selected by cell-SELEX...
July 19, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28720530/downregulation-of-protein-phosphatase-2a-by-apolipoprotein-e-implications-for-alzheimer-s-disease
#4
Veena Theendakara, Dale E Bredesen, Rammohan V Rao
The apolipoprotein E ε4 allele is the single most important genetic risk factor associated with Alzheimer's disease (AD). Tau phosphorylation and hyperphosphorylation is an underlying feature of AD and is regulated by specific kinases and phosphatases. Among phosphatases, protein phosphatase 2A (PP2A) is the principal tau dephosphorylating enzyme in the brain. Several abnormalities of PP2A have been reported in AD, including among others decreased protein levels of PP2A, decreased mRNA and protein levels of the catalytic subunit PP2AC and variable regulatory B subunits and reduced methylation of the catalytic subunit, all of which results in disruption of the PP2A phosphatase activity...
July 15, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28718373/screening-of-specific-nucleic-acid-aptamers-binding-tumor-markers-in-the-serum-of-the-lung-cancer-patients-and-identification-of-their-activities
#5
Kun Li, Chen-Lin Xiu, Li-Ming Gao, Hua-Gang Liang, Shu-Feng Xu, Ming Shi, Jian Li, Zhi-Wei Liu
Lung cancer is by far the leading cause of cancer death in the world. Despite the improvements in diagnostic methods, the status of early detection was not achieved. So, a new diagnostic method is needed. The aim of this study is to obtain the highly specific nucleic acid aptamers with strong affinity to tumor markers in the serum of the lung cancer patients for targeting the serum. Aptamers specifically binding to tumor markers in the serum of the lung cancer patients were screened from the random single-stranded DNA library with agarose beads as supports and the serum as a target by target-substituting subtractive SELEX technique and real-time quantitative polymerase chain reaction technique...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28696187/dpra-from-neisseria-meningitidis-properties-and-role-in-natural-competence-for-transformation
#6
Eirik Hovland, Getachew Tesfaye Beyene, Stephan A Frye, Håvard Homberset, Seetha V Balasingham, Marta Gómez-Muñoz, Jeremy P Derrick, Tone Tønjum, Ole H Ambur
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study...
July 12, 2017: Microbiology
https://www.readbyqxmd.com/read/28665322/pre-replicative-repair-of-oxidized-bases-maintains-fidelity-in-mammalian-genomes-the-cowcatcher-role-of-neil1-dna-glycosylase
#7
Suganya Rangaswamy, Arvind Pandey, Sankar Mitra, Muralidhar L Hegde
Genomic fidelity in the humans is continuously challenged by genotoxic reactive oxygen species (ROS) generated both endogenously during metabolic processes, and by exogenous agents. Mispairing of most ROS-induced oxidized base lesions during DNA replication induces mutations. Although bulky base adducts induced by ultraviolet light and other environmental mutagens block replicative DNA polymerases, most oxidized base lesions do not block DNA synthesis. In 8-oxo-G:A mispairs generated by the incorporation of A opposite unrepaired 8-oxo-G, A is removed by MutYH (MYH) for post-replicative repair, and other oxidized base lesions must be repaired prior to replication in order to prevent mutation fixation...
June 30, 2017: Genes
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
#8
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/28638454/downregulation-of-mitochondrial-single-stranded-dna-binding-protein-ssbp1-induces-mitochondrial-dysfunction-and-increases-the-radiosensitivity-in-non-small-cell-lung-cancer-cells
#9
You Wang, Liu Hu, Ximei Zhang, Hong Zhao, Hui Xu, Yuehua Wei, Huangang Jiang, Conghua Xie, Yunfeng Zhou, Fuxiang Zhou
Radiotherapy is one of the major therapeutic strategies for human non-small cell lung cancer (NSCLC), but intrinsic radioresistance of cancer cells makes a further improvement of radiotherapy for NSCLC challenging. Mitochondrial function is frequently dysregulated in cancer cells for adaptation to the changes of tumor microenvironment after exposure to radiation. Therefore, targeting mitochondrial biogenesis and bioenergetics is an attractive strategy to sensitize cancer cells to radiation therapy. In this study, we found that downregulation of single-strand DNA-binding protein 1 (SSBP1) in H1299 cells was associated with inducing mitochondrial dysfunction and increasing radiosensitivity to ionizing radiation...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28636604/liquid-droplet-formation-by-hp1%C3%AE-suggests-a-role-for-phase-separation-in-heterochromatin
#10
Adam G Larson, Daniel Elnatan, Madeline M Keenen, Michael J Trnka, Jonathan B Johnston, Alma L Burlingame, David A Agard, Sy Redding, Geeta J Narlikar
Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands...
July 13, 2017: Nature
https://www.readbyqxmd.com/read/28626219/base-excision-repair-proteins-couple-activation-induced-cytidine-deaminase-and-endonuclease-g-during-replication-stress-induced-mll-destabilization
#11
B Gole, E Mian, M Rall, L Wiesmüller
The breakpoint cluster region of the MLL gene (MLLbcr) is frequently rearranged in therapy-related and infant acute leukaemia, but the destabilizing mechanism is poorly understood. We recently proposed that DNA replication stress results in MLLbcr cleavage via Endonuclease G (EndoG) and represents the common denominator of genotoxic therapy-induced MLL destabilization. Here we performed a siRNA screen for new factors involved in replication stress-induced MLL rearrangements employing an EGFP-based reporter system...
June 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28623196/origin-single-stranded-dna-releases-sld3-protein-from-the-mcm2-7-complex-allowing-the-gins-tetramer-to-bind-the-mcm2-7-complex
#12
Irina Bruck, Daniel L Kaplan
No abstract text is available yet for this article.
June 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28618091/bacterial-transformation-comfa-is-a-dna-dependent-atpase-that-forms-complexes-with-comfc-and-dpra
#13
Amy Diallo, Hannah R Foster, Katarzyna A Gromek, Thomas N Perry, Annick Dujeancourt, Petya V Krasteva, Francesca Gubellini, Tanya G Falbel, Briana M Burton, Rémi Fronzes
Pneumococcal natural transformation contributes to genomic plasticity, antibiotic resistance development, and vaccine escape. Streptococcus pneumoniae, like many other naturally transformable species, has evolved sophisticated protein machinery for the binding and uptake of DNA. Two proteins encoded by the comF operon, ComFA and ComFC, are involved in transformation but their exact molecular roles remain unknown. In this study, we provide experimental evidence that ComFA binds to single stranded DNA (ssDNA) and has ssDNA-dependent ATPase activity...
June 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28615444/the-human-mitochondrial-single-strand-dna-binding-protein-displays-distinct-kinetics-and-thermodynamics-of-dna-binding-and-exchange
#14
Yufeng Qian, Kenneth A Johnson
The human mitochondrial SSB (mtSSB) is a homo-tetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain but little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB)30 and (SSB)60, defined by DNA binding site sizes of 30 and 60 nt, respectively...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28613844/assessment-of-dna-binding-and-oxidative-dna-damage-by-acrylonitrile-in-two-rat-target-tissues-of-carcinogenicity-implications-for-the-mechanism-of-action
#15
Gary M Williams, Tetyana Kobets, Jian-Dong Duan, Michael J Iatropoulos
Exposure to acrylonitrile induces formation of tumors at multiple sites in rats, with females being more sensitive. The present study assessed possible mechanisms of acrylonitrile tumorigenicity, covalent DNA binding, DNA breakage, and oxidative DNA damage, in two target tissues, the brain and Zymbal's glands, of sensitive female Fischer (F344) and Sprague-Dawley (SD) rats. One group received acrylonitrile in drinking water at 100 ppm for 28 days. Two other groups were administered either acrylonitrile in drinking water at 100 ppm or drinking water alone for 27 days, followed by a single oral gavage dose of 11 mg/kg bw (14)C-acrylonitrile on day 28...
June 29, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28609781/a-data-driven-structural-model-of-hssb1-nabp2-obfc2b-self-oligomerization
#16
Christine Touma, Mark N Adams, Nicholas W Ashton, Michael Mizzi, Serene El-Kamand, Derek J Richard, Liza Cubeddu, Roland Gamsjaeger
The maintenance of genome stability depends on the ability of the cell to repair DNA efficiently. Single-stranded DNA binding proteins (SSBs) play an important role in DNA processing events such as replication, recombination and repair. While the role of human single-stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) in the repair of double-stranded breaks has been well established, we have recently shown that it is also essential for the base excision repair (BER) pathway following oxidative DNA damage. However, unlike in DSB repair, the formation of stable hSSB1 oligomers under oxidizing conditions is an important prerequisite for its proper function in BER...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28607160/a-pria-mutant-expressed-in-two-pieces-has-almost-full-activity-in-e-coli-k-12
#17
Maxime Leroux, Niketa Jani, Steven J Sandler
The ability to restart broken DNA replication forks is essential across all domains of life. In Escherichia coli, the priA, priB, priC and dnaT genes encode the Replication Restart Proteins (RRPs) to accomplish this task. PriA plays a critical role in Replication Restart such that its absence reveals a dramatic phenotype: poor growth, high basal levels of SOS expression, poorly partitioned nucleoids (Par(-)), UV sensitivity and recombination deficiency. PriA has 733 amino acids and its structure is composed of six domains that enable it to bind to DNA replication fork-like structures, re-model the strands of DNA, interact with SSB (single-stranded DNA binding protein), PriB and DnaT, and display ATPase, helicase and translocase activities...
June 12, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28607004/rpa-activates-the-xpf-ercc1-endonuclease-to-initiate-processing-of-dna-interstrand-crosslinks
#18
Ummi B Abdullah, Joanna F McGouran, Sanja Brolih, Denis Ptchelkine, Afaf H El-Sagheer, Tom Brown, Peter J McHugh
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity...
July 14, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28606086/analysis-and-prediction-of-single-stranded-and-double-stranded-dna-binding-proteins-based-on-protein-sequences
#19
Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu, Keliang Li
BACKGROUND: DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding proteins can be categorized as single-stranded DNA-binding proteins (SSBs) and double-stranded DNA-binding proteins (DSBs). The identification of DNA-binding proteins from amino acid sequences can help to annotate protein functions and understand the binding specificity...
June 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28605670/ssb-recruitment-of-exonuclease-i-aborts-template-switching-in-escherichia-coli
#20
Laura T Laranjo, Stephen J Gross, Danna M Zeiger, Susan T Lovett
Misalignment of a nascent strand and the use of an alternative template during DNA replication, a process termed "template-switching", can give rise to frequent mutations and genetic rearrangements. Mutational hotspots are frequently found associated with imperfect inverted repeats ("quasipalindromes" or "QPs") in many organisms, including bacteriophage, bacteria, yeast and mammals. Evidence suggests that QPs mutate by a replication template-switch whereby one copy of the inverted repeat templates synthesis of the other...
June 3, 2017: DNA Repair
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