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single-stranded DNA binding protein

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https://www.readbyqxmd.com/read/28626219/base-excision-repair-proteins-couple-activation-induced-cytidine-deaminase-and-endonuclease-g-during-replication-stress-induced-mll-destabilization
#1
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
#2
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
#3
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
#4
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-mechanism-of-action
#5
Gary 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 14C-acrylonitrile on day 28...
June 14, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28609781/a-data-driven-structural-model-of-hssb1-nabp2-obfc2b-self-oligomerization
#6
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
#7
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
#8
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...
June 12, 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
#9
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
#10
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
https://www.readbyqxmd.com/read/28594346/interactive-roles-of-dna-helicases-and-translocases-with-the-single-stranded-dna-binding-protein-rpa-in-nucleic-acid-metabolism
#11
REVIEW
Sanket Awate, Robert M Brosh
Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress...
June 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28592488/dna-damage-induced-atr-kinase-activation-in-non-replicating-cells-is-regulated-by-the-xpb-subunit-of-transcription-factor-ii-h-tfiih
#12
Michael G Kemp
The role of the DNA damage response protein kinase ataxia telangiectasia and Rad-3-related (ATR) in the cellular response to DNA damage during the replicative phase of the cell cycle has been extensively studied. However, little is known about ATR kinase function in cells that are not actively replicating DNA and which constitute most cells in the human body. Using small-molecule inhibitors of ATR kinase and overexpression of a kinase-inactive form of the enzyme, I show here that ATR promotes cell death in non-replicating/non-cycling cultured human cells exposed to N-acetoxy-2-acetylaminofluorene (NA-AAF), which generates bulky DNA adducts that block RNA polymerase movement...
June 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28590137/monitoring-the-retention-of-human-pcna-at-primer-template-junctions-by-proteins-that-bind-single-stranded-dna
#13
Mark Hedglin, Mahesh Aitha, Stephen J Benkovic
In humans, PCNA sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at/near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, qualitative, and significantly deviate from physiologically-relevant conditions...
June 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28584163/protection-of-arabidopsis-blunt-ended-telomeres-is-mediated-by-a-physical-association-with-the-ku-heterodimer
#14
Sona Valuchova, Jaroslav Fulnecek, Zbynek Prokop, Paggy Stolt-Bergner, Eliska Janouskova, Ctirad Hofr, Karel Riha
Telomeres form specialized chromatin that protects natural chromosome termini from being recognized as DNA double-strand breaks. Plants possess unusual blunt-ended telomeres that are unable to form t-loops or complex with single-strand DNA binding proteins, raising the question of the mechanism behind their protection. We have previously suggested that blunt-ended telomeres in Arabidopsis thaliana are protected by Ku, a DNA repair factor with a high affinity for DNA ends. In non-homologous end joining (NHEJ), Ku loads onto broken DNA via a channel consisting of positively charged amino acids...
June 5, 2017: Plant Cell
https://www.readbyqxmd.com/read/28581365/fine-epitope-mapping-of-monoclonal-antibodies-to-the-dna-repair-protein-rada
#15
Melissa K Stuart, Deborah A Hudman, Stephanie N Nachtrab, Jacob L Hiatt, Jin Seo, Samuel J Pullen, Neil J Sargentini
Repair of DNA damage is vital to the health and survival of all organisms. In Escherichia coli, a protein known as RadA (or Sms) participates in recombinational repair, a process that uses an undamaged DNA strand in one DNA duplex to fill a gap in a homologous DNA strand in a sister DNA duplex. In a prior report, we described the production of monoclonal antibodies (MAbs) specific for RadA. Here, we investigated the epitopes recognized by two of the antibodies, MAbs 6F5 and 2A2. Premature stop codons (ochre mutations) were introduced into the radA gene at selected sites, and the truncated RadA proteins were probed by western blotting...
June 2017: Monoclonal Antibodies in Immunodiagnosis and Immunotherapy
https://www.readbyqxmd.com/read/28575448/bacillus-subtilis-dna-polymerases-polc-and-dnae-are-required-for-both-leading-and-lagging-strand-synthesis-in-spp1-origin-dependent-dna-replication
#16
Elena M Seco, Silvia Ayora
Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA 'initiation primer' on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex...
May 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28575445/quaternary-interactions-and-supercoiling-modulate-the-cooperative-dna-binding-of-agt
#17
Manana Melikishvili, Michael G Fried
Human O6-alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O6-alkylguanine and O4-alkylthymine adducts in single-stranded and duplex DNAs. The search for these lesions, through a vast excess of competing, unmodified genomic DNA, is a mechanistic challenge that may limit the repair rate in vivo. Here, we examine influences of DNA secondary structure and twist on protein-protein interactions in cooperative AGT complexes formed on lesion-free DNAs that model the unmodified parts of the genome. We used a new approach to resolve nearest neighbor (nn) and long-range (lr) components from the ensemble-average cooperativity, ωave...
May 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28574055/alternate-binding-modes-of-anti-crispr-viral-suppressors-acrf1-2-to-csy-surveillance-complex-revealed-by-cryo-em-structures
#18
Ruchao Peng, Ying Xu, Tengfei Zhu, Ningning Li, Jianxun Qi, Yan Chai, Min Wu, Xinzheng Zhang, Yi Shi, Peiyi Wang, Jiawei Wang, Ning Gao, George Fu Gao
Bacteriophages encode anti-CRISPR suppressors to counteract the CRISPR/Cas immunity of their bacterial hosts, thus facilitating their survival and replication. Previous studies have shown that two phage-encoded anti-CRISPR proteins, AcrF1 and AcrF2, suppress the type I-F CRISPR/Cas system of Pseudomonas aeruginosa by preventing target DNA recognition by the Csy surveillance complex, but the precise underlying mechanism was unknown. Here we present the structure of AcrF1/2 bound to the Csy complex determined by cryo-EM single-particle reconstruction...
June 2, 2017: Cell Research
https://www.readbyqxmd.com/read/28570838/a-high-throughput-screening-strategy-to-identify-inhibitors-of-ssb-protein-protein-interactions-in-an-academic-screening-facility
#19
Andrew F Voter, Michael P Killoran, Gene E Ananiev, Scott A Wildman, F Michael Hoffmann, James L Keck
Antibiotic-resistant bacterial infections are increasingly prevalent worldwide, and there is an urgent need for novel classes of antibiotics capable of overcoming existing resistance mechanisms. One potential antibiotic target is the bacterial single-stranded DNA binding protein (SSB), which serves as a hub for DNA repair, recombination, and replication. Eight highly conserved residues at the C-terminus of SSB use direct protein-protein interactions (PPIs) to recruit more than a dozen important genome maintenance proteins to single-stranded DNA...
May 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28561084/a-label-free-colorimetric-biosensor-for-sensitive-detection-of-vascular-endothelial-growth-factor-165
#20
Huige Zhang, Liang Peng, Maoxing Li, Ji Ma, Shengda Qi, Hongli Chen, Lei Zhou, Xingguo Chen
Sensitive detection of a low abundant protein is essential for biomedical research and clinical diagnostics. Herein, we develop a label-free colorimetric biosensor for the sensitive detection of recombinant human vascular endothelial growth factor-165 (VEGF165). This biosensor consists of an aptamer-based hairpin probe, an assistant DNA-trigger duplex and a linear template. In the presence of VEGF165, the specific binding of VEGF165 with the aptamer-based hairpin probe results in the opening of a hairpin probe and the opened hairpin probe subsequently hybridizes with the single-stranded region of the assistant DNA-trigger duplex to initiate the strand displacement amplification (SDA) to yield abundant triggers...
May 31, 2017: Analyst
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