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DNA ligase

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https://www.readbyqxmd.com/read/29786079/dissection-of-dna-double-strand-break-repair-using-novel-single-molecule-forceps
#1
Jing L Wang, Camille Duboc, Qian Wu, Takashi Ochi, Shikang Liang, Susan E Tsutakawa, Susan P Lees-Miller, Marc Nadal, John A Tainer, Tom L Blundell, Terence R Strick
Repairing DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) requires multiple proteins to recognize and bind DNA ends, process them for compatibility, and ligate them together. We constructed novel DNA substrates for single-molecule nanomanipulation, allowing us to mechanically detect, probe, and rupture in real-time DSB synapsis by specific human NHEJ components. DNA-PKcs and Ku allow DNA end synapsis on the 100 ms timescale, and the addition of PAXX extends this lifetime to ~2 s. Further addition of XRCC4, XLF and ligase IV results in minute-scale synapsis and leads to robust repair of both strands of the nanomanipulated DNA...
May 21, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29782494/ubiquitin-dependent-proteolysis-of-cxcl7-leads-to-posterior-longitudinal-ligament-ossification
#2
Michiyo Tsuru, Atsushi Ono, Hideaki Umeyama, Masahiro Takeuchi, Kensei Nagata
Ossification of the posterior longitudinal ligament (OPLL), a spinal ligament, reduces the range of motion in limbs. No treatment is currently available for OPLL, which is why therapies are urgently needed. OPLL occurs in obesity, is more common in men, and has an onset after 40 years of age. The mechanisms underlying OPLL remain unclear. In this study, we performed a serum proteomic analysis in both OPLL patients and healthy subjects to identify factors potentially involved in the development of OPLL, and found reduced levels of a protein that might underlie the pathology of OPLL...
2018: PloS One
https://www.readbyqxmd.com/read/29780465/identification-of-a-selective-dna-ligase-for-accurate-recognition-and-ultrasensitive-quantification-of-n-6-methyladenosine-in-rna-at-one-nucleotide-resolution
#3
Weiliang Liu, Jingli Yan, Zhenhao Zhang, Hongru Pian, Chenghui Liu, Zhengping Li
N 6 -Methyladenosine (m6 A) is the most frequent post-transcriptional modification in RNA, and it plays a critical role in biological processes. The functions of m6 A remain largely unexplored due to a lack of highly sensitive methods to quantitatively determine the m6 A modification fraction at a precise location. Here, we first reveal that T3 DNA ligase has significant selectivity towards the m6 A modification. On the basis of the new finding, we establish an ultrasensitive quantitation assay for accurately determining m6 A at one-nucleotide resolution in RNA...
April 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780463/simultaneous-multiple-single-nucleotide-polymorphism-detection-based-on-click-chemistry-combined-with-dna-encoded-probes
#4
Qian-Yu Zhou, Fang Yuan, Xiao-Hui Zhang, Ying-Lin Zhou, Xin-Xiang Zhang
Single nucleotide polymorphisms (SNPs) are emerging as important biomarkers for disease diagnosis, prognostics and disease pathogenesis. As one type of disease is always connected to several SNP sites, there is great demand for a reliable multiple SNP detection method. Herein, we mimicked a ligation reaction based on DNA ligase and originally utilized an enzyme-free DNA template-directed click reaction for SNP detection. With 5'-alkyne and 3'-azide groups labelled on two oligonucleotide probes, the target DNA-directed Cu(i)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction produced a new DNA strand with a triazole backbone, as a mimic of a DNA phosphodiester linkage...
April 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29778533/casein-kinase-ii-phosphorylates-the-c-terminal-region-of-lif1-to-promote-the-lif1-xrs2-interaction-needed-for-non-homologous-end-joining
#5
Kenichiro Matsuzaki, Miki Shinohara
A DNA double strand break (DSB) is one of the most cytotoxic DNA lesions, but it can be repaired by non-homologous end joining (NHEJ) or by homologous recombination. The choice between these two repair pathways depends on the cell cycle stage. Although NHEJ constitutes a simple re-ligation reaction, the regulatory mechanism(s) controlling its activity has not been fully characterized. Lif1 is a regulatory subunit of the NHEJ-specific DNA ligase IV and interacts with Xrs2 of the MRX complex which is a key factor in DSB repair...
May 17, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29775751/expression-pattern-and-functional-analysis-of-the-two-ring-box-protein-rbx-in-spermatogenesis-of-chinese-mitten-crab-eriocheir-sinensis
#6
Jia-Shun Zhang, Xue-Jie Li, Lei Yang, Wei-Wei Li, Qun Wang
Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis, termed Es-RBX1 and Es-RBX2 The full length Es-RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es-RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29773824/rnase-h-assisted-rna-primed-rolling-circle-amplification-for-targeted-rna-sequence-detection
#7
Hirokazu Takahashi, Masahiko Ohkawachi, Kyohei Horio, Toshiro Kobori, Tsunehiro Aki, Yukihiko Matsumura, Yutaka Nakashimada, Yoshiko Okamura
RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3'-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769404/dna-activates-the-nse2-mms21-sumo-e3-ligase-in-the-smc5-6-complex
#8
Nathalia Varejão, Eva Ibars, Jara Lascorz, Neus Colomina, Jordi Torres-Rosell, David Reverter
Modification of chromosomal proteins by conjugation to SUMO is a key step to cope with DNA damage and to maintain the integrity of the genome. The recruitment of SUMO E3 ligases to chromatin may represent one layer of control on protein sumoylation. However, we currently do not understand how cells upregulate the activity of E3 ligases on chromatin. Here we show that the Nse2 SUMO E3 in the Smc5/6 complex, a critical player during recombinational DNA repair, is directly stimulated by binding to DNA Activation of sumoylation requires the electrostatic interaction between DNA and a positively charged patch in the ARM domain of Smc5, which acts as a DNA sensor that subsequently promotes a stimulatory activation of the E3 activity in Nse2...
May 16, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29767233/potential-role-of-cyclin-f-mrna-expression-in-the-survival-of-skin-melanoma-patients-comprehensive-analysis-of-the-pathways-altered-due-to-cyclin-f-upregulation
#9
Maciej Gagat, Adrian Krajewski, Dariusz Grzanka, Alina Grzanka
Cyclin F is a part of the Skp, Cullin, F-box containing ligase complex. The activity of cyclin F includes cell cycle control, centrosome duplication and response to DNA damage. The cyclin F expression pattern is very similar to cyclin A, but cyclin F is an orphan cyclin without its cyclin-dependent kinase partner. There is little evidence concerning the role of cyclin F in cancer. In the present study, for the first time, we present analysis from The Cancer Genome Atlas (TCGA) data in the context of expression of cyclin F mRNA in melanoma patients...
May 16, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29760876/rinck-mediated-monoubiquitination-of-cgas-promotes-antiviral-innate-immune-responses
#10
Zhao-Shan Liu, Zi-Yu Zhang, Hong Cai, Ming Zhao, Jie Mao, Jiang Dai, Tian Xia, Xue-Min Zhang, Tao Li
Background: As an important danger signal, the presence of DNA in cytoplasm triggers potent immune responses. Cyclic GMP-AMP synthase (cGAS) is a recently characterized key sensor for cytoplasmic DNA. The engagement of cGAS with DNA leads to the synthesis of a second messenger, cyclic GMP-AMP (cGAMP), which binds and activates the downstream adaptor protein STING to promote type I interferon production. Although cGAS has been shown to play a pivotal role in innate immunity, the exact regulation of cGAS activation is not fully understood...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29754243/dna-assembly-with-the-datel-method
#11
Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, Jian Chen
Simple and reliable DNA assembly methods have become a critical technique in synthetic biology. Here, we present a protocol of the recently developed DATEL (scarless and sequence-independent DNA assembly method using thermostable exonuclease and ligase) method for the construction of genetic circuits and biological pathways from multiple DNA parts in one tube. DATEL is expected to be an applicable choice for both manual and automated high-throughput assembly of DNA fragments, which will greatly facilitate the rapid progress of synthetic biology and metabolic engineering...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29754230/combinatorial-evolution-of-dna-with-recode
#12
Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, Jian Chen
In past decades, DNA engineering protocols have led to the rapid development of synthetic biology. To engineer the natural proteins, many directed evolution methods based on molecular biology have been presented for generating genetic diversity or obtaining specific properties. Here, we provide a simple (PCR operation), efficient (larger amount of products), and powerful (multiple point mutations, deletions, insertions, and combinatorial multipoint mutagenesis) RECODE method, which is capable of reediting the target DNA flexibly to restructure regulatory regions and remodel enzymes by using the combined function of the thermostable DNA polymerase and DNA ligase in one pot...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29743367/a-screen-for-epstein-barr-virus-proteins-that-inhibit-the-dna-damage-response-reveals-a-novel-histone-binding-protein
#13
Ting-Hin Ho, Justine Sitz, Qingtang Shen, Ariane Leblanc-Lacroix, Eric I Campos, Ivan Borozan, Edyta Marcon, Jack Greenblatt, Amelie Fradet-Turcotte, Dong-Yan Jin, Lori Frappier
To replicate and persist in human cells, linear double-stranded (ds) DNA viruses, such as Epstein-Barr virus (EBV), must overcome the host DNA damage response (DDR) that is triggered by the viral genomes. Since this response is necessary to maintain cellular genome integrity, its inhibition by EBV is likely an important factor in the development of cancers associated with EBV infection, including gastric carcinoma. Here we present the first extensive screen of EBV proteins that inhibit dsDNA break signaling...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29741723/a-single-molecule-sequencing-assay-for-the-comprehensive-profiling-of-t4-dna-ligase-fidelity-and-bias-during-dna-end-joining
#14
Vladimir Potapov, Jennifer L Ong, Bradley W Langhorst, Katharina Bilotti, Dan Cahoon, Barry Canton, Thomas F Knight, Thomas C Evans, Gregory Js Lohman
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29741650/flap-endonuclease-overexpression-drives-genome-instability-and-dna-damage-hypersensitivity-in-a-pcna-dependent-manner
#15
Jordan R Becker, David Gallo, Wendy Leung, Taylor Croissant, Yee Mon Thu, Hai Dang Nguyen, Timothy K Starr, Grant W Brown, Anja-Katrin Bielinsky
Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease overexpression impedes replication fork progression and leads to an accumulation of cells in mid-S phase. This was accompanied by increased phosphorylation of the checkpoint kinase Rad53 and histone H2A-S129...
May 7, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29738775/crl4b-rbbp7-targets-huwe1-for-ubiquitination-and-proteasomal-degradation
#16
Fei Liu, Li Cao, Ting Zhang, Fen Chang, Yongjie Xu, Qin Li, Jingcheng Deng, Li Li, Genze Shao
The E3 ubiquitin ligase HUWE1/Mule/ARF-BP1 plays an important role in diverse biological processes including DNA damage repair and apoptosis. Our previous study has shown that in response to DNA damage HUWE1 was downregulated in CUL4B-mediated ubiquitination and subsequent proteasomal degradation, and CUL4B-mediated regulation of HUWE1 is important for cell survival upon DNA damage. CUL4B is a core component of the CUL4B Ring ligase complexes containing ROC1, DDB1 and a DDB1-Cullin Associated Factors (DCAFs), the latter of which are DDB1-binding WD40 adaptors critical for substrate recognition and recruitment...
May 5, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29724823/hiv-1-vpr-hijacks-edd-dyrk2-ddb1-dcaf1-to-disrupt-centrosome-homeostasis
#17
Delowar Hossain, Jérémy A Ferreira Barbosa, Éric A Cohen, William Y Tsang
Viruses exploit the host cell machinery for their own profit. To evade innate immune sensing and promote viral replication, the human immunodeficiency virus type 1 (HIV-1) subverts DNA repair regulatory proteins and induces G2/M arrest. The pre-integration complex of HIV-1 is known to traffic along microtubules and accumulate near the microtubule-organizing center. The centrosome is the major microtubule-organizing center in most eukaryotic cells, but precisely how HIV-1 impinges on centrosome biology remains poorly understood...
May 3, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29721771/oxidative-stress-stimulates-invasive-potential-in-rat-c6-and-human-u-87-mg-glioblastoma-cells-via-activation-and-cross-talk-between-pkm2-enpp2-and-ape1-enzymes
#18
Ravi P Cholia, Monisha Dhiman, Raj Kumar, Anil K Mantha
Maintaining genomic integrity is essential for cell survival and viability. Reactive oxygen species (ROS) overproduction results in oxidative stress leading to the genomic instability via generation of small base lesions in DNA and these unrepaired DNA damages lead to various cellular consequences including cancer. Recent data support the concept "oxidative stress is an indispensable participant in fostering proliferation, survival, and migration" in various cancer cell types including glioblastoma cells...
May 2, 2018: Metabolic Brain Disease
https://www.readbyqxmd.com/read/29715291/interference-with-dna-repair-after-ionizing-radiation-by-a-pyrrole-imidazole-polyamide
#19
Silvia Diaz-Perez, Nathanael Kane, Alexis A Kurmis, Fei Yang, Nicolas T Kummer, Peter B Dervan, Nicholas G Nickols
Pyrrole-imidazole (Py-Im) polyamides are synthetic non-genotoxic minor groove-binding small molecules. We hypothesized that Py-Im polyamides can modulate the cellular response to ionizing radiation. Pre-treatment of cells with a Py-Im polyamide prior to exposure to ionizing radiation resulted in a delay in resolution of phosphorylated γ-H2AX foci, increase in XRCC1 foci, and reduced cellular replication potential. RNA-sequencing of cell lines exposed to the polyamide showed induction of genes related to the ultraviolet radiation response...
2018: PloS One
https://www.readbyqxmd.com/read/29708513/dna-methyltransferase-expression-in-triple-negative-breast-cancer-predicts-sensitivity-to-decitabine
#20
Jia Yu, Bo Qin, Ann M Moyer, Somaira Nowsheen, Tongzheng Liu, Sisi Qin, Yongxian Zhuang, Duan Liu, Shijia W Lu, Krishna R Kalari, Daniel W Visscher, John A Copland, Sarah A McLaughlin, Alvaro Moreno-Aspitia, Donald W Northfelt, Richard J Gray, Zhenkun Lou, Vera J Suman, Richard Weinshilboum, Judy C Boughey, Matthew P Goetz, Liewei Wang
Triple-negative breast cancer (TNBC) is a heterogeneous disease with poor prognosis that lacks targeted therapies, especially in patients with chemotherapy-resistant disease. Since DNA methylation-induced silencing of tumor suppressors is common in cancer, reversal of promoter DNA hypermethylation by 5-aza-2'-deoxycytidine (decitabine), an FDA-approved DNA methyltransferase (DNMT) inhibitor, has proven effective in treating hematological neoplasms. However, its antitumor effect varies in solid tumors, stressing the importance of identifying biomarkers predictive of therapeutic response...
April 30, 2018: Journal of Clinical Investigation
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