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https://www.readbyqxmd.com/read/28815856/molecular-dynamics-insights-into-polyamine-dna-binding-modes-implications-for-cross-link-selectivity
#1
Emmanuelle Bignon, Chen-Hui Chan, Christophe Morell, Antonio Monari, Jean-Luc Ravanat, Elise Dumont
Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding...
August 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28814074/multifunctional-yolk-shell-nanostructure-as-a-superquencher-for-fluorescent-analysis-of-potassium-ion-using-guanine-rich-oligonucleotides
#2
Na Lu, Yanli Wen, Gang Liu, Lei Ding, Caixia Zeng, Ali Aldalbahi, Muhammad Khan, Govindasami Periyasami, Mostafizur Rahaman, Abdulaziz Alrohaili, Jiye Shi, Shiping Song, Lihua Wang, Min Zhang
The excellent performance of biosensor generally depends on the high signal-to-noise ratio, and the superquencher plays dominant role on the fluorescent sensors. Novel nanoquenchers exhibited high quenching efficiency in various fluorescent assays of bio/chemical molecules. Here, we developed a novel nanobiosensor using Fe3O4@C yolk-shell nanoparticles (YSNPs) and studied their quenching effect. We found the Fe3O4@C YSNP was a superquencher and exhibited an ultrastrong quenching ability, up to almost 100% quenching efficiency, toward fluorophores...
August 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28813147/synthesis-and-evaluation-of-asymmetric-acyclic-nucleoside-bisphosphonates-as-inhibitors-of-plasmodium-falciparum-and-human-hypoxanthine-guanine-xanthine-phosphoribosyltransferase
#3
Petr Špaček, Dianne T Keough, Marina Chavchich, Martin Dracinsky, Zlatko Janeba, Lieve Naesens, Michael D Edstein, Luke W Guddat, Dana Hocková
Acyclic nucleoside bisphosphonates (ANbPs) have previously been shown to be good inhibitors of human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and Plasmodium falciparum (Pf) hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPRT). Based on this scaffold, a new series of ANbPs was synthesized. One of these new ANbPs, [3-(guanine-9-yl)-2-((2-phosphonoethoxy)methyl)propoxy]methylphosphonic acid, exhibited Ki values of 6 and 70 nM for human HGPRT and Pf HGXPRT, respectively. These low Ki values were achieved by inserting an extra carbon atom in the linker connecting the N9 atom of guanine to one of the phosphonate groups...
August 16, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28811741/consistency-and-variability-of-dna-methylation-in-women-during-puberty-young-adulthood-and-pregnancy
#4
Su Chen, Nandini Mukherjee, Vimala Devi Janjanam, S Hasan Arshad, Ramesh J Kurukulaaratchy, John W Holloway, Hongmei Zhang, Wilfried Karmaus
Prior DNA methylation (DNA-m) analyses have identified cytosine-phosphate-guanine (CpG) sites, which show either a significant change or consistency during lifetime. However, the proportion of CpGs that are neither significantly different nor consistent over time (indifferent CpGs) is unknown. We investigated the methylation dynamics, both longitudinal changes and consistency, in women from preadolescence to late pregnancy using DNA-m of peripheral blood cells. Consistency of cell type-adjusted DNA-m between paired individuals was assessed by regressing CpGs of subsequent age on the prior, stability by intraclass correlation coefficients (>0...
2017: Genetics & Epigenetics
https://www.readbyqxmd.com/read/28810119/conformational-flexibility-of-the-benzyl-guanine-adduct-in-a-bypass-polymerase-active-site-permits-replication-insights-from-molecular-dynamics-simulations
#5
Katie A Wilson, Stacey D Wetmore
Although translesion synthesis (TLS) polymerases play key roles in replicating DNA that contains nucleobase addition products (adducts), there are many unknowns about their function. The present work gains indispensable structural insights from molecular dynamics simulations on the replication of O6-benzyl-guanine (Bz-dG) prior to bond formation during dCTP insertion opposite the adduct by Dpo4. When combined with previous X-ray crystal structures of the Bz-dG extension complex, molecular details are now available for each stage during a single TLS replication cycle for this carcinogenic lesion...
August 15, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28810083/self-cyclizing-antioxidants-to-prevent-dna-damage-caused-by-hydroxyl-radical
#6
Safnas F AbdulSalam, Purujit N Gurjar, Haizhou Zhu, Emma S Johnson, Jing Liu, Ana Luisa Kadekaro, Julio Landero-Figueroa, Edward Joseph Merino
Antioxidant therapy is a promising treatment strategy to protect DNA from damage caused by reactive oxygen species. Here we report novel self-cyclizing antioxidant reagents that are selective for hydroxyl radical. Our mechanistic investigation revealed that the reagents react with three equivalents of oxidant in a cascading reaction to form a bicyclic final product. Among the reagents synthesized 1c showed favourable properties in vitro and in cellular studies. Using As2O3, which triggers reactive oxygen species production, we showed 1c prevents formation of the guanine oxidation product 2,2,4-triamino-2H-oxazol-5-one-2'-deoxyribonucleoside and lowers levels of cellular reactive oxygen...
August 15, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28808777/phase-ii-study-of-bi-weekly-temozolomide-plus-bevacizumab-for-adult-patients-with-recurrent-glioblastoma
#7
Michael A Badruddoja, Marjorie Pazzi, Abhay Sanan, Kurt Schroeder, Kevin Kuzma, Thomas Norton, Thomas Scully, Daruka Mahadevan, Michael Malek Ahmadi
PURPOSE: Bevacizumab is an active anti-angiogenic agent in the treatment of recurrent glioblastoma. Temozolomide can prolong survival in patients with newly diagnosed glioblastoma. At recurrence, alternate dosing of temozolomide has shown to further deplete methyl-guanine-methyltransferase (MGMT) conferring added activity for patients who have progressed on the standard dosing regimen. In this study, bevacizumab plus biweekly temozolomide was evaluated for efficacy in adult patients with recurrent glioblastoma...
August 14, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28808134/vps9a-activates-the-rab5-gtpase-ara7-to-confer-distinct-pre-and-post-invasive-plant-innate-immunity
#8
Mads Eggert Nielsen, Gerd Jürgens, Hans Thordal-Christensen
Plant innate immunity can effectively prevent the proliferation of filamentous pathogens. Papilla formation at the site of attack is essential for pre-invasive immunity; in post-invasive immunity the encasement of pathogen structures inside host cells can hamper disease. Whereas papillae are highly dependent on transcytosis of premade material, little is known about encasement formation. Here we show that endosome-associated VPS9a, the conserved guanine-nucleotide exchange factor activating Rab5 GTPases, is required for both pre- and post-invasive immunity against a non-adapted powdery mildew fungus (Blumeria graminis f...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28807941/the-rac-gtpase-in-cancer-from-old-concepts-to-new-paradigms
#9
Marcelo G Kazanietz, María-José Caloca
Rho family GTPases are critical regulators of cellular functions that play important roles in cancer progression. Aberrant activity of Rho small G-proteins, particularly Rac1 and their regulators, is a hallmark of cancer, and contributes to the tumorigenic and metastatic phenotypes of cancer cells. This review examines the multiple mechanisms leading to Rac1 hyperactivation, particularly focusing on emerging paradigms that involve gain-of-function mutations in Rac and guanine nucleotide exchange factors (GEFs), defects in Rac1 degradation, and mislocalization of Rac signaling components...
August 14, 2017: Cancer Research
https://www.readbyqxmd.com/read/28807916/inhibition-of-calcineurin-or-impdh-exerts-moderate-to-potent-antiviral-activity-against-norovirus-replication
#10
Wen Dang, Yuebang Yin, Yijin Wang, Wenshi Wang, Junhong Su, Dave Sprengers, Luc J W van der Laan, Krzysztof Felczak, Krzysztof W Pankiewicz, Kyeong-Ok Chang, Marion P G Koopmans, Herold J Metselaar, Maikel P Peppelenbosch, Qiuwei Pan
Norovirus is a major cause of acute gastroenteritis worldwide and has emerged as an important issue of chronic infection in transplantation patients. Since no approved antiviral is available, we evaluated the effects of different immunosuppressants and ribavirin on norovirus and explored their mechanism-of-actions by using a human norovirus (HuNV) replicon-harboring model and a surrogate murine norovirus (MNV) infectious model. Roles of corresponding drug targets were investigated by gain- or loss-of-function approaches...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28806394/smggds-is-a-transient-nucleolar-protein-that-protects-cells-from-nucleolar-stress-and-promotes-the-cell-cycle-by-regulating-dream-complex-gene-expression
#11
P Gonyo, C Bergom, A C Brandt, S-W Tsaih, Y Sun, T M Bigley, E L Lorimer, S S Terhune, H Rui, M J Flister, R M Long, C L Williams
The chaperone protein and guanine nucleotide exchange factor SmgGDS (RAP1GDS1) is a key promoter of cancer cell proliferation and tumorigenesis. SmgGDS undergoes nucleocytoplasmic shuttling, suggesting that it has both cytoplasmic and nuclear functions that promote cancer. Previous studies indicate that SmgGDS binds cytoplasmic small GTPases and promotes their trafficking to the plasma membrane. In contrast, little is known about the functions of SmgGDS in the nucleus, or how these nuclear functions might benefit cancer cells...
August 14, 2017: Oncogene
https://www.readbyqxmd.com/read/28805722/estrogen-repression-of-micrornas-is-associated-with-high-guanine-content-in-the-terminal-loop-sequences-of-their-precursors
#12
Amit Cohen, Mario Alberto Burgos-Aceves, Tamar Kahan, Yoav Smith
Widespread microRNA (miRNA) repression is a phenomenon observed in mammals after exposure to cigarette smoke and in many types of cancer. A comprehensive reduction in miRNA expression after treatment with the hormone estrogen has also previously been described. Here, we reveal a conserved association of miRNA downregulation after estrogen exposure in zebrafish, mouse, and human breast cancer cell line, with a high guanine content in the terminal loop sequences of their precursors, and offer a possible link between estrogen-related miRNA-adducts formation and carcinogenesis...
August 14, 2017: Biomedicines
https://www.readbyqxmd.com/read/28803992/p-rex1-amplification-promotes-progression-of-cutaneous-melanoma-via-the-pak1-p38-mmp-2-pathway
#13
Jinhua Wang, Hajime Hirose, Guanhua Du, Kelly Chong, Eiji Kiyohara, Isaac P Witz, Dave S B Hoon
P-REX1 (PIP3-dependent Rac exchange factor-1) is a guanine nucleotide exchange factor that activates Rac by catalyzing exchange of GDP for GTP bound to Rac. Aberrant up-regulation of P-REX1 expression has a role in metastasis however, copy number (CN) and function of P-REX1 in cutaneous melanoma are unclear. To explore the role of P-REX1 in melanoma, SNP 6.0 and Exon 1.0 ST microarrays were assessed. There was a higher CN (2.82-fold change) of P-REX1 in melanoma cells than in melanocytes, and P-REX1 expression was significantly correlated with P-REX1 CN...
August 10, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28801461/structural-basis-of-human-prdm9-allele-c-specific-recognition-of-its-cognate-dna-sequence
#14
Anamika Patel, Xing Zhang, Robert M Blumenthal, Xiaodong Cheng
PRDM9 is the only mammalian gene that has been associated with speciation. The PR/SET domain 9 (PRDM9) protein is a major determinant of meiotic recombination hotspots, and acts through sequence-specific DNA binding via its C2H2 zinc finger (ZF) tandem array, which is highly polymorphic within and between species. The most common human variant, PRDM9 allele A (PRDM9a), contains 13 fingers (ZF1-13). Allele C (PRDM9c) is the second-most common among African populations, and differs from PRDM9a by an arginine-to-serine change (R764S) in ZF9, and by replacement of ZF11 with two other fingers, yielding 14 fingers in PRDM9c...
August 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28799328/a-tunable-signal-off-and-signal-on-electrochemical-cisplatin-sensor
#15
Yao Wu, Rebecca Y Lai
We report the first electrochemical cisplatin sensor fabricated with a thiolated and methylene blue (MB)-modified oligo-adenine(A)-guanine(G) DNA probe. Depending on the probe coverage, the sensor can behave as a "signal-off" or "signal-on" sensor. For the high-coverage sensor, formation of intrastrand Pt(II)-AG adducts rigidifies the oligo-AG probe, resulting in a concentration-dependent decrease in the MB signal. For the low-coverage sensor, the increase in probe-to-probe spacing enables binding of cisplatin via the intrastrand GNG motif (N = A), generating a bend in the probe which results in an increase in the MB current...
August 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28799234/arhgef10-knockout-inhibits-platelet-aggregation-and-protects-mice-from-thrombus-formation
#16
Dai-Hua Lu, Chun-Chieh Hsu, Shiu-Wen Huang, Huang-Ju Tu, Tur-Fu Huang, Houng-Chi Liou, Hsiao-Mei Liao, Chia-Hsiang Chen, Wen-Mei Fu, Susan Shur-Fen Gau
BACKGROUND: ARHGEF10, a member of Rho guanine nucleotide exchange factors (GEF) family, stimulates the Rho GTPases. Rho GTPases have been reported to regulate a variety of cellular behaviors such as cell polarity, cytoskeletal organization and gene transcription. ARHGEF10 SNPs are linked with the risk of ischemic stroke. However, the role of ARHGEF10 in platelet function remains unknown. OBJECTIVE: To examine the role of ARHGEF10 in platelet function. METHODS: ARHGEF10 knockout mice were generated...
August 11, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28798404/an-in-vivo-high-throughput-screening-for-riboswitch-ligands-using-a-reverse-reporter-gene-system
#17
Marion Kirchner, Kenji Schorpp, Kamyar Hadian, Sabine Schneider
Riboswitches are bacterial RNA elements that regulate gene expression in response to metabolite or ion abundance and are considered as potential drug targets. In recent years a number of methods to find non-natural riboswitch ligands have been described. Here we report a high-throughput in vivo screening system that allows identifying OFF-riboswitch modulators in a 384 well bioluminescence assay format. We use a reverse reporter gene setup in Bacillus subtilis, consisting of a primary screening assay, a secondary assay as well as counter assays to detect compounds in a library of 1,280 molecules that act on the guanine-responsive xpt riboswitch from B...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798372/multi-level-quantum-mechanics-and-molecular-mechanics-study-of-ring-opening-process-of-guanine-damage-by-hydroxyl-radical-in-aqueous-solution
#18
Peng Liu, Qiong Wang, Meixing Niu, Dunyou Wang
Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796037/functional-prediction-of-mir-3144-5p-in-human-cardiac-myocytes-based-on-transcriptome-sequencing-and-bioinformatics
#19
Lei Ruan, Yi Yang, Yi Huang, Ling Ding, Cuntai Zhang, Xiaofen Wu
BACKGROUND: RAN guanine nucleotide release factor (RANGRF) encoding protein MOG1 plays an important role in cardiac arrhythmia, so we intended to investigate the regulatory miRNA of RANGRF and explore its potential regulatory mechanism in arrhythmogenesis. METHODS: Based on bioinformatic analysis, miR-3144-5p was predicted to be a regulatory miRNA of RANGRF, which were then validated through a dual-luciferase reporter plasmid assay. Subsequently, the expression level of miR-3144-5p in human cardiac myocytes (HCMs) was detected, followed by cell transfection with miR-3144-5p mimics...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28795376/arabidopsis-prk6-interacts-specifically-with-atropgef8-12-and-induces-depolarized-growth-of-pollen-tubes-when-overexpressed
#20
Yuexuan Yu, Jiali Song, Xiaohui Tian, Haiwen Zhang, Legong Li, Huifen Zhu
The pollen receptor kinases (PRK) are critical regulators of pollen tube growth. The Arabidopsis genome encodes eight PRK genes, of which six are highly expressed in pollen tubes. The potential functions of AtPRK1 through AtPRK5, but not of AtPRK6, in pollen growth were analyzed in tobacco. Herein, AtPRK6 was cloned, and its function was identified. AtPRK6 was expressed specifically in pollen tubes. A yeast two-hybrid screen of AtPRK6 against 14 Arabidopsis Rop guanine nucleotide exchange factors (RopGEFs) showed that AtPRK6 interacted with AtRopGEF8 and AtRopGEF12...
August 8, 2017: Science China. Life Sciences
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