keyword
MENU ▼
Read by QxMD icon Read
search

Polymerase substrate specificity

keyword
https://www.readbyqxmd.com/read/28811334/argonaute-8-ago8-mediates-the-elicitation-of-primary-defense-against-herbivory
#1
Maitree Pradhan, Priyanka Pandey, Klaus Gase, Murali Shraff, Ravi K Singh, Avinash Sethi, Ian T Baldwin, Shree P Pandey
In Nicotiana attenuata, specific RNA directed RNA polymerase (RdR1) and the Dicer-like proteins (DCL3 and 4) are recruited during herbivore attack to mediate the regulation of defense responses. However, the identity and role(s) of Argonautes (AGOs) involved in herbivory remains unknown. Of the 11 AGOs in the N. attenuata genome, we silenced the expression of 10. Plants silenced in NaAGO8 expression grew normally but were highly susceptible to herbivore attack. Larvae of the Manduca sexta grew faster when consuming irAGO8 plants, but did not differ from WT when consuming plants silenced in AGO1 (a, b and c), AGO2, AGO4 (a and b), AGO7, or AGO10 expression...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28808059/linchpin-dna-binding-residues-serve-as-go-no-go-controls-in-the-replication-factor-c-catalyzed-clamp-loading-mechanism
#2
Juan Liu, Yayan Zhou, Manju M Hingorani
DNA polymerases depend on circular sliding clamps for processive replication. Clamps must be loaded onto primer-template DNA (ptDNA) by clamp loaders that open and close clamps around ptDNA in an ATP-fueled reaction. All clamp loaders share a core structure in which five subunits form a spiral chamber that binds the clamp at its base in a twisted open form and encloses ptDNA within, while binding and hydrolyzing ATP to topologically link the clamp and ptDNA. To understand how clamp loaders perform this complex task, here we focused on conserved arginines that might play a central coordinating role in the mechanism, since they can alternately contact ptDNA or Walker B glutamate in the ATPase site, and lie close to the clamp loader-clamp binding interface...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28790447/wheat-tapub1-modulates-plant-drought-stress-resistance-by-improving-antioxidant-capability
#3
Guangqiang Zhang, Meng Zhang, Zhongxian Zhao, Yuanqing Ren, Qinxue Li, Wei Wang
E3 ligases play significant roles in plant stress tolerance by targeting specific substrate proteins for post-translational modification. In a previous study, we cloned TaPUB1 from Triticum aestivum L., which encodes a U-box E3 ligase. Real-time polymerase chain reaction revealed that the gene was up-regulated under drought stress. To investigate the function of TaPUB1 in the response of plants to drought, we generated transgenic Nicotiana benthamiana (N. benthamiana) plants constitutively expressing TaPUB1 under the CaMV35S promoter...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28769016/favipiravir-t-705-a-broad-spectrum-inhibitor-of-viral-rna-polymerase
#4
Yousuke Furuta, Takashi Komeno, Takaaki Nakamura
Favipiravir (T-705; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) is an anti-viral agent that selectively and potently inhibits the RNA-dependent RNA polymerase (RdRp) of RNA viruses. Favipiravir was discovered through screening chemical library for anti-viral activity against the influenza virus by Toyama Chemical Co., Ltd. Favipiravir undergoes an intracellular phosphoribosylation to be an active form, favipiravir-RTP (favipiravir ribofuranosyl-5'-triphosphate), which is recognized as a substrate by RdRp, and inhibits the RNA polymerase activity...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28752801/virus-directed-enzyme-prodrug-therapy-and-the-assessment-of-the-cytotoxic-impact-of-some-benzimidazole-derivatives
#5
Michał Szewczuk, Karolina Boguszewska, Marta Żebrowska, Ewa Balcerczak, Marta Stasiak, Maria Świątkowska, Katarzyna Błaszczak-Świątkiewicz
Virus-directed enzyme prodrug therapy is one of the major strategy of increasing cytotoxicity of bioreductive agents. This research intended to examine new selected benzimidazole derivatives as a substrate for nitroreductase, the enzyme involved in nitroreduction which is responsible to the production of cytotoxic metabolites. In this way, the selectivity and strength of cytotoxicity can be raised. The effect of benzimidazoles on virus transfected cells and non-virus transfected cells A549 cell line was established by Annexin V + propidium iodide test, western blot, and polymerase chain reaction analysis of specific pro- and anti-apoptotic proteins in the corresponding gene expression and additionally nitroreductase gene expression...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28751463/dual-src-kinase-pretubulin-inhibitor-kx-01-sensitizes-er%C3%AE-negative-breast-cancers-to-tamoxifen-through-er%C3%AE-re-expression
#6
Muralidharan Anbalagan, Mei Sheng, Brian Fleischer, Yifang Zhang, Yuanjun Gao, Van T Hoang, Margarite D Matossian, Hope E Burks, Matthew E Burow, Bridgette M Collins-Burow, David Hangauer, Brian G Rowan
Unlike breast cancer that is positive for estrogen receptor-α (ERα), there are no targeted therapies for triple negative breast cancer (TNBC). ERα is silenced in TNBC through epigenetic changes including DNA methylation and histone acetylation. Restoring ERα expression in TNBC may sensitize patients to endocrine therapy. Expression of c-Src and ERα are inversely correlated in breast cancer suggesting that c-Src inhibition may lead to re-expression of ERα in TNBC. KX-01 is a peptide substrate-targeted Src/pretubulin inhibitor in clinical trials for solid tumors...
July 27, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28695520/use-of-inosine-monophosphate-dehydrogenase-activity-assay-to-determine-the-specificity-of-parp-1-inhibitors
#7
Sajitha Anthony, Jeffrey R Peterson, Yingbiao Ji
Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in purine nucleotide biosynthesis. It is responsible for catalyzing the oxidation of inosine monophosphate (IMP) into xanthosine monophosphate (XMP). Concurrently, the cofactor NAD(+) is reduced to NADH. Poly(ADP-ribose) polymerase 1 (PARP-1) also utilizes NAD(+) as a substrate to synthesize poly(ADP-ribose). It has been demonstrated that inhibition of PARP-1 activity can be an effective cancer therapeutic. However, most PARP-1 inhibitors, including olaparib, were developed as NAD(+) analogs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28695506/using-clickable-nad-analogs-to-label-substrate-proteins-of-parps
#8
Lu Zhang, Hening Lin
ADP-ribosylation has been well known as an important posttranslational modification, which is catalyzed by a family of enzymes called poly(ADP-ribose) polymerases (PARPs). PARPs transfer of a single or multiple adenine diphosphate ribose (ADP-ribose) units from nicotinamide adenine dinucleotide (NAD(+)) to specific amino acids on substrate proteins. Through mono- or poly-ADP-ribosylation enzymatic activities, PARPs regulate various biological processes, including DNA damage repair, chromatin remodeling, transcriptional regulation, RNA processing and metabolism...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28695500/quantification-of-parp-activity-in-human-tissues-ex-vivo-assays-in-blood-cells-and-immunohistochemistry-in-human-biopsies
#9
Eszter M Horvath, Zsuzsanna K Zsengellér, Csaba Szabo
Poly(ADP-ribosyl)ation of proteins is a posttranslational modification mediated by poly(ADP-ribose) polymerases (PARPs) that use NAD(+) as substrate to form the negatively charged polymer of poly(ADP-ribose) (PAR). After DNA damage, PARP-1 is responsible for approximately 90% of the total cellular PARylation activity. Numerous studies showed activation of PARP-1 in various conditions associated with oxidative and nitrosative stress, such as ischemia-reperfusion injury, diabetes mellitus, and inflammation, and also proved the beneficial effects of PARP inhibitors...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28678845/polymerase-free-measurement-of-microrna-122-with-single-base-specificity-using-single-molecule-arrays-detection-of-drug-induced-liver-injury
#10
David M Rissin, Barbara López-Longarela, Salvatore Pernagallo, Hugh Ilyine, A D Bastiaan Vliegenthart, James W Dear, Juan J Díaz-Mochón, David C Duffy
We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA) probe-containing a reactive amine instead of a nucleotide at a specific position in the sequence-for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase-containing an aldehyde group-that was complementary to the missing base in the probe sequence, and a reducing agent...
2017: PloS One
https://www.readbyqxmd.com/read/28665322/pre-replicative-repair-of-oxidized-bases-maintains-fidelity-in-mammalian-genomes-the-cowcatcher-role-of-neil1-dna-glycosylase
#11
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/28659472/crystal-structure-and-thermostability-characterization-of-ev-d68-3d-pol
#12
Chunnian Wang, Caiyan Wang, Qing Li, Zhong Wang, Wei Xie
Enterovirus-D68 (EV-D68) is one of the many non-polio enteroviruses that cause mild-to-severe respiratory illness. The non-structural protein 3D(pol) is an RNA-dependent RNA polymerase (RdRP) of EV-D68, which plays a critical role in the replication of the viral genome and represents a promising drug target. Here we report the first three-dimensional crystal structure of RdRP from EV-D68 in complex with the substrate GTP to 2.3-Å resolution. The RdRP structure is similar to those of other viral RdRPs, where the three domains termed the palm, fingers, and thumb form a structure resembling a cupped right hand...
June 28, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28641560/functional-and-catalytic-characterization-of-the-detoxifying-enzyme-haloalkane-dehalogenase-from-rhizobium-leguminosarum
#13
Nikolaos Georgakis, Evangelia Chronopoulou, Maria Anna Gad, Dimitrios Skliros, Rodica Efrose, Emmanouil Flemetakis, Nikolaos E Labrou
Haloalkanes are acutely toxic to animals and humans and their toxic effects are mainly observed in the liver, kidneys and central nervous system. In the present work, the haloalkane dehalogenase from Rhizobium leguminosarum bv. trifolii (DrlA) was characterized. Reverse transcription polymerase chain reaction analysis and enzyme activity assays revealed that the DrlA gene expression in R. leguminosarum bv. trifolii is induced by 1,2-dibromoethane (1,2-DBE) during the early exponential phase. The gene of the enzyme was isolated, cloned and expressed in E...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28630124/the-dna-repair-repertoire-of-mycobacterium-smegmatis-fena-includes-the-incision-of-dna-5-flaps-and-the-removal-of-5-adenylylated-products-of-aborted-nick-ligation
#14
Maria Loressa Uson, Shreya Ghosh, Stewart Shuman
We characterize Mycobacterium smegmatis FenA as a manganese-dependent 5'-flap endonuclease homologous to the 5'-exonuclease of DNA polymerase I. FenA incises a nicked 5' flap between the first and second nucleotides of the duplex segment to yield a 1-nucleotide gapped DNA, which is then further resected in dinucleotide steps. Initial FenA cleavage at a Y-flap or nick occurs between the first and second nucleotides of the duplex. However, when the template 3' single strand is eliminated to create a 5'-tailed duplex, FenA incision shifts to between the second and third nucleotides...
September 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28629775/8-oxo-7-8-dihydroguanine-friend-and-foe-epigenetic-like-regulator-versus-initiator-of-mutagenesis
#15
REVIEW
Aaron M Fleming, Cynthia J Burrows
A high flux of reactive oxygen species during oxidative stress results in oxidative modification of cellular components including DNA. Oxidative DNA "damage" to the heterocyclic bases is considered deleterious because polymerases may incorrectly read the modifications causing mutations. A prominent member in this class is the oxidized guanine base 8-oxo-7,8-dihydroguanine (OG) that is moderately mutagenic effecting G→T transversion mutations. Recent reports have identified that formation of OG in G-rich regulatory elements in the promoters of the VEGF, TNFα, and SIRT1 genes can increase transcription via activation of the base excision repair (BER) pathway...
August 2017: DNA Repair
https://www.readbyqxmd.com/read/28628207/engineered-polymerases-with-altered-substrate-specificity-expression-and-purification
#16
Ali Nikoomanzar, Matthew R Dunn, John C Chaput
Polymerase engineering is making it possible to synthesize xeno-nucleic acid polymers (XNAs) with diverse backbone structures and chemical functionality. The ability to copy genetic information back and forth between DNA and XNA has led to a new field of science known as synthetic genetics, which aims to study the genetic concepts of heredity and evolution in artificial genetic polymers. Since many of the polymerases needed to synthesize XNA polymers are not available commercially, researchers must express and purify these enzymes as recombinant proteins from E...
June 19, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28622802/rapid-multiplex-dna-amplification-on-an-inexpensive-microdevice-for-human-identification-via-short-tandem-repeat-analysis
#17
Jacquelyn A DuVall, Delphine Le Roux, Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Daniel L Mills, An-Chi Tsuei, Martin G Ensenberger, Cindy Sprecher, Douglas R Storts, Brian E Root, James P Landers
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28588250/an-atypical-phosphodiesterase-capable-of-degrading-haloalkyl-phosphate-diesters-from-sphingobium-sp-strain-tcm1
#18
Katsumasa Abe, Naoko Mukai, Yuka Morooka, Takeshi Makino, Kenji Oshima, Shouji Takahashi, Yoshio Kera
Sphingobium sp. strain TCM1 can degrade tris(2-chloroethyl) phosphate (TCEP) to inorganic phosphate and 2-chloroethanol. A phosphotriesterase (PTE), phosphodiesterase (PDE) and phosphomonoesterase (PME) are believed to be involved in the degradation of TCEP. The PTE and PME that respectively catalyze the first and third steps of TCEP degradation in TCM1 have been identified. However, no information has been reported on a PDE catalyzing the second step. In this study, we identified, purified, and characterized a PDE capable of hydrolyzing haloalkyl phosphate diesters...
June 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28570559/analysis-of-dna-polymerase-%C3%AE-function-in-meiotic-recombination-immunoglobulin-class-switching-and-dna-damage-tolerance
#19
Kei-Ichi Takata, Shelley Reh, Matthew J Yousefzadeh, Maciej J Zelazowski, Sarita Bhetawal, David Trono, Megan G Lowery, Maria Sandoval, Yoko Takata, Yue Lu, Kevin Lin, Jianjun Shen, Donna F Kusewitt, Kevin M McBride, Francesca Cole, Richard D Wood
DNA polymerase ν (pol ν), encoded by the POLN gene, is an A-family DNA polymerase in vertebrates and some other animal lineages. Here we report an in-depth analysis of pol ν-defective mice and human cells. POLN is very weakly expressed in most tissues, with the highest relative expression in testis. We constructed multiple mouse models for Poln disruption and detected no anatomic abnormalities, alterations in lifespan, or changed causes of mortality. Mice with inactive Poln are fertile and have normal testis morphology...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28559253/nucleotide-substrate-specificity-of-anti-hepatitis-c-virus-nucleoside-analogs-for-human-mitochondrial-rna-polymerase
#20
Maryam Ehteshami, Longhu Zhou, Sheida Amiralaei, Jadd R Shelton, Jong Hyun Cho, Hongwang Zhang, Hao Li, Xiao Lu, Tugba Ozturk, Richard Stanton, Franck Amblard, Tamara R McBrayer, Steven J Coats, Raymond F Schinazi
Nucleoside analog inhibitors (NAIs) are an important class of antiviral agents. Although highly effective, some NAIs with activity against hepatitis C virus (HCV) can cause toxicity, presumably due to off-target inhibition of host mitochondrial RNA polymerase (POLRMT). The in vitro nucleotide substrate specificity of POLRMT was studied in order to explore structure-activity relationships that can facilitate the identification of nontoxic NAIs. These findings have important implications for the development of all anti-RNA virus NAIs...
August 2017: Antimicrobial Agents and Chemotherapy
keyword
keyword
77441
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"