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Rnase h

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https://www.readbyqxmd.com/read/27899605/poly-a-specific-ribonuclease-regulates-the-processing-of-small-subunit-rrnas-in-human-cells
#1
Hideaki Ishikawa, Harunori Yoshikawa, Keiichi Izumikawa, Yutaka Miura, Masato Taoka, Yuko Nobe, Yoshio Yamauchi, Hiroshi Nakayama, Richard J Simpson, Toshiaki Isobe
Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899559/division-of-labor-among-mycobacterium-smegmatis-rnase-h-enzymes-rnase-h1-activity-of-rnha-or-rnhc-is-essential-for-growth-whereas-rnhb-and-rnha-guard-against-killing-by-hydrogen-peroxide-in-stationary-phase
#2
Richa Gupta, Debashree Chatterjee, Michael S Glickman, Stewart Shuman
RNase H enzymes sense the presence of ribonucleotides in the genome and initiate their removal by incising the ribonucleotide-containing strand of an RNA:DNA hybrid. Mycobacterium smegmatis encodes four RNase H enzymes: RnhA, RnhB, RnhC and RnhD. Here, we interrogate the biochemical activity and nucleic acid substrate specificity of RnhA. We report that RnhA (like RnhC characterized previously) is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27890900/in-vitro-and-in-vivo-biophysical-properties-of-oligonucleotides-containing-5-thio-nucleosides
#3
Md Ariful Islam, Reiko Waki, Aki Fujisaka, Kosuke Ramon Ito, Satoshi Obika
Phosphorothioate modification is one of the most widely investigated and promising chemical modifications in oligonucleotide (ON) based therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which a 5'-bridging oxygen is replaced with a sulfur atom, are gaining importance for ON-based research. Several reports have been published describing the synthesis of 5'-thio-modified ONs but no detailed in vitro and in vivo data are available. Here, we report the synthesis of 5'-thio-modified 2'-deoxy-5-methylcytidine...
2016: Drug Discoveries & Therapeutics
https://www.readbyqxmd.com/read/27886596/an-end-point-method-based-on-graphene-oxide-for-rnase-h-analysis-and-inhibitors-screening
#4
Chuan Zhao, Jialong Fan, Lan Peng, Lijian Zhao, Chunyi Tong, Wei Wang, Bin Liu
As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10(-3) units/ mL under optimal conditions...
November 16, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27881652/inhibition-of-human-cytomegalovirus-pul89-terminase-subunit-blocks-virus-replication-and-genome-cleavage
#5
Yan Wang, Lili Mao, Jayakanth Kankanala, Zhengqiang Wang, Robert J Geraghty
: Human cytomegalovirus terminase complex cleaves the concatemeric genomic DNA into unit lengths during genome packaging and particle assembly. This process is an attractive drug target because cleavage of concatemeric DNA is not required in mammalian cell DNA replication, indicating that drugs targeting the terminase complex could be safe and selective. One component of the human cytomegalovirus terminase complex, pUL89, provides the endonucleolytic activity for genome cleavage and the domain responsible is reported to have an RNase H-like fold...
November 23, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27881299/transient-rna-dna-hybrids-are-required-for-efficient-double-strand-break-repair
#6
Corina Ohle, Rafael Tesorero, Géza Schermann, Nikolay Dobrev, Irmgard Sinning, Tamás Fischer
RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNase H enzymes is important for maintaining genomic stability. Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair. Using a site-specific DNA double-strand break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous-recombination (HR)-mediated DSB repair process and that RNase H enzymes are essential for their degradation and efficient completion of DNA repair...
November 3, 2016: Cell
https://www.readbyqxmd.com/read/27875905/identification-of-novel-resistance-related-polymorphisms-in-hiv-1-subtype-c-rt-connection-and-rnase-h-domains-from-patients-under-virological-failure-in-brazil
#7
Maria Fernanda M Barral, Arielly K P Sousa, André F Santos, Celina M Abreu, Amilcar Tanuri, Marcelo A Soares
Mutations in the connection and RNase H C-terminal reverse transcriptase (RT) domains of HIV-1 have been shown to impact drug resistance to RT inhibitors. However, their impact in the context of non-B subtypes has been poorly assessed. This study aimed to characterize resistance-related mutations in the C-terminal portions of RT in treatment-failing patients from southern Brazil, a region with endemic HIV-1 subtype C (HIV-1C). Viral RNA was isolated and reverse transcribed from 280 infected subjects, and genomic regions were analyzed by PCR, DNA sequencing and phylogenetic analysis...
November 22, 2016: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/27830012/human-mesenchymal-stromal-cell-derived-extracellular-vesicles-alleviate-renal-ischemic-reperfusion-injury-and-enhance-angiogenesis-in-rats
#8
Xiangyu Zou, Di Gu, Xiaoyu Xing, Zhongliang Cheng, Dongliang Gong, Guangyuan Zhang, Yingjian Zhu
BACKGROUND: Mesenchymal stromal cells (MSCs) derived extracellular vesicles (EVs) were regarded as a potent medium for kidney injury repair and angiogenesis were regarded as an important step in tissue regeneration. However, the pro-angiogenesis effect of MSC-EVs in ischemia-reperfusion induced kidney injury and its potential mechanisms have yet to be determined. METHODS: EVs were isolated from the medium of human umbilical cord-derived MSCs (huMSCs) were injected in rats intravenously after unilateral kidney ischemia...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27825885/endonuclease-controlled-aggregation-of-gold-nanoparticles-for-the-ultrasensitive-detection-of-pathogenic-bacterial-dna
#9
Claire McVey, Fumin Huang, Christopher Elliott, Cuong Cao
The development of an ultrasensitive biosensor for the low-cost and on-site detection of pathogenic DNA could transform detection capabilities within food safety, environmental monitoring and clinical diagnosis. Herein, we present an innovative approach exploiting endonuclease-controlled aggregation of plasmonic gold nanoparticles (AuNPs) for label-free and ultrasensitive detection of bacterial DNA. The method utilizes RNA-functionalized AuNPs which form DNA-RNA heteroduplex structures through specific hybridization with target DNA...
October 27, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27812578/pcr-free-multiple-ligase-reactions-and-probe-cleavages-for-the-snp-detection-of-kras-mutation-with-attomole-sensitivity
#10
Joong Hyun Kim
A method to produce multiple ligated primers without PCR for a target DNA containing a single point mutation is presented. A strand displacing hairpin was introduced into the reaction, enabling separation of the ligated primer target DNA duplex without any thermal denaturing process. The ligated product was cycled to allow cleavage of fluorescence labeled substrates for RNase H on gold nanoparticles, leading to target specific fluorescence amplification. As a result, 10 attomoles of target DNA containing a point mutation in the KRAS gene were detected...
November 4, 2016: Analyst
https://www.readbyqxmd.com/read/27799545/evolutionary-trend-toward-kinetic-stability-in-the-folding-trajectory-of-rnases-h
#11
Shion A Lim, Kathryn M Hart, Michael J Harms, Susan Marqusee
Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27792457/functions-and-regulation-of-the-brr2-rna-helicase-during-splicing
#12
Eva Absmeier, Karine F Santos, Markus C Wahl
Pre-mRNA splicing entails the stepwise assembly of an inactive spliceosome, its catalytic activation, splicing catalysis and spliceosome disassembly. Transitions in this reaction cycle are accompanied by compositional and conformational rearrangements of the underlying RNA-protein interaction networks, which are driven and controlled by eight conserved superfamily 2 RNA helicases. The Ski2-like helicase, Brr2, provides the key remodeling activity during spliceosome activation and is additionally implicated in the catalytic and disassembly phases of splicing, indicating that Brr2 needs to be tightly regulated during splicing...
October 28, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27791008/differential-roles-of-the-rnases-h-in-preventing-chromosome-instability
#13
Anjali D Zimmer, Douglas Koshland
DNA:RNA hybrids can lead to DNA damage and genome instability. This damage can be prevented by degradation of the RNA in the hybrid by two evolutionarily conserved enzymes, RNase H1 and H2. Indeed, RNase H-deficient cells have increased chromosomal rearrangements. However, the quantitative and spatial contributions of the individual enzymes to hybrid removal have been unclear. Additionally, RNase H2 can remove single ribonucleotides misincorporated into DNA during replication. The relative contribution of DNA:RNA hybrids and misincorporated ribonucleotides to chromosome instability also was uncertain...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27777304/rate-limiting-pyrophosphate-release-by-hiv-reverse-transcriptase-improves-fidelity
#14
An Li, Shanzhong Gong, Kenneth A Johnson
Previous measurements of the rates of polymerization and pyrophosphate release with DNA templates showed that pyrophosphate (PPi) dissociation was fast following nucleotide incorporation so that it did not contribute to enzyme specificity (kcat/Km). Here, kinetic parameters governing nucleotide incorporation and PPi release were determined using an RNA template. Compared with a DNA template of the same sequence, the rate of chemistry increased by up to 10-fold (250 vs 24 s-1) while the rate of PPi release decreased to approximate 58 s-1, so that PPi release became the rate-limiting step...
October 24, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27777303/hiv-1-reverse-transcriptase-polymerase-and-rnase-h-active-sites-work-simultaneously-and-independently
#15
An Li, Jiawen Li, Kenneth A Johnson
HIV Reverse Transcriptase (RT) plays a central role in viral replication and requires coordination of both polymerase and RNase H activities. Although this coordination is crucial in viral replication, whether a DNA/RNA hybrid can simultaneously engage both active sites has yet to be determined since structural and kinetic analyses have provided contradictory results. Single nucleotide incorporation and RNase H cleavage were examined using pre-steady-state kinetics with global data analysis. The results revealed three interconverting RT-DNA/RNA species: 43% were active for both sites, 27% showed only polymerase activity, and the remaining 30% were nonproductive...
October 24, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27774452/rna-sequencing-of-formalin-fixed-paraffin-embedded-specimens-for-gene-expression-quantification-and-data-mining
#16
Yan Guo, Jie Wu, Shilin Zhao, Fei Ye, Yinghao Su, Travis Clark, Quanhu Sheng, Brian Lehmann, Xiao-Ou Shu, Qiuyin Cai
Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N = 16). We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27769719/analysis-of-the-cleavage-mechanism-by-protein-only-rnase-p-using-precursor-trna-substrates-with-modifications-at-the-cleavage-site
#17
Dennis Walczyk, Markus Gößringer, Walter Rossmanith, Timofei S Zatsepin, Tatiana S Oretskaya, Roland K Hartmann
Ribonuclease P (RNase P) is the enzyme that endonucleolytically removes 5'-precursor sequences from tRNA transcripts in all domains of life. RNase P activities are either ribonucleoprotein (RNP) or protein-only RNase P (PRORP) enzymes, raising the question about the mechanistic strategies utilized by these architecturally different enzyme classes to catalyze the same type of reaction. Here, we analyzed the kinetics and cleavage-site selection by PRORP3 from Arabidopsis thaliana (AtPRORP3) using precursor tRNAs (pre-tRNAs) with individual modifications at the canonical cleavage site, with either Rp- or Sp-phosphorothioate, or 2'-deoxy, 2'-fluoro, 2'-amino, or 2'-O-methyl substitutions...
October 18, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27765358/sennoside-a-derived-from-the-traditional-chinese-medicine-plant-rheum-l-is-a-new-dual-hiv-1-inhibitor-effective-on-hiv-1-replication
#18
Francesca Esposito, Ilaria Carli, Claudia Del Vecchio, Lijia Xu, Angela Corona, Nicole Grandi, Dario Piano, Elias Maccioni, Simona Distinto, Cristina Parolin, Enzo Tramontano
BACKGROUND: Despite the availability of effective antiretroviral therapies, drugs for HIV-1 treatment with new mode of action are still needed. An innovative approach is aimed to identify dual HIV-1 inhibitors, small molecules that can inhibit two viral functions at the same time. Rhubarb, originated from Rheum palmatum L. and Rheum officinale Baill., is one of the earliest and most commonly used medicinal plants in Traditional Chinese Medicine (TCM) practice. We wanted to explore TCM for the identification of new chemical scaffolds with dual action abilities against HIV-1...
November 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27755604/correction-a-computational-model-for-predicting-rnase-h-domain-of-retrovirus
#19
Sijia Wu, Xinman Zhang, Jiuqiang Han
[This corrects the article DOI: 10.1371/journal.pone.0161913.].
2016: PloS One
https://www.readbyqxmd.com/read/27723087/strand-specific-transcriptome-sequencing-using-smart-technology
#20
Magnolia Bostick, Nathalie Bolduc, Alisa Lehman, Andrew Farmer
Next-generation sequencing is empowering a deeper understanding of biology by enabling RNA expression analysis over the entire transcriptome with high sensitivity and a wide dynamic range. One powerful application within this field is stranded RNA sequencing (RNA-seq), which is necessary to distinguish overlapping genes and to conduct comprehensive annotation and quantification of long non-coding RNAs. Commonly used methods for generating strand-specific RNA-seq libraries are often complicated by protocols that require several rounds of enzymatic treatments and clean-up steps, making them time-intensive, insensitive, and unsuitable for processing several samples simultaneously...
October 10, 2016: Current Protocols in Molecular Biology
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