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Rnase h

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https://www.readbyqxmd.com/read/29126318/rnase-h-sequence-preferences-influence-antisense-oligonucleotide-efficiency
#1
Lukasz J Kielpinski, Peter H Hagedorn, Morten Lindow, Jeppe Vinther
RNase H cleaves RNA in RNA-DNA duplexes. It is present in all domains of life as well as in multiple viruses and is essential for mammalian development and for human immunodeficiency virus replication. Here, we developed a sequencing-based method to measure the cleavage of thousands of different RNA-DNA duplexes and thereby comprehensively characterized the sequence preferences of HIV-1, human and Escherichia coli RNase H enzymes. We find that the catalytic domains of E. coli and human RNase H have nearly identical sequence preferences, which correlate with the efficiency of RNase H-recruiting antisense oligonucleotides...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122886/mechanism-of-polypurine-tract-primer-generation-by-hiv-1-reverse-transcriptase
#2
Małgorzata Figiel, Miroslav Krepl, Sangwoo Park, Jarosław Poznański, Krzysztof Skowronek, Agnieszka Gołąb, Taekjip Ha, Jiři Šponer, Marcin Nowotny
HIV-1 reverse transcriptase (HIV-1 RT) possesses both DNA polymerase activity and RNase H activity that act in concert to convert single-stranded RNA of the viral genome to double-stranded DNA that is then integrated into the DNA of the infected cell. Reverse transcriptase-catalyzed reverse transcription critically relies on the proper generation of a polypurine tract (PPT) primer. However, the mechanism of PPT primer generation and the features of the PPT sequence that are critical for its recognition by HIV-1 RT remain unclear...
November 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29118447/influenza-virus-segment-5-rna-secondary-structure-and-new-targets-for-antiviral-strategies
#3
Marta Soszynska-Jozwiak, Paula Michalak, Walter N Moss, Ryszard Kierzek, Julita Kesy, Elzbieta Kierzek
Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29117130/characterization-of-nucleoside-reverse-transcriptase-inhibitor-associated-mutations-in-the-rnase-h-region-of-hiv-1-subtype-c-infected-individuals
#4
Sinaye Ngcapu, Kristof Theys, Pieter Libin, Vincent C Marconi, Henry Sunpath, Thumbi Ndung'u, Michelle L Gordon
The South African national treatment programme includes nucleoside reverse transcriptase inhibitors (NRTIs) in both first and second line highly active antiretroviral therapy regimens. Mutations in the RNase H domain have been associated with resistance to NRTIs but primarily in HIV-1 subtype B studies. Here, we investigated the prevalence and association of RNase H mutations with NRTI resistance in sequences from HIV-1 subtype C infected individuals. RNase H sequences from 112 NRTI treated but virologically failing individuals and 28 antiretroviral therapy (ART)-naive individuals were generated and analysed...
November 8, 2017: Viruses
https://www.readbyqxmd.com/read/29111294/oxygen-binding-isotope-effects-of-triazole-based-hiv-1-reverse-transcriptase-inhibitors-indicate-the-actual-binding-site
#5
Agnieszka Krzemińska, Tomasz Frączek, P Paneth
Binding isotope effects (BIEs) associated with binding of four triazole-based ligands to HIV-1 reverse transcriptase have been calculated at the QM/MM MD level of theory. Two main binding sites: allosteric cavity and RNase H active site, as well as three other sites reported in the literature (the Knuckles, the NNRTI Adjacent, and Incoming Nucleotide Binding) have been considered. The interactions between inhibitors and these protein sites have been quantified by binding free energies obtained from free energy perturbation (FEP) calculations, supported by interaction energy analysis...
October 27, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29104020/r-chip-using-inactive-rnase-h-reveals-dynamic-coupling-of-r-loops-with-transcriptional-pausing-at-gene-promoters
#6
Liang Chen, Jia-Yu Chen, Xuan Zhang, Ying Gu, Rui Xiao, Changwei Shao, Peng Tang, Hao Qian, Daji Luo, Hairi Li, Yu Zhou, Dong-Er Zhang, Xiang-Dong Fu
R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing...
October 31, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29100074/plexin-b2-mediates-physiologic-and-pathologic-functions-of-angiogenin
#7
Wenhao Yu, Kevin A Goncalves, Shuping Li, Hiroko Kishikawa, Guangjie Sun, Hailing Yang, Nil Vanli, Yunxia Wu, Yuxiang Jiang, Miaofen G Hu, Roland H Friedel, Guo-Fu Hu
Angiogenin (ANG) is a secreted ribonuclease (RNase) with cell-type- and context-specific roles in growth, survival, and regeneration. Although these functions require receptor-mediated endocytosis and appropriate subcellular localization, the identity of the cell surface receptor remains undefined. Here, we show that plexin-B2 (PLXNB2) is the functional receptor for ANG in endothelial, cancer, neuronal, and normal hematopoietic and leukemic stem and progenitor cells. Mechanistically, PLXNB2 mediates intracellular RNA processing that contribute to cell growth, survival, and regenerative capabilities of ANG...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29099294/introducing-the-new-bacterial-branch-of-the-rnase-a-superfamily
#8
Bonnie J Cuthbert, Kalistyn H Burley, Celia W Goulding
Bovine pancreatic ribonuclease (RNase A) is the founding member of the RNase A superfamily. Members of this superfamily of ribonucleases have high sequence diversity, but possess a similar structural fold, together with a conserved His-Lys-His catalytic triad and structural disulfide bonds. Until recently, RNase A proteins had exclusively been identified in eukaryotes within vertebrae. Here, we discuss the discovery by Batot et al. of a bacterial RNase A superfamily member, CdiA-CT(Ykris): a toxin that belongs to an inter-bacterial competition system from Yersinia kristensenii...
November 3, 2017: RNA Biology
https://www.readbyqxmd.com/read/29053842/differential-expression-of-water-channel-and-noncoding-rna-biogenesis-related-genes-in-three-lines-of-chickens-under-a-short-term-water-restriction
#9
S Orlowski, J Flees, N Anthony, S Dridi
Genetic selection for high growth rate has resulted in tremendous changes not only in feed efficiency, but also in water consumption between modern broilers and their ancestor jungle fowl (JF). However molecular mechanisms involved in water homeostasis are still not well defined. This study aimed, therefore, to determine the effect of short-term water restriction on the expression of water channel- and noncoding RNA biogenesis-related genes in the kidney and whole blood of JF, broiler population from the 1990s (RB1995), and modern broiler population developed in 2015 (ARB2015)...
October 5, 2017: Poultry Science
https://www.readbyqxmd.com/read/29052506/the-proposed-new-species-cacao-red-vein-virus-and-three-previously-recognized-badnavirus-species-are-associated-with-cacao-swollen-shoot-disease
#10
Nomatter Chingandu, Koffie Kouakou, Romain Aka, George Ameyaw, Osman A Gutierrez, Hans-Werner Herrmann, Judith K Brown
BACKGROUND: Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only ~50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. METHODS: The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing...
October 19, 2017: Virology Journal
https://www.readbyqxmd.com/read/29037807/dicer1-related-sertoli-leydig-cell-tumor-and-gynandroblastoma-clinical-and-genetic-findings-from-the-international-ovarian-and-testicular-stromal-tumor-registry
#11
Kris Ann P Schultz, Anne K Harris, Michael Finch, Louis P Dehner, Jubilee B Brown, David M Gershenson, Robert H Young, Amanda Field, Weiying Yu, Joyce Turner, Nicholas G Cost, Dominik T Schneider, Douglas R Stewart, A Lindsay Frazier, Yoav Messinger, D Ashley Hill
BACKGROUND: Ovarian sex cord-stromal tumors (OSCST) include juvenile granulosa cell tumors (JGCT), Sertoli-Leydig cell tumor (SLCT) and gynandroblastoma (GAB) among others. These ovarian sex cord-stromal tumors as well as other tumors including pleuropulmonary blastoma (PPB) may be associated with DICER1 mutations. We sought to describe the clinical and genetic findings from the first 107 individuals enrolled in the International Ovarian and Testicular Stromal Tumor Registry. METHODS: Medical and family history were obtained for individuals consecutively enrolled in the International Ovarian and Testicular Stromal Tumor Registry...
October 13, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29036477/a-single-active-site-in-the-mariner-transposase-cleaves-dna-strands-of-opposite-polarity
#12
Corentin Claeys Bouuaert, Ronald Chalmers
The RNase H structural fold defines a large family of nucleic acid metabolizing enzymes that catalyze phosphoryl transfer reactions using two divalent metal ions in the active site. Almost all of these reactions involve only one strand of the nucleic acid substrates. In contrast, cut-and-paste transposases cleave two DNA strands of opposite polarity, which is usually achieved via an elegant hairpin mechanism. In the mariner transposons, the hairpin intermediate is absent and key aspects of the mechanism by which the transposon ends are cleaved remained unknown...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29031062/design-synthesis-and-biological-evaluations-of-n-hydroxy-thienopyrimidine-2-4-diones-as-inhibitors-of-hiv-reverse-transcriptase-associated-rnase-h
#13
Jayakanth Kankanala, Karen A Kirby, Andrew D Huber, Mary C Casey, Daniel J Wilson, Stefan G Sarafianos, Zhengqiang Wang
Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture...
December 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28980684/a-label-free-and-enzyme-free-signal-amplification-strategy-for-a-sensitive-rnase-h-activity-assay
#14
Chang Yeol Lee, Hyowon Jang, Ki Soo Park, Hyun Gyu Park
We herein describe a label-free and enzyme-free signal amplification strategy for the sensitive determination of ribonuclease H (RNase H) activity, which relies on the target-triggered catalytic hairpin assembly (CHA) in conjunction with a G-quadruplex specific fluorescent binder, N-methyl mesoporphyrin IX (NMM). In the absence of RNase H, the RNA/DNA duplex serving as a substrate for RNase H cannot initiate the execution of CHA that produces G-quadruplexes; so NMM shows a low fluorescence signal. In contrast, the presence of RNase H that degrades RNA in the RNA/DNA duplex releases DNA designed to function as the catalyst for CHA...
November 2, 2017: Nanoscale
https://www.readbyqxmd.com/read/28978041/sperm-carried-rnas-play-critical-roles-in-mouse-embryonic-development
#15
Lei Guo, Shi-Bin Chao, Lu Xiao, Zhen-Bo Wang, Tie-Gang Meng, Yuan-Yuan Li, Zhi-Ming Han, Ying-Chun Ouyang, Yi Hou, Qing-Yuan Sun, Xiang-Hong Ou
Recently, numerous studies have reported that the mature sperm contains both coding and non-coding RNAs and the sperm delivers some RNAs to the oocyte at fertilization. However, the functions of the RNAs carried to the oocyte by sperm at fertilization in embryonic development remains a mystery. In this study, the mature spermatozoa were treated with lysolecithin, pronase and RNases (RNase A and RNase H) to remove the sperm-carried RNAs, and then injected into normal mature oocyte. The results showed that after the treatment, the content of the sperm RNAs was decreased by about 90%...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977560/dynamic-nucleoplasmic-and-nucleolar-localization-of-mammalian-rnase-h1-in-response-to-rnap-i-transcriptional-r-loops
#16
Wen Shen, Hong Sun, Cheryl L De Hoyos, Jeffrey K Bailey, Xue-Hai Liang, Stanley T Crooke
An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migration of RNase H1 and R-loops from nucleoli to perinucleolar ring structures was observed upon inhibition of RNAP I transcription. Treatment with camptothecin which transiently stabilized nucleolar R-loops recruited RNase H1 to the nucleoli...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28970564/influence-of-mismatched-and-bulged-nucleotides-on-snp-preferential-rnase-h-cleavage-of-rna-antisense-gapmer-heteroduplexes
#17
Dorota Magner, Ewa Biala, Jolanta Lisowiec-Wachnicka, Ryszard Kierzek
This study focused on determining design rules for gapmer-type antisense oligonucleotides (ASOs), that can differentiate cleavability of two SNP variants of RNA in the presence of ribonuclease H based on the mismatch type and position in the heteroduplex. We describe the influence of structural motifs formed by several arrangements of multiple mismatches (various types of mismatches and their position within the ASO/target RNA duplex) on RNase H cleavage selectivity of five different SNP types. The targets were mRNA fragments of APP, SCA3, SNCA and SOD1 genes, carrying C-to-G, G-to-C, G-to-A, A-to-G and C-to-U substitutions...
October 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28959243/rnase-h-as-gene-modifier-driver-of-evolution-and-antiviral-defense
#18
REVIEW
Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi Sunagawa
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931690/conformational-changes-in-the-5-end-of-the-hiv-1-genome-dependent-on-the-debranching-enzyme-dbr1-during-early-stages-of-infection
#19
Alvaro E Galvis, Hugh E Fisher, Hung Fan, David Camerini
Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation, but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 shRNA followed 48 hours later by infection with an HIV-1 derived vector containing an RNase H deficient reverse transcriptase...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28926069/rna-directed-off-on-switch-of-rnase-h-activity-using-boronic-ester-formation
#20
Maëva Reverte, Ivan Barvik, Jean-Jacques Vasseur, Michael Smietana
RNase H is a non-specific endonuclease which degrades selectively the RNA strand in DNA/RNA duplexes. We demonstrate in the present study that 5'-boronic acid modified oligonucleotides hybridized to a RNA target sequence converts RNase H to an inactivated enzyme complex. The dynamic formation of a boronate ester upon addition of a diol moiety disrupts the enzyme-inhibitor complex and reactivates RNase H. Moreover, we show that reactivation of RNase H function can also be engineered through short RNA trimers inputs that fashion RNase H from a non-specific DNA-guided enzyme into an informational and programmable RNA-guided one...
October 4, 2017: Organic & Biomolecular Chemistry
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