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https://www.readbyqxmd.com/read/28525600/a-novel-double-kink-turn-module-in-euryarchaeal-rnase-p-rnas
#1
Lien B Lai, Akiko Tanimoto, Stella M Lai, Wen-Yi Chen, Ila A Marathe, Eric Westhof, Vicki H Wysocki, Venkat Gopalan
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525279/double-winged-3-hydroxypyrimidine-2-4-diones-potent-and-selective-inhibition-against-hiv-1-rnase-h-with-significant-antiviral-activity
#2
Sanjeev Kumar V Vernekar, Jing Tang, Bulan Wu, Andrew D Huber, Mary C Casey, Nataliya S Myshakina, Daniel J Wilson, Jayakanth Kankanala, Karen A Kirby, Michael A Parniak, Stefan G Sarafianos, Zhengqiang Wang
Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function yet to be exploited as an antiviral target. One of the possible challenges may be that targeting HIV RNase H is confronted with a steep substrate barrier. We have previously reported a 3-hydroxypyrimidine-2,4-dione (HPD) subtype that potently and selectively inhibited RNase H without inhibiting HIV in cell culture. We report herein a critical redesign of the HPD chemotype featuring an additional wing at the C5 position that led to drastically improved RNase H inhibition and significant antiviral activity...
May 19, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28498974/strong-transcription-blockage-mediated-by-r-loop-formation-within-a-g-rich-homopurine-homopyrimidine-sequence-localized-in-the-vicinity-of-the-promoter
#3
Boris P Belotserkovskii, Jane Hae Soo Shin, Philip C Hanawalt
Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28496054/days-weaving-the-lagging-strand-synthesis-of-dna-a-personal-recollection-of-the-discovery-of-okazaki-fragments-and-studies-on-discontinuous-replication-mechanism
#4
Tsuneko Okazaki
At DNA replication forks, the overall growth of the antiparallel two daughter DNA chains appears to occur 5'-to-3' direction in the leading-strand and 3'-to-5' direction in the lagging-strand using enzyme system only able to elongate 5'-to-3' direction, and I describe in this review how we have analyzed and proved the lagging strand multistep synthesis reactions, called Discontinuous Replication Mechanism, which involve short RNA primer synthesis, primer-dependent short DNA chains (Okazaki fragments) synthesis, primer removal from the Okazaki fragments and gap filling between Okazaki fragments by RNase H and DNA polymerase I, and long lagging strand formation by joining between Okazaki fragments with DNA ligase...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28495858/comparative-functional-analysis-of-ribonuclease-1-homologs-molecular-insights-into-evolving-vertebrate-physiology
#5
Jo E Lomax, Chelcie H Eller, Ronald T Raines
Pancreatic-type ribonucleases (ptRNases) comprise a class of highly conserved secretory endoribonucleases in vertebrates. The prototype of this enzyme family is ribonuclease 1 (RNase 1). Understanding the physiological roles of RNase 1 is becoming increasingly important, as engineered forms of the enzyme progress through clinical trials as chemotherapeutic agents for cancer. Here we present an in-depth biochemical characterization of RNase 1 homologs from a broad range of mammals (human, bat, squirrel, horse, cat, mouse, and cow) and non-mammalian species (chicken, lizard, and frog)...
May 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28477335/2-%C3%AE-fluoro-tricyclo-nucleic-acids-2-f-tc-ana-thermal-duplex-stability-structural-studies-and-rnase-h-activation
#6
Alena Istrate, Adam Katolik, Andrei Istrate, Christian Joerg Leumann
We describe the synthesis, thermal stability and structural and RNase H activation properties of 2'β-fluoro-tricyclo nucleic acids (2'F-tc-ANA). Three 2'F-tc-ANA nucleosides (T, 5MeC and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements...
May 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28465635/berberine-displays-antitumor-activity-in-esophageal-cancer-cells-in-vitro
#7
Shu-Xian Jiang, Bo Qi, Wen-Jian Yao, Cheng-Wei Gu, Xiu-Feng Wei, Yi Zhao, Yu-Zhen Liu, Bao-Sheng Zhao
AIM: To investigate the effects of berberine on esophageal cancer (EC) cells and its molecular mechanisms. METHODS: Human esophageal squamous cell carcinoma cell line KYSE-70 and esophageal adenocarcinoma cell line SKGT4 were used. The effects of berberine on cell proliferation were evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. For cell cycle progression, KYSE-70 cells were stained with propidium iodide (PI) staining buffer (10 mg/mL PI and 100 mg/mL RNase A) for 30 min and cell cycle was analyzed using a BD FACSCalibur flow cytometer...
April 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28451245/protecting-micrornas-from-rnase-degradation-with-steric-dna-nanostructures
#8
H Qian, C Y Tay, M I Setyawati, S L Chia, D S Lee, D T Leong
Tumor suppressive microRNAs are potent molecules that might cure cancer, one day. Despite the many advanced strategies for delivery of these microRNAs to the cell, there are few therapeutic microRNAs in clinical use. Progress in microRNA bioapplications is hindered by a high vulnerability of exogeneous microRNA molecules to RNase degradation that occurs in extra- and intracellular physiological conditions. In this proof-of-concept study, we use a programmable self-assembled DNA nanostructure bearing a "shuriken" shape to not only deliver but more importantly protect a tumor suppressive microRNA-145 for a sufficiently long time to exert its therapeutic effect in human colorectal cancer cells...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28442387/establishment-of-microrna-delivery-system-by-pp7-bacteriophage-like-particles-carrying-cell-penetrating-peptide
#9
Yanli Sun, Yanhua Sun, Ronglan Zhao
MicroRNAs have great therapeutic potential in cancer and other diseases. However, their instability and low in vivo delivery efficiency limits their application. Recombinant PP7 bacteriophage-based virus-like particles (VLPs) could protect microRNAs against rapid degradation by RNase by packaging specific exogenous pre-microRNAs using the pac site. Insertion of a cell-penetrating peptide (CPP) into the AB-loop of VLPs could significantly improve the delivery efficiency of microRNAs into mammalian cells. Unlike other microRNA delivery methods (viral or non-viral vectors), recombinant PP7 VLPs carrying a CPP and microRNA could be efficiently expressed in Escherichia coli using the one-plasmid double expression system...
April 22, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28437166/virus-like-particles-of-mrna-with-artificial-minimal-coat-proteins-particle-formation-stability-and-transfection-efficiency
#10
Shehrazade Jekhmane, Rob de Haas, Omar Paulino da Silva Filho, Alexander H van Asbeck, Marco Emanuele Favretto, Armando Hernandez Garcia, Roland Brock, Renko de Vries
RNA has enormous potential as a therapeutic, yet, the successful application depends on efficient delivery strategies. In this study, we demonstrate that a designed artificial viral coat protein, which self-assembles with DNA to form rod-shaped virus-like particles (VLPs), also encapsulates and protects mRNA encoding enhanced green fluorescent protein (EGFP) and luciferase, and yields cellular expression of these proteins. The artificial viral coat protein consists of an oligolysine (K12) for binding to the oligonucleotide, a silk protein-like midblock S10 = (GAGAGAGQ)10 that self-assembles into stiff rods, and a long hydrophilic random coil block C that shields the nucleic acid cargo from its environment...
February 21, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/28408394/a-close-up-look-at-the-spliceosome-at-last
#11
John Abelson
Major developments in cryo-electron microscopy in the past three or four years have led to the solution of a number of spliceosome structures at high resolution, e.g., the fully assembled but not yet active spliceosome (Bact), the spliceosome just after the first step of splicing (C), and the spliceosome activated for the second step (C*). Therefore 30 years of genetics and biochemistry of the spliceosome can now be interpreted at the structural level. I have closely examined the RNase H domain of Prp8 in each of the structures...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28402412/effects-of-neutral-salts-and-ph-on-the-activity-and-stability-of-human-rnase-h2
#12
Misato Baba, Kenji Kojima, Rihoko Nakase, Shota Imai, Tomomi Yamasaki, Teisuke Takita, Robert J Crouch, Kiyoshi Yasukawa
Ribonuclease H (RNase H) specifically degrades the RNA of RNA/DNA hybrid. Recent study has shown that a single ribonucleotide is embedded in DNA double strand at every few thousand base pairs in human genome, and human RNase H2 is involved in its removal. Here, we examined the effects of neutral salts and pH on the activity and stability of human RNase H2. NaCl, KCl, RbCl, and NaBr increased the activity to 170-390% at 10-60 mM, while LiCl, LiBr, and CsCl inhibited it, suggesting that species of cation, but not anion, is responsible for the effect on activity...
April 11, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28400719/reduction-of-huntington-s-disease-rna-foci-by-cag-repeat-targeting-reagents
#13
Martyna O Urbanek, Agnieszka Fiszer, Wlodzimierz J Krzyzosiak
In several human polyglutamine diseases caused by expansions of CAG repeats in the coding sequence of single genes, mutant transcripts are detained in nuclear RNA foci. In polyglutamine disorders, unlike other repeat-associated diseases, both RNA and proteins exert pathogenic effects; therefore, decreases of both RNA and protein toxicity need to be addressed in proposed treatments. A variety of oligonucleotide-based therapeutic approaches have been developed for polyglutamine diseases, but concomitant assays for RNA foci reduction are lacking...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28384548/synthesis-biological-evaluation-and-molecular-modeling-of-2-hydroxyisoquinoline-1-3-dione-analogues-as-inhibitors-of-hiv-reverse-transcriptase-associated-ribonuclease-h-and-polymerase
#14
Jing Tang, Sanjeev Kumar V Vernekar, Yue-Lei Chen, Lena Miller, Andrew D Huber, Nataliya Myshakina, Stefan G Sarafianos, Michael A Parniak, Zhengqiang Wang
Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function not clinically validated as an antiviral target. 2-Hydroxyisoquinoline-1,3-dione (HID) is known to confer active site directed inhibition of divalent metal-dependent enzymatic functions, such as HIV RNase H, integrase (IN) and hepatitis C virus (HCV) NS5B polymerase. We report herein the synthesis and biochemical evaluation of a few C-5, C-6 or C-7 substituted HID subtypes as HIV RNase H inhibitors...
June 16, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28383274/past-current-and-future-developments-of-therapeutic-agents-for-treatment-of-chronic-hepatitis-b-virus-infection
#15
Yameng Pei, Chunting Wang, S Frank Yan, Gang Liu
For decades, treatment of hepatitis B virus (HBV) infection has been relying on interferon (IFN)-based therapies and nucleoside/nucleotide analogues (NAs) that selectively target the viral polymerase reverse transcriptase (RT) domain and thereby disrupt HBV viral DNA synthesis. We have summarized here the key steps in the HBV viral life cycle, which could potentially be targeted by novel anti-HBV therapeutics. A wide range of next-generation direct antiviral agents (DAAs) with distinct mechanisms of actions are discussed, including entry inhibitors, transcription inhibitors, nucleoside/nucleotide analogues, inhibitors of viral ribonuclease H (RNase H), modulators of viral capsid assembly, inhibitors of HBV surface antigen (HBsAg) secretion, RNA interference (RNAi) gene silencers, antisense oligonucleotides (ASOs), and natural products...
April 21, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28373864/chelation-motifs-affecting-metal-dependent-viral-enzymes-n-acylhydrazone-ligands-as-dual-target-inhibitors-of-hiv-1-integrase-and-reverse-transcriptase-ribonuclease-h-domain
#16
Mauro Carcelli, Dominga Rogolino, Anna Gatti, Nicolino Pala, Angela Corona, Alessia Caredda, Enzo Tramontano, Christophe Pannecouque, Lieve Naesens, Francesca Esposito
Human immunodeficiency virus type 1 (HIV-1) infection, still represent a serious global health emergency. The chronic toxicity derived from the current anti-retroviral therapy limits the prolonged use of several antiretroviral agents, continuously requiring the discovery of new antiviral agents with innovative strategies of action. In particular, the development of single molecules targeting two proteins (dual inhibitors) is one of the current main goals in drug discovery. In this contest, metal-chelating molecules have been extensively explored as potential inhibitors of viral metal-dependent enzymes, resulting in some important classes of antiviral agents...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28362255/ribonuclease-l-mediates-the-cell-lethal-phenotype-of-double-stranded-rna-editing-enzyme-adar1-deficiency-in-a-human-cell-line
#17
Yize Li, Shuvojit Banerjee, Stephen A Goldstein, Beihua Dong, Christina Gaughan, Sneha Rath, Jesse Donovan, Alexei Korennykh, Robert H Silverman, Susan R Weiss
ADAR1 isoforms are adenosine deaminases that edit and destabilize double-stranded RNA reducing its immunostimulatory activities. Mutation of ADAR1 leads to a severe neurodevelopmental and inflammatory disease of children, Aicardi-Goutiéres syndrome. In mice, Adar1 mutations are embryonic lethal but are rescued by mutation of the Mda5 or Mavs genes, which function in IFN induction. However, the specific IFN regulated proteins responsible for the pathogenic effects of ADAR1 mutation are unknown. We show that the cell-lethal phenotype of ADAR1 deletion in human lung adenocarcinoma A549 cells is rescued by CRISPR/Cas9 mutagenesis of the RNASEL gene or by expression of the RNase L antagonist, murine coronavirus NS2 accessory protein...
March 31, 2017: ELife
https://www.readbyqxmd.com/read/28352859/how-rnase-hi-escherichia-coli-promoted-site-selective-hydrolysis-works-on-rna-in-duplex-with-carba-lna-and-lna-substituted-antisense-strands-in-an-antisense-strategy-context
#18
Oleksandr Plashkevych, Qing Li, Jyoti Chattopadhyaya
A detailed kinetic study of 36 single modified AON-RNA heteroduplexes shows that substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The experiments have been performed using RNase HI of Escherichia coli. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs...
May 2, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28330193/a-rapid-method-for-isolation-of-genomic-dna-from-food-borne-fungal-pathogens
#19
S Umesha, H M Manukumar, Sri Raghava
Food contaminated with fungal pathogens can cause extremely harmful effects to human even when present in low concentrations. Researchers now pay more attention towards rapid DNA extraction for the quick screening, which is highly demanded in diverse research field. Molecular description of many fungal species is identified by different molecular characteristics. Hence, the efficient isolation of genomic DNA and amplification using PCR is a prerequisite for molecular characterization. Here, we used an improved Sodium dodecyl sulfate-Cetyltrimethyl ammonium bromide-Chloroform-isoamyl alcohol method by combining Sodium dodecyl sulfate with cetyl methylammonium bromide without addition of proteinase K, RNase K, and β-mercaptoethanol...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28317959/packing-energetics-determine-the-folding-routes-of-the-rnase-h-proteins
#20
Shilpa Yadahalli, Shachi Gosavi
Comparative studies of proteins from a family have been used to understand the factors that determine the folding routes of proteins. It has been conjectured that the folding mechanism of ribonuclease-H (RNase-H) proteins is determined by the topology of their fold. To test this hypothesis, we computationally studied the folding of four proteins from the RNase-H family, which have the overall RNase-H fold, but whose topologies differ in the region termed CORE in E. coli RNase-H. We simulated the folding of these proteins using molecular dynamics (MD) simulations of a coarse-grained structure-based model (SBM) which captures the effects of topology and found that the four proteins had similar folding routes...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
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