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https://www.readbyqxmd.com/read/28437166/virus-like-particles-of-mrna-with-artificial-minimal-coat-proteins-particle-formation-stability-and-transfection-efficiency
#1
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
#2
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 13, 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
#3
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
#4
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
#5
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...
March 29, 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
#6
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
#7
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-the-double-stranded-rna-editing-enzyme-adar1-in-a-human-cell-line
#8
Yize Li, Shuvojit Banerjee, Stephen A Goldstein, Beihua Dong, Christina Gaughan, Sneha Rath, Jesse Donovan, Alexei V 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
#9
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...
March 29, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28330193/a-rapid-method-for-isolation-of-genomic-dna-from-food-borne-fungal-pathogens
#10
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
#11
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
https://www.readbyqxmd.com/read/28306242/excision-repair-initiated-enzyme-assisted-bicyclic-cascade-signal-amplification-for-ultrasensitive-detection-of-uracil-dna-glycosylase
#12
Li-Juan Wang, Ming Ren, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus, the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification...
March 29, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28302473/quantitative-relationship-between-chemical-properties-and-bioactivities-of-anti-microrna-oligonucleotides-targeted-to-tumor-associated-microrna-21
#13
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
Synthetic anti-microRNA oligonucleotides (AMOs) are promising drug candidates to inactivate disease-related microRNAs because of their sequence-specific binding to their targets and the variety of chemical modifications available. Over the last decade, the qualitative relationships between the chemical properties of AMOs and bioactivity (inactivation of their target miRNAs) have been studied to enhance their bioactivity. On the other hand, in real-world drug development, drugs must be designed case-by-case, taking many factors into account...
March 13, 2017: Biochimie
https://www.readbyqxmd.com/read/28299484/characterization-of-a-new-badnavirus-from-wisteria-sinensis
#14
Yongqiang Li, Congliang Deng, Yan Qiao, Xiaoli Zhao, Qi Zhou
The complete genome sequence of a previously undescribed badnavirus isolated from a wisteria plant exhibiting mosaic and crinkle symptoms in Beijing, China, was determined. The circular double-stranded DNA genome of this virus was 7362 bp in size with four open reading frames (ORFs 1 to 4) on the plus strand. Sequence analysis showed that this virus shared the highest (69%) nucleotide (nt) sequence identity with pagoda yellow mosaic associated virus (PYMAV). In the RT-RNase H region of the ORF-3 encoded polyprotein, this virus shared 74% nt sequence identity with PYMAV...
March 15, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28281253/microrna-biosensing-with-two-dimensional-surface-plasmon-resonance-imaging
#15
Ho Pui Ho, Fong Chuen Loo, Shu Yuen Wu, Dayong Gu, Ken-Tye Yong, Siu Kai Kong
Two-dimensional surface plasmon resonance (2D-SPR) imaging, which provides a real-time, sensitive, and high-throughput analysis of surface events in a two dimensional manner, is a valuable tool for studying biomolecular interactions and biochemical reactions without using any tag labels. The sensing principle of 2D-SPR includes angular, wavelength, and phase interrogation. In this chapter, the 2D-SPR imaging technique is applied for sensing a target microRNA by its corresponding oligonucleotide probes, with sequence complementarity, immobilized on the gold SPR sensing surface...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28278199/monitoring-integrity-and-localization-of-modified-single-stranded-rna-oligonucleotides-using-ultrasensitive-fluorescence-methods
#16
Philipp Heissig, Waldemar Schrimpf, Philipp Hadwiger, Ernst Wagner, Don C Lamb
Short single-stranded oligonucleotides represent a class of promising therapeutics with diverse application areas. Antisense oligonucleotides, for example, can interfere with various processes involved in mRNA processing through complementary base pairing. Also RNA interference can be regulated by antagomirs, single-stranded siRNA and single-stranded microRNA mimics. The increased susceptibility to nucleolytic degradation of unpaired RNAs can be counteracted by chemical modification of the sugar phosphate backbone...
2017: PloS One
https://www.readbyqxmd.com/read/28271277/sequence-specific-backbone-resonance-assignments-and-microsecond-timescale-molecular-dynamics-simulation-of-human-eosinophil-derived-neurotoxin
#17
Donald Gagné, Chitra Narayanan, Khushboo Bafna, Laurie-Anne Charest, Pratul K Agarwal, Nicolas Doucet
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response...
March 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28268090/both-r-loop-removal-and-ribonucleotide-excision-repair-activities-of-rnase-h2-contribute-substantially-to-chromosome-stability
#18
Deborah A Cornelio, Hailey N C Sedam, Jessica A Ferrarezi, Nadia M V Sampaio, Juan Lucas Argueso
Cells carrying deletions of genes encoding H-class ribonucleases display elevated rates of chromosome instability. The role of these enzymes is to remove RNA-DNA associations including persistent mRNA-DNA hybrids (R-loops) formed during transcription, and ribonucleotides incorporated into DNA during replication. RNases H1 and H2 can degrade the RNA component of R-loops, but only RNase H2 can initiate accurate ribonucleotide excision repair (RER). In order to examine the specific contributions of these activities to chromosome stability, we measured rates of loss-of-heterozygosity (LOH) in diploid Saccharomyces cerevisiae yeast strains carrying the rnh201-RED separation-of-function allele, encoding a version of RNase H2 that is RER-defective, but partly retains its other activity...
April 2017: DNA Repair
https://www.readbyqxmd.com/read/28258464/sequential-fragment-ion-filtering-and-endoglycosidase-assisted-identification-of-intact-glycopeptides
#19
Zixiang Yu, Xinyuan Zhao, Fang Tian, Yang Zhao, Yong Zhang, Yi Huang, Xiaohong Qian, Wantao Ying
Detailed characterization of glycoprotein structures requires determining both the sites of glycosylation as well as the glycan structures associated with each site. In this work, we developed an analytical strategy for characterization of intact N-glycopeptides in complex proteome samples. In the first step, tryptic glycopeptides were enriched using ZIC-HILIC. Secondly, a portion of the glycopeptides was treated with endoglycosidase H (Endo H) to remove high-mannose (Man) and hybrid N-linked glycans. Thirdly, a fraction of the Endo H-treated glycopeptides was further subjected to PNGase F treatment in (18)O water to remove the remaining complex glycans...
March 3, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28254698/natural-product-inspired-esters-and-amides-of-ferulic-and-caffeic-acid-as-dual-inhibitors-of-hiv-1-reverse-transcriptase
#20
Vijay P Sonar, Angela Corona, Simona Distinto, Elias Maccioni, Rita Meleddu, Benedetta Fois, Costantino Floris, Nilesh V Malpure, Stefano Alcaro, Enzo Tramontano, Filippo Cottiglia
Using an HIV-1 Reverse Transcriptase (RT)-associated RNase H inhibition assay as lead, bioguided fractionation of the dichloromethane extract of the Ocimum sanctum leaves led to the isolation of five triterpenes (1-5) along with three 3-methoxy-4-hydroxy phenyl derivatives (6-8). The structure of this isolates were determined by 1D and 2D NMR experiments as well as ESI-MS. Tetradecyl ferulate (8) showed an interesting RNase H IC50 value of 12.4 μM and due to the synthetic accessibility of this secondary metabolite, a structure-activity relationship study was carried out...
April 21, 2017: European Journal of Medicinal Chemistry
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