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https://www.readbyqxmd.com/read/28918041/gapmer-antisense-oligonucleotides-suppress-the-mutant-allele-of-col6a3-and-restore-functional-protein-in-ullrich-muscular-dystrophy
#1
Elena Marrosu, Pierpaolo Ala, Francesco Muntoni, Haiyan Zhou
Dominant-negative mutations in the genes that encode the three major α chains of collagen type VI, COL6A1, COL6A2, and COL6A3, account for more than 50% of Ullrich congenital muscular dystrophy patients and nearly all Bethlem myopathy patients. Gapmer antisense oligonucleotides (AONs) are usually used for gene silencing by stimulating RNA cleavage through the recruitment of an endogenous endonuclease known as RNase H to cleave the RNA strand of a DNA-RNA duplex. In this study, we exploited the application of the allele-specific silencing approach by gapmer AON as a potential therapy for Collagen-VI-related congenital muscular dystrophy (COL6-CMD)...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918018/locked-nucleic-acid-gapmers-and-conjugates-potently-silence-adam33-an-asthma-associated-metalloprotease-with-nuclear-localized-mrna
#2
Hannah M Pendergraff, Pranathi Meda Krishnamurthy, Alexandre J Debacker, Michael P Moazami, Vivek K Sharma, Liisa Niitsoo, Yong Yu, Yen Nee Tan, Hans Michael Haitchi, Jonathan K Watts
Two mechanisms dominate the clinical pipeline for oligonucleotide-based gene silencing, namely, the antisense approach that recruits RNase H to cleave target RNA and the RNAi approach that recruits the RISC complex to cleave target RNA. Multiple chemical designs can be used to elicit each pathway. We compare the silencing of the asthma susceptibility gene ADAM33 in MRC-5 lung fibroblasts using four classes of gene silencing agents, two that use each mechanism: traditional duplex small interfering RNAs (siRNAs), single-stranded small interfering RNAs (ss-siRNAs), locked nucleic acid (LNA) gapmer antisense oligonucleotides (ASOs), and novel hexadecyloxypropyl conjugates of the ASOs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917670/morphological-characterization-and-biocontrol-effects-of-vibrio-vulnificus-phages-against-vibriosis-in-the-shrimp-aquaculture-environment
#3
P Srinivasan, P Ramasamy
The re-emerging field of phage therapy is the potential biocontrol agents for the transfer of virulence factor and to kill their bacterial hosts. In this study, the lytic Vibrio vulnificus phages were studied to provide a better understanding of phage-host interactions and development of phage therapy. Four new V. vulnificus phages were detected from shrimp aquaculture system, named VV1, VV2, VV3 and VV4. All lytic V. vulnificus phages are the Tecviruses of the family Tectiviridae with typical double layered elongated icosahedral head and tailless morphology...
September 13, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28911227/a-fluorescence-assay-for-ribonuclease-h-based-on-non-labeled-substrate-and-dnazyme-assisted-cascade-amplification
#4
Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang, Chunyi Tong
As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA-RNA chimeric strands. DNAzyme, a synthetic single-stranded DNA consisting of binding and catalytic sites, can cleave RNA in the presence of cofactors. In this study, we establish a highly sensitive RNase H assay assisted with DNAzyme's cleavage property. A DNA-RNA chimeric strand, which contains DNAzyme sequences, is used as the hydrolysis substrate of RNase H. The RNase H hydrolysis of the chimeric substrate results in the release of DNAzyme...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28911100/genome-wide-analysis-of-influenza-viral-rna-and-nucleoprotein-association
#5
Nara Lee, Valerie Le Sage, Adalena V Nanni, Dan J Snyder, Vaughn S Cooper, Seema S Lakdawala
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28905148/building-a-pgc-lc-ms-n-glycan-retention-library-and-elution-mapping-resource
#6
Jodie L Abrahams, Matthew P Campbell, Nicolle H Packer
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS...
September 13, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28887590/transcriptome-and-phytohormone-analysis-reveals-a-comprehensive-phytohormone-and-pathogen-defence-response-in-pear-self-cross-pollination
#7
Dongqing Shi, Chao Tang, Runze Wang, Chao Gu, Xiao Wu, Shi Hu, Jin Jiao, Shaoling Zhang
Candidate genes were identified and the role of phytohormones such as JA-Me and ABA in the synthesis of S-RNase was emphasized in pear self-incompatibility. Self-incompatibility (SI) occurs widely in flowering plants as an intraspecific reproductive barrier. This phenomenon promotes variation within species, but for some species such as Pyrus, SI is a nuisance rather than a benefit in agricultural production. Although many studies have been conducted on SI in pears, its mechanism remains unclear. In this study, high-throughput Illumina RNA sequencing (RNA-seq) was used to identify SI-related genes in pear styles...
September 8, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28877580/characterization-of-echinostoma-cinetorchis-endoribonuclease-rnase-h
#8
Sung-Bin Lim, Seok Ho Cha, Seung Jegal, Hojong Jun, Seo Hye Park, Bo-Young Jeon, Jhang Ho Pak, Young Yil Bakh, Tong-Soo Kim, Hyeong-Woo Lee
Echinostoma cinetorchis is an oriental intestinal fluke causing significant pathological damage to the small intestine. The aim of this study was to determine a full-length cDNA sequence of E. cinetorchis endoribonuclease (RNase H; EcRNH) and to elucidate its molecular biological characters. EcRNH consisted of 308 amino acids and showed low similarity to endoribonucleases of other parasites (<40%). EcRNH had an active site centered on a putative DDEED motif instead of DEDD conserved in other species. A recombinant EcRNH produced as a soluble form in Escherichia coli showed enzymatic activity to cleave the 3'-O-P bond of RNA in a DNA-RNA duplex, producing 3'-hydroxyl and 5'-phosphate...
August 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28859311/design-synthesis-and-antiviral-evaluation-of-novel-heteroarylcarbothioamide-derivatives-as-dual-inhibitors-of-hiv-1-reverse-transcriptase-associated-rnase-h-and-rddp-functions
#9
Angela Corona, Valentina Onnis, Alessandro Deplano, Giulia Bianco, Monica Demurtas, Simona Distinto, Yung-Chi Cheng, Stefano Alcaro, Francesca Esposito, Enzo Tramontano
In the continuous effort to identify new HIV-1 inhibitors endowed with innovative mechanisms, the dual inhibition of different viral functions would provide a significant advantage against drug-resistant variants. The HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) is the only viral-encoded enzymatic activity that still lacks an efficient inhibitor. We synthesized a library of 3,5-diamino-N-aryl-1H-pyrazole-4-carbothioamide and 4-amino-5-benzoyl-N-phenyl-2-(substituted-amino)-1H-pyrrole-3-carbothioamide derivatives and tested them against RNase H activity...
August 31, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28857104/analysing-the-microenvironment-of-2-p-toluidinylnaphthalene-6-sulfonate-tns-in-solvents-and-in-different-conformational-states-of-proteins-in-relation-to-its-fluorescence-properties-a-computational-study
#10
Neshatul Haque, Krishnakanth Baratam, N Prakash Prabhu
Characterization of different conformational states of proteins is essential to understand their stability and activity. Biophysical techniques aid in analysing these conformational states and molecular fluorescence is one of the most reliable and quickly accessible methods. Apart from the intrinsic fluorescence of proteins, external fluorescence dyes such as TNS, ANS, nile red and thioflavin are also used to characterize partially unfolded, aggregated and fibrillar states of proteins, though their exact molecular-level interactions with proteins are yet to be completely unravelled...
August 31, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28854731/multiplexed-analysis-of-fixed-tissue-rna-using-ligation-in-situ-hybridization
#11
Joel J Credle, Christopher Y Itoh, Tiezheng Yuan, Rajni Sharma, Erick R Scott, Rachael E Workman, Yunfan Fan, Franck Housseau, Nicolas J Llosa, W Robert Bell, Heather Miller, Sean X Zhang, Winston Timp, H Benjamin Larman
Clinical tissues are prepared for histological analysis and long-term storage via formalin fixation and paraffin embedding (FFPE). The FFPE process results in fragmentation and chemical modification of RNA, rendering it less suitable for analysis by techniques that rely on reverse transcription (RT) such as RT-qPCR and RNA-Seq. Here we describe a broadly applicable technique called 'Ligation in situ Hybridization' ('LISH'), which is an alternative methodology for the analysis of FFPE RNA. LISH utilizes the T4 RNA Ligase 2 to efficiently join adjacent chimeric RNA-DNA probe pairs hybridized in situ on fixed RNA target sequences...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28852760/an-aptamer-bio-barcode-abc-assay-using-spr-rnase-h-and-probes-with-rna-and-gold-nanorods-for-anti-cancer-drug-screening
#12
Jacky Fong-Chuen Loo, Chengbin Yang, Hing Lun Tsang, Pui Man Lau, Ken-Tye Yong, Ho Pui Ho, Siu Kai Kong
With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer])...
August 30, 2017: Analyst
https://www.readbyqxmd.com/read/28829437/control-of-phosphorothioate-stereochemistry-substantially-increases-the-efficacy-of-antisense-oligonucleotides
#13
Naoki Iwamoto, David C D Butler, Nenad Svrzikapa, Susovan Mohapatra, Ivan Zlatev, Dinah W Y Sah, Meena, Stephany M Standley, Genliang Lu, Luciano H Apponi, Maria Frank-Kamenetsky, Jason Jingxin Zhang, Chandra Vargeese, Gregory L Verdine
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers...
September 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28827284/rhinovirus-infection-of-ormdl3-transgenic-mice-is-associated-with-reduced-rhinovirus-viral-load-and-airway-inflammation
#14
Dae Jin Song, Marina Miller, Andrew Beppu, Peter Rosenthal, Sudipta Das, Maya Karta, Christine Vuong, Amit Kumar Mehta, Michael Croft, David H Broide
Orosomucoid like 3 (ORMDL3), a gene localized to chromosome 17q21, has been linked in epidemiologic studies to childhood asthma and rhinovirus (RV) infections. As the single nucleotide polymorphisms linking ORMDL3 to asthma are associated with increased expression of ORMDL3, we have used hORMDL3(zp3-Cre) mice (which have universal increased expression of human ORMDL3) to determine whether infection of these transgenic mice with RV influences levels of airway inflammation or RV viral load. RV infection of hORMDL3(zp3-Cre) mice resulted in reduced RV viral load assessed by quantitative real-time PCR (lung and airway epithelium), as well as reduced airway inflammation (total bronchoalveolar lavage cells, neutrophils, macrophages, and lymphocytes) compared with RV-infected wild-type mice...
August 21, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28821455/rnase-hii-saves-rnha-mutant-escherichia-coli-from-r-loop-associated-chromosomal-fragmentation
#15
Elena A Kouzminova, Farid F Kadyrov, Andrei Kuzminov
The rnhAB mutant Escherichia coli, deficient in two RNase H enzymes that remove both R-loops and incorporated ribonucleotides (rNs) from DNA, grow slowly, suggesting accumulation of rN-containing DNA lesions (R-lesions). We report that the rnhAB mutants have reduced viability, form filaments with abnormal nucleoids, induce SOS, and fragment their chromosome, revealing replication and/or segregation stress. R-loops are known to interfere with replication forks, and sensitivity of the double rnhAB mutants to translation inhibition points to R-loops as precursors for R-lesions...
August 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28768728/extracellular-micrornas-induce-potent-innate-immune-responses-via-tlr7-myd88-dependent-mechanisms
#16
Yan Feng, Lin Zou, Dan Yan, Hongliang Chen, Ganqiong Xu, Wenling Jian, Ping Cui, Wei Chao
Tissue ischemia, such as transient myocardial ischemia, leads to release of cellular RNA including microRNA(miRNA) into the circulation and extracellular (ex-) space, but the biological function of the ex-RNA is poorly understood. We recently reported that cardiac RNA of both human and rodent origins induced cytokine production and immune cell activation. However, the identity of the ex-RNA responsible for the proinflammatory effect remains unclear. In the current study, using an miRNA array, we profiled the plasma miRNAs 4 h after transient myocardial ischemia (45 min) or sham procedure...
August 2, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28766290/polyadenylation-site-based-analysis-of-transcript-expression-by-3-reads
#17
Dinghai Zheng, Bin Tian
Deep sequencing of the 3' end region of poly(A)+ RNA identifies the cleavage and polyadenylation site (PAS) and measures transcript abundance. However, mispriming at internal A-rich regions by the oligo-dT oligo in reverse transcription can lead to falsely identified PASs. This problem can be resolved by direct ligation of an adapter to the 3' end of RNA. However, ligation-based methods are often inefficient. Here, we describe 3'READS+, an accurate and sensitive method for deep sequencing of the 3' end of poly(A)+ RNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28760905/a-2-hydroxyisoquinoline-1-3-dione-active-site-rnase-h-inhibitor-binds-in-multiple-modes-to-hiv-1-reverse-transcriptase
#18
Karen A Kirby, Nataliya A Myshakina, Martin T Christen, Yue-Lei Chen, Hilary A Schmidt, Andrew D Huber, Zhaoyong Xi, Seongmi Kim, Rohit K Rao, Skyler T Kramer, Qiongying Yang, Kamalendra Singh, Michael A Parniak, Zhengqiang Wang, Rieko Ishima, Stefan G Sarafianos
The ribonuclease H (RNH) function of HIV-1 reverse transcriptase (RT) plays an essential part in the viral life cycle. We report the characterization of YLC2-155, a 2-hydroxyisoquinoline-1,3-dione-(HID)-based active site RNH inhibitor. YLC2-155 inhibits both polymerase (IC50 = 2.6 μM) and RNH functions (IC50 = 0.65 μM) of RT, but is more effective against RNH. X-ray crystallography, NMR, and molecular modeling were used to show that YLC2-155 binds at the RNH active site in multiple conformations.
July 31, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28704808/enhanced-reactive-oxygen-species-production-acidic-cytosolic-ph-and-upregulated-na-h-exchanger-nhe-in-dicer-deficient-cd4-t-cells
#19
Yogesh Singh, Yuetao Zhou, Shaqiu Zhang, Khalid N M Abdelazeem, Bernat Elvira, Madhuri S Salker, Florian Lang
BACKGROUND: MicroRNAs (miRNAs) negatively regulate gene expression at a post-transcriptional level. Dicer, a cytoplasmic RNase III enzyme, is required for the maturation of miRNAs from precursor miRNAs. Dicer, therefore, is a critical enzyme involved in the biogenesis and processing of miRNAs. Several biological processes are controlled by miRNAs, including the regulation of T cell development and function. T cells generate reactive oxygen species (ROS) with parallel H+ extrusion accomplished by the Na+/H+-exchanger 1 (NHE1)...
July 14, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28679714/rnase-h-10-mg-ml-dnase-free
#20
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
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