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https://www.readbyqxmd.com/read/29792692/small-molecule-targeted-recruitment-of-a-nuclease-to-rna
#1
Matthew G Costales, Yasumasa Matsumoto, Sai Pradeep Velagapudi, Matthew D Disney
The choreography between RNA synthesis and degradation is a key determinant in biology. Engineered systems such as CRISPR have been developed to rid a cell of RNAs. Here, we show that a small molecule can recruit a nuclease to a specific transcript, triggering its destruction. A small molecule that selectively binds the oncogenic microRNA(miR)-96 hairpin precursor was appended with a short 2'-5' poly(A) oligonucleotide. The conjugate locally activated endogenous, latent ribonuclease (RNase L), which selectively cleaved the miR-96 precursor in cancer cells in a catalytic and sub-stoichiometric fashion...
May 24, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29792572/galnac-sirna-conjugates-leading-the-way-for-delivery-of-rnai-therapeutics
#2
Aaron D Springer, Steven F Dowdy
Short-interfering RNA (siRNA)-induced RNAi responses have great potential to treat a wide variety of human diseases from cancer to pandemic viral outbreaks to Parkinson's Disease. However, before siRNAs can become drugs, they must overcome a billion years of evolutionary defenses designed to keep invading RNAs on the outside cells from getting to the inside of cells. Not surprisingly, significant effort has been placed in developing a wide array of delivery technologies. Foremost of these has been the development of N-acetylgalactosamine (GalNAc) siRNA conjugates for delivery to liver...
May 24, 2018: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29790953/identifying-and-avoiding-off-target-effects-of-rnase-h-dependent-antisense-oligonucleotides-in-mice
#3
Peter H Hagedorn, Malene Pontoppidan, Tina S Bisgaard, Marco Berrera, Andreas Dieckmann, Martin Ebeling, Marianne R Møller, Heidi Hudlebusch, Marianne L Jensen, Henrik F Hansen, Troels Koch, Morten Lindow
Antisense oligonucleotides that are dependent on RNase H for cleavage and subsequent degradation of complementary RNA are being developed as therapeutics. Besides the intended RNA target, such oligonucleotides may also cause degradation of unintended RNA off-targets by binding to partially complementary target sites. Here, we characterized the global effects on the mouse liver transcriptome of four oligonucleotides designed as gapmers, two targeting Apob and two targeting Pcsk9, all in different regions on their respective intended targets...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29789502/detection-of-dystrophin-dp71-in-human-skeletal-muscle-using-an-automated-capillary-western-assay-system
#4
Tatsuya Kawaguchi, Emma Tabe Eko Niba, Abdul Qawee Mahyoob Rani, Yoshiyuki Onishi, Makoto Koizumi, Hiroyuki Awano, Masaaki Matsumoto, Masashi Nagai, Shinobu Yoshida, Sachiko Sakakibara, Naoyuki Maeda, Osamu Sato, Hisahide Nishio, Masafumi Matsuo
BACKGROUND: Dystrophin Dp71 is one of the isoforms produced by the DMD gene which is mutated in patients with Duchenne muscular dystrophy (DMD). Although Dp71 is expressed ubiquitously, it has not been detected in normal skeletal muscle. This study was performed to assess the expression of Dp71 in human skeletal muscle. METHODS: Human skeletal muscle RNA and tissues were obtained commercially. Mouse skeletal muscle was obtained from normal and DMDmdx mice. Dp71 mRNA and protein were determined by reverse-transcription PCR and an automated capillary Western assay system, the Simple Western, respectively...
May 23, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29789410/a-randomised-open-label-parallel-group-phase-2-study-of-antisense-oligonucleotide-therapy-in-acromegaly
#5
Peter J Trainer, John Newell-Price, John Ayuk, Simon Aylwin, D Aled Rees, Wm Drake, Philippe Chanson, Thierry Brue, Susan M Webb, Carmen Fajardo Montañana, Javier Aller, Ann I McCormack, David J Torpy, George Tachas, Lynne Atley, David Ryder, Martin Bidlingmaier
OBJECTIVE: ATL1103 is a second-generation antisense oligomer targeting the human GH receptor. This phase 2 randomised, open-label, parallel-group study assessed the potential of ATL1103 as a treatment for acromegaly. DESIGN: 26 patients with active acromegaly (IGF-I >130% upper limit of normal) were randomised to subcutaneous ATL1103 200 mg either once- or twice-weekly for 13 weeks, and monitored for a further 8-week washout period. METHODS: The primary efficacy measures were change in IGF-I at week 14, compared to baseline and between cohorts...
May 22, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29787751/the-n-terminal-domain-of-gastrulation-brain-homeobox-2-gbx2-is-required-for-iridophore-specification-in-zebrafish
#6
Shunya Hozumi, Masaki Shirai, Jingxin Wang, Shun Aoki, Yutaka Kikuchi
Although body color pattern formation by pigment cells plays critical roles in animals, pigment cell specification has not yet been fully elucidated. In zebrafish, there are three chromatophores: melanophore, iridophore, and xanthophore, that are derived from neural crest cells (NCCs). A recent study has reported the differentially expressed genes between melanophores and iridophores. Based on transcriptome data, we identified that Gbx2 is required for iridophore specification during development. In support of this, iridophore formation is suppressed by gbx2 knockdown by morpholino antisense oligonucleotide, at 72 h post fertilization (hpf) in zebrafish...
May 19, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29787736/g-quadruplexes-in-the-bap1-promoter-positively-regulate-its-expression
#7
Yingzhou Li, Xiao Zhang, Yang Gao, Jinming Shi, Liping Tang, Guangchao Sui
Accumulating evidence suggests a key role of BAP1 in oncogenesis, but mechanisms regulating BAP1 gene expression remain unexplored. In this report, we revealed that the BAP1 promoter contains multiple G-tracts in its negative strand with high potential of forming G-quadruplex (G4) structures. In circular dichroism studies, synthesized oligonucleotides within these G-rich regions upstream the BAP1 transcription start site showed molar ellipticity at specific wavelengths characteristic of G4 structures. Analyses of these oligonucleotides by native polyacrylamide gel electrophoresis revealed formation of multiple types of G4 structures...
May 19, 2018: Experimental Cell Research
https://www.readbyqxmd.com/read/29786706/hg-ii-interactions-with-t-rich-regions-in-oligonucleotides-effects-of-positional-variations-on-the-electrochemical-properties
#8
Ajar Kamal, Renu Sharma, Zhe She, Heinz-Bernhard Kraatz
Hg(ii) binding to thymine-rich oligonucleotides (ODNs) is investigated electrochemically. The focus of this study is to probe the effects of position on the electrochemical response. For this purpose, three oligonucleotides were investigated in which the position of a hexa-thymine repeat is varied within a surface-supported oligonucleotide. The hexa repeats were placed in the top, middle, and bottom positions within the strand with respect to the gold surface. The effects were monitored by electrochemical impedance spectroscopy and scanning electrochemical microscopy...
May 22, 2018: Analyst
https://www.readbyqxmd.com/read/29786096/reversal-of-sirna-mediated-gene-silencing-in-vivo
#9
Ivan Zlatev, Adam Castoreno, Christopher R Brown, June Qin, Scott Waldron, Mark K Schlegel, Rohan Degaonkar, Svetlana Shulga-Morskaya, Huilei Xu, Swati Gupta, Shigeo Matsuda, Akin Akinc, Kallanthottathil G Rajeev, Muthiah Manoharan, Martin A Maier, Vasant Jadhav
We report rapid, potent reversal of GalNAc-siRNA-mediated RNA interference (RNAi) activity in vivo with short, synthetic, high-affinity oligonucleotides complementary to the siRNA guide strand. We found that 9-mers with five locked nucleic acids (LNAs) have the highest potency across several targets. Our modular, sequence-specific approach, named REVERSIR, may enhance the therapeutic profile of any long-acting GalNAc-siRNA (short interfering RNA) conjugate by enabling control of RNAi pharmacology.
May 14, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29784403/enzymatic-amplification-of-oligonucleotides-in-paper-substrates
#10
Abootaleb Sedighi, Ulrich J Krull
Several solution-based methods have recently been adapted for use in paper substrates for enzymatic amplification to increase the number of copies of DNA sequences. There is limited information available about the impact of a paper matrix on DNA amplification by enzymatic processes, and about how to optimize conditions to maximize yields. The work reported herein provides insights about the impact of physicochemical properties of a paper matrix, using nuclease-assisted amplification by exonuclease III and nicking endonuclease Nt...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29784358/short-probe-based-duplex-specific-nuclease-signal-amplification-strategy-enables-imaging-of-endogenous-micrornas-in-living-cells-with-ultrahigh-specificity
#11
Yingjun Ma, Jun Chen, Danping Chen, Yuzhi Xu, Li Zhang, Zong Dai, Xiaoyong Zou
Specific nucleic acids amplification at a constant and mild temperature is important for imaging assay of endogenous microRNAs (miRNAs) in living cells. Duplex-specific nuclease (DSN) is attractive in one-step isothermal assay of miRNA; however, its intrinsic limitations of low amplification specificity and high reaction temperature greatly restrict the application scope. Herein, we present a short-probe-based DSN signal amplification (spDSNSA) strategy enabling analysis of miRNAs at body temperature with significantly high specificity...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29782009/construction-of-synthetic-phage-displayed-fab-library-with-tailored-diversity
#12
Ganggang Huang, Zhenwei Zhong, Shane Miersch, Sachdev S Sidhu, Shin-Chen Hou, Donghui Wu
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development...
May 1, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781489/probing-the-competition-between-duplex-and-g-quadruplex-i-motif-structures-using-a-conformation-sensitive-fluorescent-nucleoside-probe
#13
Pramod M Sabale, Arun A Tanpure, Seergazhi G Srivatsan
Double-stranded segments of a genome that can potentially form G-quadruplex (GQ) and/or i-motif (iM) structures are considered to be important regulatory elements. Hence, the development of a common probe that can detect GQ and iM structures and also distinguish them from a duplex structure will be highly useful in understanding the propensity of such segments to adopt duplex or non-canonical four-stranded structures. Here, we describe the utility of a conformation-sensitive fluorescent nucleoside analog, which was originally developed as a GQ sensor, in detecting the iM structures of C-rich DNA oligonucleotides (ONs)...
May 21, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29780463/simultaneous-multiple-single-nucleotide-polymorphism-detection-based-on-click-chemistry-combined-with-dna-encoded-probes
#14
Qian-Yu Zhou, Fang Yuan, Xiao-Hui Zhang, Ying-Lin Zhou, Xin-Xiang Zhang
Single nucleotide polymorphisms (SNPs) are emerging as important biomarkers for disease diagnosis, prognostics and disease pathogenesis. As one type of disease is always connected to several SNP sites, there is great demand for a reliable multiple SNP detection method. Herein, we mimicked a ligation reaction based on DNA ligase and originally utilized an enzyme-free DNA template-directed click reaction for SNP detection. With 5'-alkyne and 3'-azide groups labelled on two oligonucleotide probes, the target DNA-directed Cu(i)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction produced a new DNA strand with a triazole backbone, as a mimic of a DNA phosphodiester linkage...
April 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29779110/translocation-of-oligonucleotide-oligosaccharide-complexes-into-cells-of-the-brain
#15
N N Dygalo, T S Kalinina, D A Lanshakov
Irradiation of a mixture of oligonucleotides with dextran resulted in the formation of a complex that is detected by a decelerated migration of an irradiated sample in electrophoretic gel compared to a non-irradiated one. When injected into the brain of neonatal rats, the formed complex penetrated into the cells 3 times easier compared to the original oligonucleotide, thus indicating that the use of radiation crosslinking of oligonucleotides with oligosaccharides is promising to enhance the efficiency of delivery of gene-targeted oligonucleotide drugs into cells...
March 2018: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29778198/molecular-characterization-of-dermatophytes-isolated-from-cattle-in-plateau-state-nigeria
#16
James S Dalis, Haruna M Kazeem, Jacob K P Kwaga, Clara N Kwanashie, Bitrus Yakubu, Olajide A Owolodun, Anvou R Jambol
Dermatophytes from cattle were successfully characterized to species and strain levels for the first time in Nigeria. This study was undertaken to isolate and characterize dermatophytes from cattle in Plateau State, Nigeria. Two molecular techniques were utilized. The first was the use of polymerase chain reaction (PCR) to amplify the internal transcribed spacer regions of the ribosomal DNA using ITS-1 and ITS-4 as primers. This was followed by restriction fragment length polymorphism analysis of the amplified ITS regions using the enzyme MvaI to identify dermatophyte species...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29777795/sirna-in-ovarian-cancer-delivery-strategies-and-targets-for-therapy
#17
REVIEW
Dirk van den Brand, Vicky Mertens, Leon F A G Massuger, Roland Brock
Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy, and the sixth leading cause of cancer related death in women overall. Despite improved surgical techniques and advances in chemotherapy, mortality hardly decreased over the last twenty years. The major problem is that (micro)metastases persevere in the abdominal cavity, causing incurable tumor recurrence. Therefore, there is an imminent need for new therapeutic strategies. Oligonucleotide (ON) based therapies such as RNA interference (RNAi) provide the possibility to specifically address disease-related pathways...
May 16, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/29776372/curation-of-microarray-oligonucleotides-and-corresponding-ests-cdnas-used-for-gene-expression-analysis-in-zebra-finches
#18
Peter V Lovell, Nicole A Huizinga, Abel Getachew, Brianna Mees, Samantha R Friedrich, Morgan Wirthlin, Claudio V Mello
OBJECTIVES: Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches...
May 18, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29775740/eriocheir-sinensis-microrna-7-targets-crab-myd88-to-enhance-white-spot-syndrome-virus-replication
#19
Ying Huang, Wen Wang, Zhiqiang Xu, Jianlin Pan, Zhe Zhao, Qian Ren
MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression at the posttranscriptional level. In this study, the function of microRNA-7 (miR-7) in host-virus interaction was investigated. Replication of White spot syndrome virus (WSSV) was enhanced with the overexpression of miR-7 and inhibited with the downregulation of miR-7 by using anti-miRNA oligonucleotide AMO-miR-7. The target gene of miR-7 was predicted using bioinformatics methods. Results showed that crab myeloid differentiation factor 88 (Myd88) could be targeted by miR-7...
May 15, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29775643/myocardial-infarction-induced-hippocampal-microtubule-damage-by-cardiac-originating-microrna-1-in-mice
#20
Lin-Lin Sun, Ming-Jing Duan, Ji-Chao Ma, Ling Xu, Meng Mao, Das Biddyut, Qin Wang, Chao Yang, Shuai Zhang, Yi Xu, Lin Yang, You Tian, Ying Liu, Sheng-Nan Xia, Ke-Xin Li, Zhuo Jin, Qiaojie Xiong, Jing Ai
Cardiovascular diseases are risk factors for dementia, but the mechanisms remain elusive. Here, we report that myocardial infarction (MI) generated by the ligation of the left coronary artery (LCA) could lead to increased miR-1 levels in the hippocampus and blood with neuronal microtubule damage and decreased TPPP/p25 protein expression in the hippocampus. These changes could be prevented by a knockdown of miR-1 using hippocampal stereotaxic injections of anti-miR-1 oligonucleotide fragments carried by a lentivirus vector (lenti-pre-AMO-miR-1)...
May 15, 2018: Journal of Molecular and Cellular Cardiology
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