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https://www.readbyqxmd.com/read/29346415/acute-multi-sgrna-knockdown-of-keops-complex-genes-reproduces-the-microcephaly-phenotype-of-the-stable-knockout-zebrafish-model
#1
Tilman Jobst-Schwan, Johanna Magdalena Schmidt, Ronen Schneider, Charlotte A Hoogstraten, Jeremy F P Ullmann, David Schapiro, Amar J Majmundar, Amy Kolb, Kaitlyn Eddy, Shirlee Shril, Daniela A Braun, Annapurna Poduri, Friedhelm Hildebrandt
Until recently, morpholino oligonucleotides have been widely employed in zebrafish as an acute and efficient loss-of-function assay. However, off-target effects and reproducibility issues when compared to stable knockout lines have compromised their further use. Here we employed an acute CRISPR/Cas approach using multiple single guide RNAs targeting simultaneously different positions in two exemplar genes (osgep or tprkb) to increase the likelihood of generating mutations on both alleles in the injected F0 generation and to achieve a similar effect as morpholinos but with the reproducibility of stable lines...
2018: PloS One
https://www.readbyqxmd.com/read/29341934/advances-in-the-delivery-of-antisense-oligonucleotides-for-combating-bacterial-infectious-diseases
#2
REVIEW
Xiao-Yan Xue, Xing-Gang Mao, Ying Zhou, Zhou Chen, Yue Hu, Zheng Hou, Ming-Kai Li, Jing-Ru Meng, Xiao-Xing Luo
Discovery and development of new antibacterial drugs against multidrug resistant bacterial strains have become more and more urgent. Antisense oligonucleotides (ASOs) show immense potential to control the spread of resistant microbes due to its high specificity of action, little risk to human gene expression, and easy design and synthesis to target any possible gene. However, efficient delivery of ASOs to their action sites with enough concentration remains a major obstacle, which greatly hampers their clinical application...
January 13, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29341839/activation-of-frataxin-protein-expression-by-antisense-oligonucleotides-targeting-the-mutant-expanded-repeat
#3
Liande Li, Xiulong Shen, Zhongtian Liu, Michaela Norrbom, Thazha P Prakash, Daniel O'Reilly, Vivek K Sharma, Masad J Damha, Jonathan K Watts, Frank Rigo, David R Corey
Friedreich's Ataxia (FA) is an inherited neurologic disorder caused by an expanded GAA repeat within intron 1 of the frataxin (FXN) gene that reduces expression of FXN protein. Agents that increase expression of FXN have the potential to alleviate the disease. We previously reported that duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) complementary to the GAA repeat could enhance expression of FXN protein. We now explore the potential of a diverse group of chemically modified dsRNAs and ASOs to define the breadth of repeat-targeted synthetic nucleic acids as a platform for therapeutic development for FA...
January 17, 2018: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29341438/natural-antisense-transcripts-in-diseases-from-modes-of-action-to-targeted-therapies
#4
REVIEW
Elżbieta Wanowska, Magdalena Regina Kubiak, Wojciech Rosikiewicz, Izabela Makałowska, Michał Wojciech Szcześniak
Antisense transcription is a widespread phenomenon in mammalian genomes, leading to production of RNAs molecules referred to as natural antisense transcripts (NATs). NATs apply diverse transcriptional and post-transcriptional regulatory mechanisms to carry out a wide variety of biological roles that are important for the normal functioning of living cells, but their dysfunctions can be associated with human diseases. In this review, we attempt to provide a molecular basis for the involvement of NATs in the etiology of human disorders such as cancers and neurodegenerative and cardiovascular diseases...
January 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29340361/a-curcumin-loaded-polymeric-micelle-as-a-carrier-of-a-microrna-21-antisense-oligonucleotide-for-enhanced-anti-tumor-effects-in-a-glioblastoma-animal-model
#5
Xiaonan Tan, Gyeungyun Kim, Dahee Lee, Jungju Oh, Minkyung Kim, Chunxian Piao, Jaewon Lee, Min Sang Lee, Ji Hoon Jeong, Minhyung Lee
A glioblastoma is a common primary brain tumor that expresses microRNA-21 (miR-21), which inhibits the expression of pro-apoptotic genes such as phosphatase and tensin homologue (PTEN) and programmed cell death 4 (PDCD4). Therefore, an antisense-oligonucleotide against miR-21 (miR21ASO) could have therapeutic effects for glioblastomas. In this study, curcumin was loaded into deoxycholic acid-conjugated polyethylenimine (DP) micelles. The curcumin-loaded DP micelle (DP-Cur) was evaluated as a carrier for the combined delivery of curcumin and miR21ASO...
January 17, 2018: Biomaterials Science
https://www.readbyqxmd.com/read/29339976/detection-of-dioxin-induced-demethylation-of-mouse-cyp1a1-gene-promoter-by-a-new-labeling-method-for-short-dna-fragments-possessing-5-methylcytosine-at-the-end
#6
Hisaka Kurita, Toshiki Aiba, Toshiyuki Saito, Seiichiroh Ohsako
Environmental factors stimulate alteration of DNA methylation level. Investigation of the genome-wide DNA methylation status is important for environmental health studies. We here designed a genomic DNA amplification and labeling protocol using a methylation-sensitive restriction enzyme HinP1 I. This method can specifically amplify genomic DNA fragments possessing methyl-CpG at the end. The fragments are a relatively short size and dominantly located on CpG-islands. By using the samples prepared by this method, a dioxin-induced change in the methylation level of the mouse Cyp1a1 promoter was successfully evaluated using oligonucleotide probes covalently bound onto a glass plate...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/29339778/a-novel-human-muscle-cell-model-of-duchenne-muscular-dystrophy-created-by-crispr-cas9-and-evaluation-of-antisense-mediated-exon-skipping
#7
Takenori Shimo, Kana Hosoki, Yusuke Nakatsuji, Toshifumi Yokota, Satoshi Obika
Oligonucleotide-mediated splicing modulation is a promising therapeutic approach for Duchenne muscular dystrophy (DMD). Recently, eteplirsen, a phosphorodiamidate morpholino oligomer-based splice-switching oligonucleotide (SSO) targeting DMD exon 51, was approved by the U.S. Food and Drug Administration as the first antisense-based drug for DMD patients. For further exploring SSOs targeting other exons in the DMD gene, the efficacy of exon skipping and protein rescue with each SSO sequence needs evaluations in vitro...
January 16, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29339495/streamlined-circular-proximity-ligation-assay-provides-high-stringency-and-compatibility-with-low-affinity-antibodies
#8
Roxana Jalili, Joe Horecka, James R Swartz, Ronald W Davis, Henrik H J Persson
Proximity ligation assay (PLA) is a powerful tool for quantitative detection of protein biomarkers in biological fluids and tissues. Here, we present the circular proximity ligation assay (c-PLA), a highly specific protein detection method that outperforms traditional PLA in stringency, ease of use, and compatibility with low-affinity reagents. In c-PLA, two proximity probes bind to an analyte, providing a scaffolding that positions two free oligonucleotides such that they can be ligated into a circular DNA molecule...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29338211/highly-stable-rna-capture-by-dense-cationic-polymer-brushes-for-the-design-of-cytocompatible-serum-stable-sirna-delivery-vectors
#9
Danyang Li, Amir S Sharili, John Connelly, Julien E Gautrot
The high density of polymer brushes confers to these coatings unique physico-chemical properties, in particular for the regulation of biomolecular interaction and the design of highly selective coatings for biosensors and protein patterning. Here we show that high density poly(dimethylaminoethyl methacrylate) cationic polymer brushes enable the stable uptake of high levels of oligonucleotides. This is proposed to result from the high degree of crowding and associated increase in entropic driving force for the binding of polyelectrolytes such as nucleic acid molecules...
January 16, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/29336444/the-structural-diversity-of-c-rich-dna-aggregates-unusual-self-assembly-of-beetle-like-nanostructures
#10
A D Protopopova, V B Tsvetkov, A M Varizhuk, N A Barinov, V V Podgorsky, D V Klinov, G E Pozmogova
We studied the ability of oligonucleotides CnT25 (n = 2, 5, 7, 9, 12, 25) to form an intermolecular i-motif using circular dichroism, ultra-violet spectroscopy, nuclear magnetic resonance, high-resolution atomic force microscopy, high-performance liquid chromatography, and molecular dynamics simulations. The arrangement of single-stranded oligonucleotides in multimer i-motifs was very unusual: C-tracts of different oligonucleotides followed each other consecutively in order to fold into a closed intermolecular i-motif core with minimal loops (one cytidine in a loop spanning over a minor groove, three cytidines in a loop over a major groove); intact T-tracts protruded from predefined loci allowing visualization of beetle-like nanostructures by atomic force microscopy...
January 16, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29335794/effect-of-a-calcitonin-gene-related-peptide-binding-l-rna-aptamer-on-neuronal-activity-in-the-rat-spinal-trigeminal-nucleus
#11
Michael J M Fischer, Jakob Schmidt, Stanislav Koulchitsky, Sven Klussmann, Axel Vater, Karl Messlinger
BACKGROUND: Calcitonin gene-related peptide (CGRP) plays a major role in the pathogenesis of migraine and other primary headaches. Spinal trigeminal neurons integrate nociceptive afferent input from trigeminal tissues including intracranial afferents, and their activity is thought to reflect facial pain and headache in man. CGRP receptor inhibitors and anti-CGRP antibodies have been demonstrated to be therapeutically effective in migraine. In parallel, CGRP receptor inhibition has been shown to lower spinal trigeminal neuron activity in animal models of meningeal nociception...
January 15, 2018: Journal of Headache and Pain
https://www.readbyqxmd.com/read/29335405/author-correction-myoblasts-and-macrophages-are-required-for-therapeutic-morpholino-antisense-oligonucleotide-delivery-to-dystrophic-muscle
#12
James S Novak, Marshall W Hogarth, Jessica F Boehler, Marie Nearing, Maria C Vila, Raul Heredia, Alyson A Fiorillo, Aiping Zhang, Yetrib Hathout, Eric P Hoffman, Jyoti K Jaiswal, Kanneboyina Nagaraju, Sebahattin Cirak, Terence A Partridge
In the original version of this Article, financial support was not fully acknowledged. The PDF and HTML versions of the Article have now been corrected to include support from the CRI Light Microscopy and Image Analysis Core.
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29334995/antisense-suppression-of-the-nonsense-mediated-decay-factor-upf3b-as-a-potential-treatment-for-diseases-caused-by-nonsense-mutations
#13
Lulu Huang, Audrey Low, Sagar S Damle, Melissa M Keenan, Steven Kuntz, Susan F Murray, Brett P Monia, Shuling Guo
BACKGROUND: About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncated proteins, but also often result in  decreased mRNA abundance due to  nonsense-mediated mRNA decay (NMD). Although pharmacological inhibition of NMD could be an attractive therapeutic approach for the treatment of diseases caused by nonsense mutations, NMD also regulates the expression of 10-20% of the normal transcriptome...
January 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29334984/new-insights-into-angplt3-in-controlling-lipoprotein-metabolism-and-risk-of-cardiovascular-diseases
#14
REVIEW
Xin Su, Dao-Quan Peng
Dyslipidemia, characterized by elevation of plasma low density lipoprotein cholesterol (LDL-C), triglyceride (TG) and reduction of plasma high density lipoprotein cholesterol (HDL-C), has been verified as a causal risk factor for cardiovascular diseases (CVD), leading to a high mortality rate in general population. It is important to understand the molecular metabolism underlying dyslipidemia in order to reduce the risk and to develop effective therapeutic approaches against CVD. ANGPTL3 (human) or Angptl3 (mouse), one member of the angiopoietin-like protein (ANGPTL) family, has been identified as an important regulator of lipid metabolism by inhibiting LPL and EL activity...
January 15, 2018: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29332345/correlation-between-mir-19a-inhibition-and-radiosensitivity-in-siha-cervical-cancer-cells
#15
Yina Wang, Yang Wang, Wei Zhong, Kuerban Gulina
PURPOSE: MicroRNAs (miRs) have been implicated in many aspects of tumor cell development and survival, including sensitivity to radiotherapy. In particular, miR-19a regulates the proliferation of cervical cancer cells, but its role in radiosensitivity is not known. Here, we describe the consequence of silencing miR-19a using antisense oligonucleotides (ASO) on the radiosensitivity of human cervical cancer SiHa cells. METHODS: Following transfection with miR-19a-ASO or control-ASO, SiHa cells were exposed to X-rays to determine their proliferation...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29331427/water-soluble-mercury-ion-sensing-based-on-the-thymine-hg2-thymine-base-pair-using-retroreflective-janus-particle-as-an-optical-signaling-probe
#16
Hyeong Jin Chun, Saemi Kim, Yong Duk Han, Dong Woo Kim, Ka Ram Kim, Hyo-Sop Kim, Jae-Ho Kim, Hyun C Yoon
Herein, we report an optical sensing platform for mercury ions (Hg2+) in water based on the integration of Hg2+-mediated thymine-thymine (T-T) stabilization, a biotinylated stem-loop DNA probe, and a streptavidin-modified retroreflective Janus particle (SA-RJP). Two oligonucleotide probes, including a stem-loop DNA probe and an assistant DNA probe, were utilized. In the absence of Hg2+, the assistant DNA probe does not hybridize with the stem-loop probe due to their T-T mismatch, so the surface-immobilized stem-loop DNA probe remains a closed hairpin structure...
January 6, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29330203/personalized-rna-medicine-for-pancreatic-cancer
#17
Maud-Emmanuelle Gilles, Liangliang Hao, Ling Huang, Rajesha Rupaimoole, Pedro P Lopez-Casas, Emilia Pulver, Jong Cheol Jeong, Senthil K Muthuswamy, Manuel Hidalgo, Sangeeta N Bhatia, Frank J Slack
PURPOSE: Since drug responses vary between patients, it is crucial to develop pre-clinical or co-clinical strategies that forecast patient response. In this study, we tested whether RNA-based therapeutics were suitable for personalized medicine by using patient-derived-organoid (PDO) and patient-derived-xenograft (PDX) models.  Experimental Design: We performed microRNA (miRNA) profiling of PDX samples to determine the status of miRNA deregulation in individual pancreatic ductal adenocarcinoma (PDAC) patients...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29330129/estradiol-up-regulates-l-type-ca2-channels-via-membrane-bound-estrogen-receptor-phosphoinositide-3kinase-akt-camp-response-element-binding-protein-signaling-pathway
#18
Xiaoyan Yang, Xiaofang Mao, Gao Xu, Shasha Xing, Ansuman Chattopadhyay, Si Jin, Guy Salama
BACKGROUND: In long QT type-2 (LQT2), women are more prone to lethal arrhythmias called Torsade de Pointes (TdP) than men. We previously reported that 17-β-estradiol (E2) upregulates L-type Ca2+-channels and current (ICa,L) (∼30%) in rabbit ventricular myocytes by a classical genomic-mechanism mediated by estrogen-receptor-α (ER)α. In LQT2 ( IKr-blockade or bradycardia), the higher Ca2+ influx via ICa,L, causes Ca2+-overload, spontaneous sarcoplasmic reticulum Ca2+-release, and re-activation of ICa,L that trigger early afterdepolarizations (EADs) and TdP...
January 9, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/29329816/structural-polymorphism-of-a-cytosine-rich-dna-sequence-forming-i-motif-structure-exploring-ph-based-biosensors
#19
Saami Ahmed, Mahima Kaushik, Swati Chaudhary, Shrikant Kukreti
Sequence recognition and conformational polymorphism enable DNA to emerge out as a substantial tool in fabricating the devices within nano-dimensions. These DNA associated nano devices work on the principle of conformational switches, which can be facilitated by many factors like sequence of DNA/RNA strand, change in pH or temperature, enzyme or ligand interactions etc. Thus, controlling these DNA conformational changes to acquire the desired function is significant for evolving DNA hybridization biosensor, used in genetic screening and molecular diagnosis...
January 9, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29328971/ultrasensitive-electrochemical-sensing-of-hg2-based-on-thymine-hg2-thymine-interaction-and-signal-amplification-of-alkaline-phosphatase-catalyzed-silver-deposition
#20
Aigui Xu, Long Chao, Hongbo Xiao, Yuyun Sui, Jia Liu, Qingji Xie, Shouzhuo Yao
We report an ultrasensitive electrochemical sensor for Hg2+ detection, on the basis of two Hg2+-specific oligonucleotide probes (a thiolated capture probe and a biotinated signal probe), "terminal" signal amplification of alkaline phosphatase catalyzed deposition of silver and in situ microliter-droplet anodic stripping voltammetry (ASV). The thiolated capture probe is immobilized on an Au-plated glassy carbon electrode, and the biotinated signal probe is then attached to the electrode surface through the thymine-Hg2+-thymine interaction in the presence of Hg2+...
January 5, 2018: Biosensors & Bioelectronics
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