Interference Interfering RNA-Mediated RNA Inhibition Of
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Xfect™ RNA Transfection Reagent Protocol-At-A-Glance
Xfect™ RNA Transfection Reagent Protocol-At-A-Glance I. Introduction A. Summary This Protocol-At-A-Glance is provided for transfection of cells with RNA using the Xfect RNA Transfection Reagent (Cat. No. 631450). It describes transfection of mammalian cells with RNA (mRNA, sgRNA, microRNA, or shRNA) in a 12-well plate format. For formats other than 12-well plates, see Tables I and II for appropriate reaction volumes. Transfections can be carried out entirely in the presence of serum. The protocol is divided into two sections: Section II describes transfection of cells with RNA only, without the cotransfection of DNA. Section III describes cotransfection of cells with both RNA and DNA. NOTE: When transfecting cells with mRNA, expression may be increased by using serum-free medium during transfection, since serum may contain RNases that can reduce the amount of full-length mRNA. B. General Considerations Storage & handling Store the Xfect RNA Transfection Polymer at –20°C. Do not thaw until ready to use. Once thawed, store at 4°C for up to 12 months. NOTE: The Xfect RNA Transfection Polymer is a milky suspension and should be vortexed briefly prior to use to ensure that it is fully resuspended. Thaw Xfect Reaction Buffer at room temperature just prior to use. Vortex after thawing. Once thawed, store Xfect Reaction Buffer at 4°C for up to 12 months. Xfect Polymer The protocol for cotransfection with DNA (Section III) requires the use of the Xfect Polymer (not included; sold as part of the DNA Xfect Transfection Reagent, Cat. Nos. 631317, 631318). -
Mrna Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection
International Journal of Molecular Sciences Review mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection 1, 1, 2 1,3, Shuqin Xu y, Kunpeng Yang y, Rose Li and Lu Zhang * 1 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200438, China; [email protected] (S.X.); [email protected] (K.Y.) 2 M.B.B.S., School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; [email protected] 3 Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China * Correspondence: [email protected]; Tel.: +86-13524278762 These authors contributed equally to this work. y Received: 30 July 2020; Accepted: 30 August 2020; Published: 9 September 2020 Abstract: Messenger ribonucleic acid (mRNA)-based drugs, notably mRNA vaccines, have been widely proven as a promising treatment strategy in immune therapeutics. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have enabled them to become prevalent in pre-clinical and clinical trials against various infectious diseases and cancers. Recent technological advancements have alleviated some issues that hinder mRNA vaccine development, such as low efficiency that exist in both gene translation and in vivo deliveries. mRNA immunogenicity can also be greatly adjusted as a result of upgraded technologies. In this review, we have summarized details regarding the optimization of mRNA vaccines, and the underlying biological mechanisms of this form of vaccines. Applications of mRNA vaccines in some infectious diseases and cancers are introduced. It also includes our prospections for mRNA vaccine applications in diseases caused by bacterial pathogens, such as tuberculosis. -
Malaria Parasites Both Repress Host CXCL10 and Use It As a Cue for Growth Acceleration
ARTICLE https://doi.org/10.1038/s41467-021-24997-7 OPEN Malaria parasites both repress host CXCL10 and use it as a cue for growth acceleration Yifat Ofir-Birin 1, Hila Ben Ami Pilo1, Abel Cruz Camacho1, Ariel Rudik1, Anna Rivkin1, Or-Yam Revach1, Netta Nir1, Tal Block Tamin1, Paula Abou Karam1, Edo Kiper1, Yoav Peleg2, Reinat Nevo1, Aryeh Solomon3, Tal Havkin-Solomon1, Alicia Rojas1, Ron Rotkopf 4, Ziv Porat 5, Dror Avni6,7, Eli Schwartz6,7, Thomas Zillinger 8, Gunther Hartmann 8, Antonella Di Pizio 9, Neils Ben Quashie 10,11, Rivka Dikstein1, Motti Gerlic12, Ana Claudia Torrecilhas 13, Carmit Levy14, Esther N. M. Nolte-‘t Hoen15, ✉ Andrew G. Bowie 16 & Neta Regev-Rudzki 1 1234567890():,; Pathogens are thought to use host molecular cues to control when to initiate life-cycle transitions, but these signals are mostly unknown, particularly for the parasitic disease malaria caused by Plasmodium falciparum. The chemokine CXCL10 is present at high levels in fatal cases of cerebral malaria patients, but is reduced in patients who survive and do not have complications. Here we show a Pf ‘decision-sensing-system’ controlled by CXCL10 concentration. High CXCL10 expression prompts P. falciparum to initiate a survival strategy via growth acceleration. Remarkably, P. falciparum inhibits CXCL10 synthesis in monocytes by disrupting the association of host ribosomes with CXCL10 transcripts. The underlying inhi- bition cascade involves RNA cargo delivery into monocytes that triggers RIG-I, which leads to HUR1 binding to an AU-rich domain of the CXCL10 3’UTR. These data indicate that when the parasite can no longer keep CXCL10 at low levels, it can exploit the chemokine as a cue to shift tactics and escape. -
INTRODUCTION Sirna and Rnai
J Korean Med Sci 2003; 18: 309-18 Copyright The Korean Academy ISSN 1011-8934 of Medical Sciences RNA interference (RNAi) is the sequence-specific gene silencing induced by dou- ble-stranded RNA (dsRNA). Being a highly specific and efficient knockdown tech- nique, RNAi not only provides a powerful tool for functional genomics but also holds Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National a promise for gene therapy. The key player in RNAi is small RNA (~22-nt) termed University, Seoul, Korea siRNA. Small RNAs are involved not only in RNAi but also in basic cellular pro- cesses, such as developmental control and heterochromatin formation. The inter- Received : 19 May 2003 esting biology as well as the remarkable technical value has been drawing wide- Accepted : 23 May 2003 spread attention to this exciting new field. V. Narry Kim, D.Phil. Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, San 56-1, Shillim-dong, Gwanak-gu, Seoul 151-742, Korea Key Words : RNA Interference (RNAi); RNA, Small interfering (siRNA); MicroRNAs (miRNA); Small Tel : +82.2-887-8734, Fax : +82.2-875-0907 hairpin RNA (shRNA); mRNA degradation; Translation; Functional genomics; Gene therapy E-mail : [email protected] INTRODUCTION established yet, testing 3-4 candidates are usually sufficient to find effective molecules. Technical expertise accumulated The RNA interference (RNAi) pathway was originally re- in the field of antisense oligonucleotide and ribozyme is now cognized in Caenorhabditis elegans as a response to double- being quickly applied to RNAi, rapidly improving RNAi stranded RNA (dsRNA) leading to sequence-specific gene techniques. -
Annale D890ahlfors.Pdf (5.211Mb)
TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS SARJA - SER. D OSA - TOM. 890 MEDICA - ODONTOLOGICA INTERLEUKIN-4 INDUCED LEUKOCYTE DIFFERENTIATION by Helena Ahlfors TURUN YLIOPISTO UNIVERSITY OF TURKU Turku 2009 From Turku Centre for Biotechnology, University of Turku and Åbo Akademi University; Department of Medical Biochemistry and Molecular Biology, University of Turku and National Graduate School of Informational and Structural Biology Supervised by Professor Riitta Lahesmaa, M.D., Ph.D. Turku Centre for Biotechnology University of Turku and Åbo Akademi University Turku, Finland Reviewed by Professor Risto Renkonen M.D., Ph.D. Transplantation laboratory Haartman Institute University of Helsinki Helsinki, Finland and Docent Panu Kovanen, M.D., Ph.D. Haartman Institute Department of Pathology University of Helsinki Helsinki, Finland Opponent Assistant Professor Mohamed Oukka, Ph.D. Seattle Children’s Research Institute Department of Immunology University of Washington Seattle, USA ISBN 978-951-29-4183-4 (PRINT) ISBN 978-951-29-4184-1 (PDF) ISSN 0355-9483 Painosalama Oy – Turku, Finland 2009 Think where mans glory most begins and ends, and say my glory was I had such friends. William Butler Yeats (1865 – 1939) ABSTRACT Helena Ahlfors Interleukin-4 induced leukocyte differentiation Turku Centre for Biotechnology, University of Turku and Åbo Akademi University Department of Medical Biochemistry and Genetics, University of Turku National Graduate School of Informational and Structural Biology, 2009 Monocytes, macrophages and dendritic cells (DCs) are important mediators of innate immune system, whereas T lymphocytes are the effector cells of adaptive immune responses. DCs play a crucial role in bridging innate and adaptive immunity. Naïve CD4+ Th progenitors (Thp) differentiate to functionally distinct effector T cell subsets including Th1, Th2 and Th17 cells, which while being responsible for specific immune functions have also been implicated in pathological responses, such as autoimmunity, asthma and allergy. -
Efficient Sirna Delivery and Gene Silencing Using a Lipopolypeptide Hybrid Vector Mediated by a Caveolae-Mediated and Temperatur
Kasai et al. J Nanobiotechnol (2019) 17:11 https://doi.org/10.1186/s12951-019-0444-8 Journal of Nanobiotechnology RESEARCH Open Access Efcient siRNA delivery and gene silencing using a lipopolypeptide hybrid vector mediated by a caveolae‑mediated and temperature‑dependent endocytic pathway Hironori Kasai1, Kenji Inoue1, Kentaro Imamura1,2, Carlo Yuvienco3, Jin K. Montclare3,4,5,6 and Seiichi Yamano1* Abstract Background: We developed a non-viral vector, a combination of HIV-1 Tat peptide modifed with histidine and cysteine (mTat) and polyethylenimine, jetPEI (PEI), displaying the high efciency of plasmid DNA transfection with lit- tle toxicity. Since the highest efciency of INTERFERin (INT), a cationic amphiphilic lipid-based reagent, for small inter- fering RNA (siRNA) transfection among six commercial reagents was shown, we hypothesized that combining mTat/ PEI with INT would improve transfection efciency of siRNA delivery. To elucidate the efcacy of the hybrid vector for siRNA silencing, β-actin expression was measured after siRNA β-actin was transfected with mTat/PEI/INT or other vec- tors in HSC-3 human oral squamous carcinoma cells. Results: mTat/PEI/INT/siRNA produced signifcant improvement in transfection efciency with little cytotoxicity com- pared to other vectors and achieved 100% knockdown of β-actin expression compared to non-treated cells. The electric charge of mTat/PEI/INT/siRNA≈ was signifcantly higher than INT/siRNA. The particle size of mTat/PEI/INT/siRNA was signifcantly smaller than INT/siRNA. Filipin III and β-cyclodextrin, an inhibitor of caveolae-mediated endocyto- sis, signifcantly inhibited mTat/PEI/INT/siRNA transfection, while chlorpromazine, an inhibitor of clathrin-mediated endocytosis, did not inhibit mTat/PEI/INT/siRNA transfection. -
Beyond Microrna Â
Cancer Letters xxx (2013) xxx–xxx Contents lists available at SciVerse ScienceDirect Cancer Letters journal homepage: www.elsevier.com/locate/canlet Mini-review Beyond microRNA – Novel RNAs derived from small non-coding RNA and their implication in cancer ⇑ Elena S. Martens-Uzunova , Michael Olvedy, Guido Jenster Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands article info abstract Article history: Over the recent years, Next Generation Sequencing (NGS) technologies targeting the microRNA transcrip- Available online xxxx tome revealed the existence of many different RNA fragments derived from small RNA species other than microRNA. Although initially discarded as RNA turnover artifacts, accumulating evidence suggests that Keywords: RNA fragments derived from small nucleolar RNA (snoRNA) and transfer RNA (tRNA) are not just random snoRNA-derived RNA (sdRNA) degradation products but rather stable entities, which may have functional activity in the normal and tRNA fragment (tRF) malignant cell. Next generation sequencing This review summarizes new findings describing the detection and alterations in expression of Cancer snoRNA-derived (sdRNA) and tRNA-derived (tRF) RNAs. We focus on the possible interactions of sdRNAs microRNA Non-coding RNA and tRFs with the canonical microRNA pathways in the cell and present current hypotheses on the func- tion of these RNAs. Ó 2013 Elsevier Ireland Ltd. All rights reserved. 1. Introduction Alongside with miRNA, other types of small regulatory ncRNAs like exogenous and endogenous small interfering RNAs (siRNAs Within less than a decade since the sequencing of the human and endo-siRNAs) [6–8] and PiWi-interacting RNAs (piRNAs) [9] genome it became clear that over ninety percent of our genes en- are also involved in gene regulation and genome defense and share code for RNA transcripts that never get translated to protein. -
Dan Graur Department of Biology & Biochemistry University Of
Down with ncRNA! Long live fRNA and jRNA! Dan Graur Department of Biology & Biochemistry University of Houston Science & Research Building 2 3455 Cullen Blvd. Suite #342 Houston, TX 77204-5001 Voice: 713-743-7236 Fax: 713-743-2636 Email: [email protected] 1 Abstract Noncoding RNA (ncRNA) and long noncoding RNA (lncRNA) are scientifically invalid terms because they define molecular entities according to properties they do not possess and functions they do not perform. Here, I suggest retiring these two terms. Instead, I suggest using an evolutionary classification of genomic function, in which every RNA molecule is classified as either “functional” or “junk” according to its selected effect function. Dealing with RNA molecules whose functional status is unknown require us to phrase Popperian nomenclatures that spell out the conditions for their own refutation. Thus, in the absence of falsifying evidence, RNA molecules of unknown function must be considered junk RNA (jRNA). 2 Negative descriptions in biology are generally considered invalid. That is, biological entities cannot be solely defined by what they do not possess or do not do. Hence, for instance, the taxon Pisces (fishes) has been deemed scientifically invalid even before its monophyletic status was refuted, because the definition of Pisces involved a single negative character state—the lack of limbs with digits. The same principles should apply to the taxonomy of molecular entities. In the scientific literature, the modifiers “non-coding,” “noncoding,” and “nc” are widely used as prefixes for “DNA” and “RNA.” As of September 1, 2017, these terms appear more than 45,000 times in Google Scholar. -
Method for Efficient Transfection of in Vitro-Transcribed Mrna Into SK-N-AS and HEK293 Cells: Difference in the Toxicity of Nuclear EGFP Compared to Cytoplasmic EGFP
1011-1016 2/5/06 13:15 Page 1011 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 17: 1011-1016, 2006 Method for efficient transfection of in vitro-transcribed mRNA into SK-N-AS and HEK293 cells: Difference in the toxicity of nuclear EGFP compared to cytoplasmic EGFP KATARINA EJESKÄR1,2, SUSANNE FRANSSON2, FATEN ZAIBAK1 and PANAYIOTIS A. IOANNOU1 1Murdoch Children's Research Institute, Melbourne University, Royal Children's Hospital, 3052 Parkville, VIC, Australia; 2Department of Clinical Genetics, Göteborg University, SU/Östra, SE-416 85 Gothenburg, Sweden Received December 2, 2005; Accepted January 20, 2006 Abstract. Here we report a method for efficient transfection Introduction of in vitro-transcribed mRNA into two different types of human adherent cells, the neuroblastoma cell line SK-N-AS, A major challenge today is to analyze the functions of many and the transformed kidney cell line HEK293. By using newly genes at the cellular level (1). It is possible to conduct high- trypsinized adherent cells in suspension and Lipofectamine™ throughput screening through transfectional microarrays (2) 2000, we detected a transfection efficiency of 80-90% in both but, for many research groups, this is not an option because it cell lines and a cell viability of 90% in SK-N-AS and 60% in requires costly equipment and, for many research projects, it HEK293, 24 h after transfection when using cytoplasmic might not be necessary to test thousands of genes. enhanced green fluorescent protein (EGFP)-mRNA. We have The major issue in functional gene studies in living cells evaluated the different effects of the generally used EGFP that is good transfection efficiency, and there are numerous different mainly localizes to the cytoplasm and nuclear EGFP, where the methods for DNA/RNA delivery available, all with advantages nuclear EGFP are more toxic to the cells than the cytoplasmic and drawbacks (3). -
Exportin-5 Mediates the Nuclear Export of Pre-Micrornas and Short Hairpin Rnas
Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION Exportin-5 mediates the miRNA biogenesis is the nuclear excision of the upper part of this RNA hairpin to give the ∼65-nt pre-miRNA nuclear export of intermediate (Lee et al. 2002; Zeng and Cullen 2003). pre-microRNAs and short This processing step is performed by human RNAse III, also called ‘Drosha’ (Lee et al. 2003). The pre-miRNA hairpin RNAs intermediate, which in the case of human miR-30 con- sists of a 63-nt hairpin bearing a 2-nt 3Ј overhang, is then 2 3 3 Rui Yi, Yi Qin, Ian G. Macara, and exported to the cytoplasm by a currently unknown Bryan R. Cullen1,2,4 mechanism. Once there, the pre-miRNA is processed by a second RNAse III family member called ‘Dicer’ to give 1 2 Howard Hughes Medical Institute and Department of the mature ∼22-nt miRNA (Grishok et al. 2001; Molecular Genetics and Microbiology, Duke University Hutvágner et al. 2001; Ketting et al. 2001). The miRNA Medical Center, Durham, North Carolina 27710, USA; is then incorporated into the RNA-induced silencing 3 Center for Cell Signaling, University of Virginia, complex (RISC), where it functions to guide RISC to ap- Charlottesville, Virginia 22908, USA propriate mRNA targets (Hammond et al. 2000; Martinez et al. 2002; Mourelatos et al. 2002; Schwarz et al. 2002). MicroRNAs (miRNAs) are initially expressed as long In addition to miRNAs, cells can also generate similar ∼ transcripts that are processed in the nucleus to yield 65- ∼22-nt noncoding RNAs called small interfering RNAs nucleotide (nt) RNA hairpin intermediates, termed pre- (siRNA), by Dicer processing of long double-stranded miRNAs, that are exported to the cytoplasm for addi- RNAs (dsRNAs; Zamore et al. -
Transfection of Ssdna Donor Oligonucleotides for HDR-Mediated Gene Modifications Using the Dharmacon™ Edit-R™ System
PROTOCOL Transfection of ssDNA donor oligonucleotides for HDR-mediated gene modifications using the Dharmacon™ Edit-R™ system Table of Contents Guidelines for HDR-mediated gene modification co-transfection using the Edit-R platform and ssDNA donor oligonucleotides (oligos) ....1 Materials required ....................................................................................................................................................................................................................................... 1 Reagents to be supplied by user ........................................................................................................................................................................................................... 2 Co-transfection of donor oligos with Edit-R Cas9 Nuclease mRNA and Edit-R synthetic guide RNA .......................................................................... 2 Co-transfection of donor oligos with Edit-R Cas9 Nuclease protein NLS and Edit-R synthetic guide RNA ............................................................... 3 Appendix .............................................................................................................................................................................................................................................................4 Additional references ..................................................................................................................................................................................................................................4 -
RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges
1521-0081/72/4/862–898$35.00 https://doi.org/10.1124/pr.120.019554 PHARMACOLOGICAL REVIEWS Pharmacol Rev 72:862–898, October 2020 Copyright © 2020 by The Author(s) This is an open access article distributed under the CC BY-NC Attribution 4.0 International license. ASSOCIATE EDITOR: RHIAN M. TOUYZ RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges Ai-Ming Yu, Young Hee Choi, and Mei-Juan Tu Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.) Abstract. ....................................................................................863 Significance Statement ......................................................................863 I. Introduction. ..............................................................................863 II. Classification and General Features of RNA-Based Therapeutics .............................864 III. RNAs as Therapeutic Drugs .................................................................865 A. The Rise and Promise of RNA Therapeutics ..............................................865 B. Types of RNA Drugs and Mechanisms of Action ..........................................866 1. Antisense Oligonucleotides ...........................................................866 Downloaded from 2. Small Interfering RNAs . ............................................................868