Please click on the subheadings to see the Resource links.
Please email hotpapers@oligotherapeutics.org with additional resource link suggestions!
Essential Guidelines
- PFRED: A computational platform for siRNA and antisense oligonucleotides design.
Sciabola S, Xi H, Cruz D, Cao Q, Lawrence C, Zhang T, Rotstein S, Hughes JD, Caffrey DR, Stanton RV. PLoS One. 2021 Jan 22;16(1):e0238753.
- Guidelines for Experiments Using Antisense Oligonucleotides and Double-Stranded RNAs.
Gagnon KT, Corey DR.
Nucleic Acid Ther. 2019 Jun;29(3):116-22.
- Advancing Nucleic Acid Therapeutics by Setting Uniform Standards for Experimental Controls – Accompanying Editorial by the past and current OTS Presidents Prof. Annemieke Aartsma-Rus and Dr. Arthur M. Krieg
- “Paper of the Month” highlight of the article //www.oligotherapeutics.org/april-2019-paper-of-the-month/
Legacy papers
- Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide.
Zamecnik PC, Stephenson ML.
Proc Natl Acad Sci U S A. 1978 Jan;75(1):280-4.
- Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide.
Stephenson ML, Zamecnik PC.
Proc Natl Acad Sci U S A. 1978 Jan;75(1):285-8.
Reviews
- Treating Disease at the RNA Level with Oligonucleotides.
Levin AA.
N Engl J Med. 2019 Jan 3;380(1):57-70.
- The chemical evolution of oligonucleotide therapies of clinical utility.
Khvorova A, Watts JK.
Nat Biotechnol. 2017 Mar;35(3):238-248.
- Therapeutic Oligonucleotides: State of the Art.
Smith CIE, Zain R.
Annu Rev Pharmacol Toxicol. 2019 Jan 6;59:605-630.
- Oligonucleotide Therapies: The Past and the Present.
Lundin KE, Gissberg O, Smith CI.
Hum Gene Ther. 2015 Aug;26(8):475-85.
- Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs.
Shen X, Corey DR.
Nucleic Acids Res. 2018 Feb 28;46(4):1584-1600.
Webinars & Educational videos
- Dr. Art Krieg “Oligonucleotide Therapeutics: New Drugs That Could Stop COVID-19”
- Dr. Art Krieg “Efforts by the OTS community to combat SARS-CoV-2 and COVID-19”
- Prof. David R. Corey “Guidelines for Experiments using Antisense Oligonucleotides and Double-Stranded RNAs”
- Dr. Dan O’Reilly “Patient Representative Webinar” – A good general introduction for lay audience
Software & databases
- ViennaRNA Web services (inc RNAfold)
- UNAfold (mfold & DINAMelt)
- RNAstructure
- Sfold
- RNAComposer
- Prediction of large RNA 3D structures.
- GGGenome
- PFRED
Scrambled oligo generators
(these say siRNA but are usable for ASO too)
Other general resources
- Nature Milestones in Antisense RNA – A collection of articles on significant milestones and a timeline
- Advances in Nucleic Acid Therapeutics – A book with introductory articles on all areas of oligonucleotide therapeutics
Splicing switching oligonucleotides
Legacy papers
- Antisense RNA inhibits splicing of pre-mRNA in vitro.
Munroe SH.
EMBO J. 1988 Aug;7(8):2523-32.
- Surveying cis-acting sequences of pre-mRNA by adding antisense 2′-O-methyl oligoribonucleotides to a splicing reaction.
Mayeda A, Hayase Y, Inoue H, Ohtsuka E, Ohshima Y.
J Biochem. 1990 Sep;108(3):399-405.
- Restoration of correct splicing in thalassemic pre-mRNA by antisense oligonucleotides.
Dominski Z, Kole R.
Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8673-7.
- Modulation of in vitro splicing of the upstream intron by modifying an intra-exon sequence which is deleted from the dystrophin gene in dystrophin Kobe.
Takeshima Y, Nishio H, Sakamoto H, Nakamura H, Matsuo M.
J Clin Invest. 1995 Feb;95(2):515-20.
- Induction of exon skipping of the dystrophin transcript in lymphoblastoid cells by transfecting an antisense oligodeoxynucleotide complementary to an exon recognition sequence.
Pramono ZA, Takeshima Y, Alimsardjono H, Ishii A, Takeda S, Matsuo M.
Biochem Biophys Res Commun. 1996 Sep 13;226(2):445-9.
- Modification of splicing in the dystrophin gene in cultured Mdx muscle cells by antisense oligoribonucleotides.
Dunckley MG, Manoharan M, Villiet P, Eperon IC, Dickson G.
Hum Mol Genet. 1998 Jul;7(7):1083-90.
- Specific removal of the nonsense mutation from the mdx dystrophin mRNA using antisense oligonucleotides.
Wilton SD, Lloyd F, Carville K, Fletcher S, Honeyman K, Agrawal S, Kole R.
Neuromuscul Disord. 1999 Jul;9(5):330-8.
- Antisense-induced exon skipping restores dystrophin expression in DMD patient derived muscle cells.
van Deutekom JC, Bremmer-Bout M, Janson AA, Ginjaar IB, Baas F, den Dunnen JT, van Ommen GJ.
Hum Mol Genet. 2001 Jul 15;10(15):1547-54.
Reviews
- Invention and Early History of Exon Skipping and Splice Modulation.
Lim KRQ, Yokota T.
Methods Mol Biol. 2018;1828:3-30.
- Exon skipping: a first in class strategy for Duchenne muscular dystrophy.
Niks EH, Aartsma-Rus A.
Expert Opin Biol Ther. 2017 Feb;17(2):225-236.
- Overview on applications of antisense-mediated exon skipping.
van Roon-Mom WM, Aartsma-Rus A.
Methods Mol Biol. 2012;867:79-96
- Antisense-mediated modulation of splicing: therapeutic implications for Duchenne muscular dystrophy.
Aartsma-Rus A.
RNA Biol. 2010 Jul-Aug;7(4):453-61.
Webinars & Educational videos
-
- Prof. Annemieke Aartsma-Rus “Design of Exon Skipping Oligonucleotides”
Software & databases
- Human Splicing Finder
Calculates consensus values of potential splice sites and searches for branch points.
- SpliceDetector
Detection of alternative splicing events in human and model organisms directly from transcript IDs.
Design of splice switching oligonucleotides
- Guidelines for antisense oligonucleotide design and insight into splice-modulating mechanisms.
Aartsma-Rus A, van Vliet L, Hirschi M, Janson AA, Heemskerk H, de Winter CL, de Kimpe S, van Deutekom JC, ‘t Hoen PA, van Ommen GJ.
Mol Ther. 2009 Mar;17(3):548-53.
- Design of phosphorodiamidate morpholino oligomers (PMOs) for the induction of exon skipping of the human DMD gene.
Popplewell LJ, Trollet C, Dickson G, Graham IR.
Mol Ther. 2009 Mar;17(3):554-61.
- Exonic sequences provide better targets for antisense oligonucleotides than splice site sequences in the modulation of Duchenne muscular dystrophy splicing.
Aartsma-Rus A, Houlleberghs H, van Deutekom JC, van Ommen GJ, ‘t Hoen PA.
Oligonucleotides. 2010 Apr;20(2):69-77.
- Development of therapeutic splice-switching oligonucleotides.
Disterer P, Kryczka A, Liu Y, Badi YE, Wong JJ, Owen JS, Khoo B.
Hum Gene Ther. 2014 Jul;25(7):587-98.
- Overview on AON design.
Aartsma-Rus A.
Methods Mol Biol. 2012;867:117-29.
- A prospective study in the rational design of efficient antisense oligonucleotides for exon skipping in the DMD gene.
Pramono ZA, Wee KB, Wang JL, Chen YJ, Xiong QB, Lai PS, Yee WC.
Hum Gene Ther. 2012 Jul;23(7):781-90.
- In silico screening based on predictive algorithms as a design tool for exon skipping oligonucleotides in Duchenne muscular dystrophy.
Echigoya Y, Mouly V, Garcia L, Yokota T, Duddy W.
PLoS One. 2015 Mar 27;10(3):e0120058.
Regulatory perspective:
- Development of Exon Skipping Therapies for Duchenne Muscular Dystrophy: A Critical Review and a Perspective on the Outstanding Issues.
Aartsma-Rus A, Straub V, Hemmings R, Haas M, Schlosser-Weber G, Stoyanova-Beninska V, Mercuri E, Muntoni F, Sepodes B, Vroom E, Balabanov P.
Nucleic Acid Ther. 2017 Oct;27(5):251-259.
- Translational and regulatory challenges for exon skipping therapies.
Aartsma-Rus A, Ferlini A, Goemans N, Pasmooij AM, Wells DJ, Bushby K, Vroom E, Balabanov P.
Hum Gene Ther. 2014 Oct;25(10):885-92.
Legacy papers
- Site specific enzymatic cleavage of RNA.
Donis-Keller H.
Nucleic Acids Res. 1979 Sep 11;7(1):179-92.
Reviews
- Cellular uptake and trafficking of antisense oligonucleotides.
Crooke ST, Wang S, Vickers TA, Shen W, Liang XH.
Nat Biotechnol. 2017 Mar;35(3):230-237.
- Therapeutic Antisense Oligonucleotides Are Coming of Age.
Bennett CF.
Annu Rev Med. 2019 Jan 27;70:307-321.
Webinars & Educational videos
-
- Dr. Robert MacLeod “Antisense Oligonucleotides- Mechanisms of Action and Rational Design”
- OTS Young Investigator Award 2019
Dr. Holly Kordasiewicz “Antisense oligonucleotides for the treatment of neurodegenerative diseases”
- OTS Paper of the Year Award 2019
Dr. Xue-hai Liang “Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index”
Software & databases
Design of RNaseH-based ASOs
ASO off target effects
- Antisense oligonucleotide treatment produces a type I interferon response that protects against diet-induced obesity.
McCabe KM, Hsieh J, Thomas DG, Molusky MM, Tascau L, Feranil JB, Qiang L, Ferrante AW Jr, Tall AR.
Mol Metab. 2020 Apr;34:146-156.
- Development of DNA aptamers using Cell-SELEX.
Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W.
Nat Protoc. 2010 Jun;5(6):1169-85.
- By-product formation in repetitive PCR amplification of DNA libraries during SELEX.
Tolle F, Wilke J, Wengel J, Mayer G.
PLoS One. 2014 Dec 9;9(12):e114693.
- Analysis of In Vitro Aptamer Selection Parameters.
McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC.
J Mol Evol. 2015 Dec;81(5-6):150-61.
- Aptamer Selection Technology and Recent Advances.
Blind M, Blank M.
Mol Ther Nucleic Acids. 2015;4(1):e223.
- Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity.
Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK.
Front Mol Biosci. 2018 May 14;5:41.
- Applications of aptamers as sensors.
Cho EJ, Lee JW, Ellington AD.
Annu Rev Anal Chem (Palo Alto Calif). 2009;2:241-64.
Quadruplex forming
- Apta-Index™ (Aptamer Database) //www.aptagen.com/apta-index/To PEGylate or Not To PEGylate Therapeutics?
Maier KE, Rusconi CP, Levy M.
Cell Chem Biol. 2019 May 16;26(5):615-616.
Some guidelines at the end of this paper:
- Applications of aptamers as sensors.
Cho EJ, Lee JW, Ellington AD.
Annu Rev Anal Chem (Palo Alto Calif). 2009;2:241-64.
Legacy papers
- Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
Tuerk C, Gold L.
Science. 1990 Aug 3;249(4968):505-10.
- In vitro selection of RNA molecules that bind specific ligands.
Ellington AD, Szostak JW.
Nature. 1990 Aug 30;346(6287):818-22.
Reviews
- Aptamers and the RNA world, past and present. a historical view
Gold L, Janjic N, Jarvis T, Schneider D, Walker JJ, Wilcox SK, Zichi D.
Cold Spring Harb Perspect Biol. 2012 Mar 1;4(3).
- Aptamers as therapeutics.
Keefe AD, Pai S, Ellington A.
Nat Rev Drug Discov. 2010 Jul;9(7):537-50.
- Aptamer chemistry.
Röthlisberger P, Hollenstein M.
Adv Drug Deliv Rev. 2018 Sep;134:3-21.
- Aptamers as targeted therapeutics: current potential and challenges.
Zhou J, Rossi J.
Nat Rev Drug Discov. 2017 Mar;16(3):181-202.
- Aptamer-siRNA Chimeras: Discovery, Progress, and Future Prospects.
Kruspe S, Giangrande PH.
Biomedicines. 2017 Aug 9;5(3).
- Aptamers as Diagnostic Tools in Cancer.
Ruiz Ciancio D, Vargas MR, Thiel WH, Bruno MA, Giangrande PH, Mestre MB.
Pharmaceuticals (Basel). 2018 Sep 11;11(3).
- An RNA toolbox for cancer immunotherapy.
Pastor F, Berraondo P, Etxeberria I, Frederick J, Sahin U, Gilboa E, Melero I.
Nat Rev Drug Discov. 2018 Oct;17(10):751-767.
- Aptamers as Therapeutics.
Nimjee SM, White RR, Becker RC, Sullenger BA.
Annu Rev Pharmacol Toxicol. 2017 Jan 6;57:61-79.
- Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers.
Trachman RJ, Ferré-D’Amaré AR.
Q Rev Biophys. 2019 Aug 19;52:e8.
- Aptamers in Drug Design: An Emerging Weapon to Fight a Losing Battle.
Jose J, Thomas AM, Mendonsa D, Al-Sanea MM, Uddin MS, Parambi DGT, Charyulu RN, Mathew B.
Curr Drug Targets. 2019;20(16):1624-1635.
Recent papers of interest:
- Independent control of the thermodynamic and kinetic properties of aptamer switches.
Wilson BD, Hariri AA, Thompson IAP, Eisenstein M, Soh HT.
Nat Commun. 2019 Nov 7;10(1):5079.
- Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology.
Panigaj M, Johnson MB, Ke W, McMillan J, Goncharova EA, Chandler M, Afonin KA.
ACS Nano. 2019 Nov 5.
- Cell fishing with DNA aptamers.
Chen YY.
Nat Biomed Eng. 2019 Oct;3(10):757-758.
- Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs.
Chen X, Zhang D, Su N, Bao B, Xie X, Zuo F, Yang L, Wang H, Jiang L, Lin Q, Fang M, Li N, Hua X, Chen Z, Bao C, Xu J, Du W, Zhang L, Zhao Y, Zhu L, Loscalzo J, Yang Y.
Nat Biotechnol. 2019 Nov;37(11):1287-1293.
High-profile papers:
- Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay.
Pastor F, Kolonias D, Giangrande PH, Gilboa E.
Nature. 2010 May 13;465(7295):227-30.
- Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors.
Dassie JP, Liu XY, Thomas GS, Whitaker RM, Thiel KW, Stockdale KR, Meyerholz DK, McCaffrey AP, McNamara JO 2nd, Giangrande PH.
Nat Biotechnol. 2009 Sep;27(9):839-49.
- Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras.
McNamara JO 2nd, Andrechek ER, Wang Y, Viles KD, Rempel RE, Gilboa E, Sullenger BA, Giangrande PH.
Nat Biotechnol. 2006 Aug;24(8):1005-15.
- Development of universal antidotes to control aptamer activity.
Oney S, Lam RT, Bompiani KM, Blake CM, Quick G, Heidel JD, Liu JY, Mack BC, Davis ME, Leong KW, Sullenger BA.
Nat Med. 2009 Oct;15(10):1224-8.
- Multifunctional aptamer-miRNA conjugates for targeted cancer therapy.
Esposito CL, Cerchia L, Catuogno S, De Vita G, Dassie JP, Santamaria G, Swiderski P, Condorelli G, Giangrande PH, de Franciscis V.
Mol Ther. 2014 Jun;22(6):1151-1163.
- Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients With Stable Coronary Heart Disease.
Ganz P, Heidecker B, Hveem K, Jonasson C, Kato S, Segal MR, Sterling DG, Williams SA.
JAMA. 2016 Jun 21;315(23):2532-41.
- Traceless aptamer-mediated isolation of CD8+ T cells for chimeric antigen receptor T-cell therapy.
Kacherovsky N, Cardle II, Cheng EL, Yu JL, Baldwin ML, Salipante SJ, Jensen MC, Pun SH.
Nat Biomed Eng. 2019 Oct;3(10):783-795.
Webinars & Educational videos
- Prof. Paloma Giangrande “Aptamers and SELEX: The Past, The Present, and The Future”
- Prof. Günter Mayer “Advances in SELEX technologies for Aptamers”
- Dr. David Porciani and Prof. Donald H. Burke “Targeted delivery using aptamers”
Software & databases
- ViennaRNA Web services (inc RNAfold)
- UNAfold (mfold & DINAMelt)
- RNAstructure
- Sfold
- RNAComposer
- Prediction of large RNA 3D structures.
Fluorescent aptamers
Introduction
- //blog.addgene.org/the-fluorescent-vegetables-in-aptamer-soup
- //blog.addgene.org/plasmids-101-aptamer-fluorophores
Reviews
- Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers.
Trachman RJ, Ferré-D’Amaré AR.
Q Rev Biophys. 2019 Aug 19;52:e8.
- RNA-Based Fluorescent Biosensors for Detecting Metabolites in vitro and in Living Cells.
Jaffrey SR.
Adv Pharmacol. 2018;82:187-203.
- Structural Principles of Fluorescent RNA Aptamers.
Trachman RJ 3rd, Truong L, Ferré-D’Amaré AR.
Trends Pharmacol Sci. 2017 Oct;38(10):928-939.
Singh, A.S. Narang, et al. Subcellular fate and off-target effects of siRNA, shRNA, and miRNA. Pharmaceutical Research 28, 2996–3015 (2011).
- D.R. Caffrey, J. Zhao, et al. siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS One 6, e21503 (2011).
- E. Anderson, Q. Boese, et al. Identifying siRNA-induced off-targets by microarray analysis. Methods in Molecular Biology 442, 45–63 (2008).
- A. Birmingham, E.M. Anderson, et al. 3′-UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature Methods 3(3), 199-204 (2006).
- A. Reynolds, E.M. Anderson, et al. Induction of the interferon response by siRNA is cell type and duplex length dependent. RNA 12(6), 988–993 (2006).
- Federov, E.M. Anderson, et al. Off-targeting by siRNA can induce toxic phenotype. RNA 12(7), 1188–1196 (2006).
- Lin, X. Ruan, et al. siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Research 33(14), 4527–4535 (2005).
- Fedorov, A. King, et al. Different delivery methods-different expression profiles. Nature Methods 2(4), 241 (2005).
- Reynolds, D. Leake, et al. Rational siRNA design for RNA interference. Nature Biotechnology 22(3), 326-330 (2004).
- L. Jackson, S.R. Bartz et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnology 21(6), 635–637 (2003).
- Khvorova, A. Reynolds, et al. Functional siRNAs and miRNAs exhibit strand bias. Cell 115 (2), 209–216 (2003).
Legacy papers
- Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC.
Nature. 1998 Feb 19;391(6669):806-11.
- Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells.
Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T.
Nature. 2001 May 24;411(6836):494-8.
- Precise and efficient siRNA design: a key point in competent gene silencing.
Fakhr E, Zare F, Teimoori-Toolabi L.
Cancer Gene Ther. 2016 Apr;23(4):73-82.
Reviews
- RNA interference.
Hannon GJ.
Nature. 2002 Jul 11;418(6894):244-51.
- Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins?
Nakanishi K.
Wiley Interdiscip Rev RNA. 2016 Sep;7(5):637-60.
- RNA Interference (RNAi)-Based Therapeutics: Delivering on the Promise?
Bobbin ML, Rossi JJ.
Annu Rev Pharmacol Toxicol. 2016;56:103-22.
- The current state and future directions of RNAi-based therapeutics.
Setten RL, Rossi JJ, Han SP.
Nat Rev Drug Discov. 2019 Jun;18(6):421-446.
Protocols
Webinars & Educational videos
Prof. Anastasia Khvorova “Oligonucleotide Therapeutics: Technology Evolution for Clinically Relevant Tissue Delivery”
- Dr. Bruno Godhino “Divalent siRNA Scaffold for Robust Gene Modulation in the Central Nervous System”
- Dr. Alan M Gewirtz Memorial Scholarship Award 2019
- Dr. Garrett Rettig “Planning and executing siRNA experiments”
- Dr. Garrett Rettig “In vivo RNAi: Considerations and examples – a panel presentation”
Software & databases
siRNA design
Remember to check if our siRNA design knocks down (all) your intended target splice isoform(s)
- RNAxs (siRNA)
- i-Score Designer (siRNA)
- Custom Dicer-Substrate siRNA (DsiRNA)
- siRNA Wizard (siRNA)
- E-RNAi (esiRNA + siRNA)
- Kay Lab siRNA/shRNA/Oligo Optimal design (siRNA + shRNA)
- BLOCK-iT RNAi Designer (siRNA + shRNA)
- DSIR (siRNA + shRNA)
- GPP Web Portal (shRNA)
Other
RNAi phenotype database
siRNA off target
DO NOT use GFP siRNA as a control!
- Misinterpreting the therapeutic effects of small interfering RNA caused by immune stimulation.
Robbins M, Judge A, Ambegia E, Choi C, Yaworski E, Palmer L, McClintock K, MacLachlan I.
Hum Gene Ther. 2008 Oct;19(10):991-9. - Sequence- and target-independent angiogenesis suppression by siRNA via TLR3.
Kleinman ME, Yamada K, Takeda A, Chandrasekaran V, Nozaki M, Baffi JZ, Albuquerque RJ, Yamasaki S, Itaya M, Pan Y, Appukuttan B, Gibbs D, Yang Z, Karikó K, Ambati BK, Wilgus TA, DiPietro LA, Sakurai E, Zhang K, Smith JR, Taylor EW, Ambati J.
Nature. 2008 Apr 3;452(7187):591-7.
Legacy papers
- Nucleoside phosphorothioates.
Eckstein F.
J Am Chem Soc. 1970 Jul 29;92(15):4718-23.
- Efficient RNase H-directed cleavage of RNA promoted by antisense DNA or 2’F-ANA constructs containing acyclic nucleotide inserts.
Mangos MM, Min KL, Viazovkina E, Galarneau A, Elzagheid MI, Parniak MA, Damha MJ. J Am Chem Soc. 2003 Jan 22;125(3):654-61.
Reviews
- Morpholino antisense oligomers: design, preparation, and properties.
Summerton J, Weller D.
Antisense Nucleic Acid Drug Dev. 1997 Jun;7(3):187-95.
- The Medicinal Chemistry of Therapeutic Oligonucleotides.
Wan WB, Seth PP.
J Med Chem. 2016 Nov 10;59(21):9645-9667.
- The Medicinal Chemistry of RNase H-activating Antisense Oligonucleotides
Seth, P.P. and Swayze, E.E.
In Advances in Nucleic Acid Therapeutics edited by Agrawal, S. and Gait, M.J.
The Royal Society of Chemistry, 2019, pp. 32-61.
- Nucleic Acids in Chemistry and Biology: Edition 3 edited by Blackburn, G.M., Gait, M.J., Loakes, D. and Williams, D.M.
The Royal Society of Chemistry, 2006.
- Exploring Atypical Fluorine-Hydrogen Bonds and Their Effects on Nucleoside Conformations.
O’Reilly D, Stein RS, Patrascu MB, Jana SK, Kurian J, Moitessier N, Damha MJ. Chemistry. 2018 Nov 2;24(61):16432-16439
- Designing chemically modified oligonucleotides for targeted gene silencing.
Deleavey GF, Damha MJ. Chem Biol. 2012 Aug 24;19(8):937-54.
Protocols
Webinars & Educational videos
Dr. Muthiah (Mano) Manoharan “Chemistry of Oligonucleotide Therapeutics 101
Dr. Muthiah (Mano) Manoharan “Chemistry of Therapeutic Oligonucleotides: A Brief Overview
Dr. Muthiah (Mano) Manoharan “Living in the World of Oligonucleotide Therapeutics”
OTS Lifetime Achievement Award 2019
Prof Marvin H. Caruthers “Chemical Synthesis DNA/RNA and Biological Activity of Selected Analogues”
OTS Lifetime Achievement Award 2018
Prof Michael J. Gait “A Life’s work in Oligonucleotides: From chemical Synthesis to Peptide-PMO for treatment of Neuromuscular Diseases”
OTS Lifetime Achievement Award 2017
Prof. Fritz Eckstein “50 Years of Phosphorothioate Nucleic Acids”
OTS Lifetime Achievement Award 2016
Legacy papers
Reviews
Protocols
Webinars & Educational videos
Dr. Jana L. McCaskill “Broad-Spectrum, host-targeted miRNA Therapeutics for the Treatment of Respiratory Viral Infections”
Dr. Alan Gewirtz Memorial Scholarship 2015 Award Lecture
Prof. Andrea Kasinski “Design of microRNA therapeutics”
Mr. Simone Detassis “Pitfalls and problems of miRNA expression analysis”
Embed //youtu.be/1yRMvoPHPns
Software & databases
MicroRNA design
- AmiRNA Designer (microRNA)
- miR-Synth (multiple target microRNA)
- miRNAsong (microRNA sponge)
Databases
- miRBase: the microRNA database
- miRWalk2.0: a comprehensive atlas of microRNA-target interactions
- miRTarBase
- TargetScan
- PicTar
Legacy papers
Reviews
- CpG still rocks! Update on an accidental drug.
Krieg AM.
Nucleic Acid Ther. 2012 Apr;22(2):77-89. - Nucleic Acid Immunity.
Hartmann G.
Adv Immunol. 2017;133:121-169. - Therapeutically exploiting STAT3 activity in cancer – using tissue repair as a road map.
Huynh J, Chand A, Gough D, Ernst M.
Nat Rev Cancer. 2019 Feb;19(2):82-96. doi: 10.1038/s41568-018-0090-8. - STAT3 Inhibition Combined with CpG Immunostimulation Activates Antitumor Immunity to Eradicate Genetically Distinct Castration-Resistant Prostate Cancers.
Moreira D, Adamus T, Zhao X, Su YL, Zhang Z, White SV, Swiderski P, Lu X, DePinho RA, Pal SK, Kortylewski M.
Clin Cancer Res. 2018 Dec 1;24(23):5948-5962
Protocols
Webinars & Educational videos
Dr. Art Krieg “How to test for immune activation by your therapeutic oligonucleotide”
Dr. Art Krieg “Screening for Immunostimulation”
Dr. Art Krieg “Oligo Meeting 2017 – Immune Stimulatory Oligos”
Software & databases
Legacy papers
- Recommendations for safety pharmacology evaluations of oligonucleotide-based therapeutics.
Berman CL, Cannon K, Cui Y, Kornbrust DJ, Lagrutta A, Sun SZ, Tepper J, Waldron G, Younis HS.
Nucleic Acid Ther. 2014 Aug;24(4):291-301. doi: 10.1089/nat.2013.0477. Epub 2014 Jun 19. Review.
PMID: 24946015
- Considerations for the Characterization and Interpretation of Results Related to Alternative Complement Activation in Monkeys Associated with Oligonucleotide-Based Therapeutics.
Henry SP, Seguin R, Cavagnaro J, Berman C, Tepper J, Kornbrust D.
Nucleic Acid Ther. 2016 Aug;26(4):210-5. doi: 10.1089/nat.2015.0593. Epub 2016 Mar 16. Review.
PMID: 26981618
Reviews
Protocols
Webinars & Educational videos
Dr. Patrik Andersson “Safety of Therapeutic Oligonucleotides”
Dr. Seokjoo Yoon “New Approach for Safety Evaluation of Oligonucleotide Therapeutics Using RNAseq”
Dr. Sebastien Burel “Unraveling the Mechanisms of ASO Mediated Toxicity”
Dr. Sabine Sewing “AON Safety Screening – In vitro Assays Capturing Toxicity Risks”
Software & databases
Reviews
- Messenger RNA as a Novel Therapeutic Approach
Stanton, M.G. and Murphy-Benenato, K.E.
- In RNA Therapeutics edited by Garner, A.L.
Springer, Cham, 2018, pp. 237-253
- mRNA vaccines – a new era in vaccinology.
Pardi N, Hogan MJ, Porter FW, Weissman D. Nat Rev Drug Discov. 2018 Apr;17(4):261-279.
- Current Status of Messenger RNA Delivery Systems.
Stanton MG. Nucleic Acid Ther. 2018 Jun;28(3):158-165.
Protocols
Webinars & Educational videos
Dr. Matthew Stanton “Messenger RNA as a Novel Therapeutic Approach”
Software & databases
Legacy papers
- The product of the H19 gene may function as an RNA.
Brannan CI, Dees EC, Ingram RS, Tilghman SM.
Mol Cell Biol. 1990 Jan;10(1):28-36.
- A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome.
Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF.
Nature. 1991 Jan 3;349(6304):38-44.
- Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.
Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S. Nature. 2012 Nov 15;491(7424):454-7.
Reviews
- A guide to naming human non-coding RNA genes.
Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O’Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA.
EMBO J. 2020 Feb 24:e103777.
Recent papers
- Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins.
Lee S, Kopp F, Chang TC, Sataluri A, Chen B, Sivakumar S, Yu H, Xie Y, Mendell JT.
Cell. 2016 Jan 14;164(1-2):69-80.
- Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA.
Hosono Y, Niknafs YS, Prensner JR, Iyer MK, Dhanasekaran SM, Mehra R, Pitchiaya S, Tien J, Escara-Wilke J, Poliakov A, Chu SC, Saleh S, Sankar K, Su F, Guo S, Qiao Y, Freier SM, Bui HH, Cao X, Malik R, Johnson TM, Beer DG, Feng FY, Zhou W, Chinnaiyan AM.
Cell. 2017 Dec 14;171(7):1559-1572.e20.
- Melanoma addiction to the long non-coding RNA SAMMSON.
Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, Radaelli E, Eyckerman S, Leonelli C, Vanderheyden K, Rogiers A, Hermans E, Baatsen P, Aerts S, Amant F, Van Aelst S, van den Oord J, de Strooper B, Davidson I, Lafontaine DL, Gevaert K, Vandesompele J, Mestdagh P, Marine JC.
Nature. 2016 Mar 24;531(7595):518-22.
Protocols
Webinars & Educational videos
- Kim Lennox “Knockdown of lncRNAs: Exploring RNAi and antisense oligo methods”
Software & databases
Legacy papers
- Small dsRNAs induce transcriptional activation in human cells.
Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R.
Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17337-42.
- Activating gene expression in mammalian cells with promoter-targeted duplex RNAs.
Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE, Corey DR.
Nat Chem Biol. 2007 Mar;3(3):166-73.
Reviews
- Developing small activating RNA as a therapeutic: current challenges and promises.
Kwok A, Raulf N, Habib N.
Ther Deliv. 2019 Mar;10(3):151-164.
- Regulation of mammalian transcription and splicing by Nuclear RNAi.
Kalantari R, Chiang CM, Corey DR.
Nucleic Acids Res. 2016 Jan 29;44(2):524-37.
- RNA-mediated gene activation.
Jiao AL, Slack FJ.
Epigenetics. 2014 Jan;9(1):27-36.
- Small RNA and transcriptional upregulation.
Portnoy V, Huang V, Place RF, Li LC.
Wiley Interdiscip Rev RNA. 2011 Sep-Oct;2(5):748-60.
- Development and Mechanism of Small Activating RNA Targeting CEBPA, a Novel Therapeutic in Clinical Trials for Liver Cancer.
Voutila J, Reebye V, Roberts TC, Protopapa P, Andrikakou P, Blakey DC, Habib R, Huber H, Saetrom P, Rossi JJ, Habib NA.
Mol Ther. 2017 Dec 6;25(12):2705-2714.
Protocols
Webinars & Educational videos
Software & databases
Legacy papers
- Circular RNAs are a large class of animal RNAs with regulatory potency.
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N.
Nature. 2013 Mar 21;495(7441):333-8
- Natural RNA circles function as efficient microRNA sponges.
Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J.
Nature. 2013 Mar 21;495(7441):384-8.
Reviews
Guidelines for necessary experiments can be found here:
- Artificial Circular RNA Sponges Targeting MicroRNAs as a Novel Tool in Molecular Biology.
Rossbach O.
Mol Ther Nucleic Acids. 2019 Sep 6;17:452-454.
- The biogenesis, biology and characterization of circular RNAs.
Kristensen LS, Andersen MS, Stagsted LVW, Ebbesen KK, Hansen TB, Kjems J.
Nat Rev Genet. 2019 Nov;20(11):675-691.
- Circular RNAs: analysis, expression and potential functions.
Barrett SP, Salzman J. Development. 2016 Jun 1;143(11):1838-47.
Protocols
- Production and Purification of Artificial Circular RNA Sponges for Application in Molecular Biology and Medicine.
Breuer J, Rossbach O. Methods Protoc. 2020 May 26;3(2):E42.
Webinars & Educational videos
- Prof. Grace Chen “Circular RNA Immunity”
Embed //youtu.be/K3xwrfwCZDI
Software & databases
- circBase
Public circRNA datasets
- Circular RNA Interactome
Prediction and mapping of binding sites for RBPs and miRNAs on reported circRNAs
- CircR2Disease
A curated database of experimentally supported associations between circRNAs and diseases
- circRNADb
A database of circular RNA molecules in humans containing 32,914 annotated exonic circRNAs
- MiOncoCirc
A compendium of circular RNAs compiled from cancer clinical samples at the University of Michigan
Legacy papers
Reviews
- Nucleic Acid Therapeutics Special Issue: Delivery of RNA Therapeutics
June 2018; 28(3)
- Strategies, design, and chemistry in siRNA delivery systems.
Dong Y, Siegwart DJ, Anderson DG.
Adv Drug Deliv Rev. 2019 Apr;144:133-147.
- Lipid Nanoparticle Technology for Clinical Translation of siRNA Therapeutics.
Kulkarni JA, Witzigmann D, Chen S, Cullis PR, van der Meel R.
Acc Chem Res. 2019 Sep 17;52(9):2435-2444.
- Selective tissue targeting of synthetic nucleic acid drugs.
Seth PP, Tanowitz M, Bennett CF.
J Clin Invest. 2019 Mar 1;129(3):915-925.
- Overcoming cellular barriers for RNA therapeutics.
Dowdy SF.
Nat Biotechnol. 2017 Mar;35(3):222-229.
- Intracellular Trafficking and Endosomal Release of Oligonucleotides: What We Know and What We Don’t.
Juliano RL.
Nucleic Acid Ther. 2018 Jun;28(3):166-177.
- Receptor-Mediated Uptake of Phosphorothioate Antisense Oligonucleotides in Different Cell Types of the Liver.
Miller CM, Tanowitz M, Donner AJ, Prakash TP, Swayze EE, Harris EN, Seth PP.
Nucleic Acid Ther. 2018 Jun;28(3):119-127.
- Oligonucleotide therapies for disorders of the nervous system.
Khorkova O, Wahlestedt C.
Nat Biotechnol. 2017 Mar;35(3):249-263.
- The delivery of therapeutic oligonucleotides.
Juliano RL.
Nucleic Acids Res. 2016 Aug 19;44(14):6518-48.
- RNA Therapeutics (Almost) Comes of Age: Targeting, Delivery and Endosomal Escape.
Dowdy SF, Levy M.
Nucleic Acid Ther. 2018 Jun;28(3):107-108.
- Current Status of Messenger RNA Delivery Systems.
Stanton MG.
Nucleic Acid Ther. 2018 Jun;28(3):158-165.
- A Novel Amino Lipid Series for mRNA Delivery: Improved Endosomal Escape and Sustained Pharmacology and Safety in Non-human Primates.
Sabnis S, Kumarasinghe ES, Salerno T, Mihai C, Ketova T, Senn JJ, Lynn A, Bulychev A, McFadyen I, Chan J, Almarsson Ö, Stanton MG, Benenato KE.
Mol Ther. 2018 Jun 6;26(6):1509-1519.
Webinars & Educational videos
Prof. Steven Dowdy “Delivery of Macromolecular Therapeutics: Tackling a Billion Year Old Barrier”
Prof. Anastasia Khvorova “Oligonucleotide Therapeutics: Technology Evolution for Clinically Relevant Tissue Delivery”
Protocols
Software & databases
with aptamers
- Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras.
McNamara JO 2nd, Andrechek ER, Wang Y, Viles KD, Rempel RE, Gilboa E, Sullenger BA, Giangrande PH.
Nat Biotechnol. 2006 Aug;24(8):1005-15.
- Design and Preparation of Aptamer-siRNA Chimeras (AsiCs) for Targeted Cancer Therapy.
Kruspe S, Giangrande PH.
Methods Mol Biol. 2017;1632:175-186.
- Nucleic acids delivering nucleic acids.
Catuogno S, Esposito CL, Condorelli G, de Franciscis V.
Adv Drug Deliv Rev. 2018 Sep;134:79-93.
with GalNAc
- GalNAc-siRNA Conjugates: Leading the Way for Delivery of RNAi Therapeutics.
Springer AD, Dowdy SF.
Nucleic Acid Ther. 2018 Jun;28(3):109-118.
- Multivalent N-acetylgalactosamine-conjugated siRNA localizes in hepatocytes and elicits robust RNAi-mediated gene silencing.
Nair JK, Willoughby JL, Chan A, Charisse K, Alam MR, Wang Q, Hoekstra M, Kandasamy P, Kel’in AV, Milstein S, Taneja N, O’Shea J, Shaikh S, Zhang L, van der Sluis RJ, Jung ME, Akinc A, Hutabarat R, Kuchimanchi S, Fitzgerald K, Zimmermann T, van Berkel TJ, Maier MA, Rajeev KG, Manoharan M.
J Am Chem Soc. 2014 Dec 10;136(49):16958-61.
- Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity.
Janas MM, Schlegel MK, Harbison CE, Yilmaz VO, Jiang Y, Parmar R, Zlatev I, Castoreno A, Xu H, Shulga-Morskaya S, Rajeev KG, Manoharan M, Keirstead ND, Maier MA, Jadhav V.
Nat Commun. 2018 Feb 19;9(1):723.
- Safety evaluation of 2′-deoxy-2′-fluoro nucleotides in GalNAc-siRNA conjugates.
Janas MM, Zlatev I, Liu J, Jiang Y, Barros SA, Sutherland JE, Davis WP, Liu J, Brown CR, Liu X, Schlegel MK, Blair L, Zhang X, Das B, Tran C, Aluri K, Li J, Agarwal S, Indrakanti R, Charisse K, Nair J, Matsuda S, Rajeev KG, Zimmermann T, Sepp-Lorenzino L, Xu Y, Akinc A, Fitzgerald K, Vaishnaw AK, Smith PF, Manoharan M, Jadhav V, Wu JT, Maier MA.
Nucleic Acids Res. 2019 Apr 23;47(7):3306-3320.
- Impact of enhanced metabolic stability on pharmacokinetics and pharmacodynamics of GalNAc-siRNA conjugates.
Nair JK, Attarwala H, Sehgal A, Wang Q, Aluri K, Zhang X, Gao M, Liu J, Indrakanti R, Schofield S, Kretschmer P, Brown CR, Gupta S, Willoughby JLS, Boshar JA, Jadhav V, Charisse K, Zimmermann T, Fitzgerald K, Manoharan M, Rajeev KG, Akinc A, Hutabarat R, Maier MA.
Nucleic Acids Res. 2017 Nov 2;45(19):10969-10977.
with TLR9
- In vivo delivery of siRNA to immune cells by conjugation to a TLR9 agonist enhances antitumor immune responses.
Kortylewski M, Swiderski P, Herrmann A, Wang L, Kowolik C, Kujawski M, Lee H, Scuto A, Liu Y, Yang C, Deng J, Soifer HS, Raubitschek A, Forman S, Rossi JJ, Pardoll DM, Jove R, Yu H.
Nat Biotechnol. 2009 Oct;27(10):925-32.
- Intracellular processing of immunostimulatory CpG-siRNA: Toll-like receptor 9 facilitates siRNA dicing and endosomal escape.
Nechaev S, Gao C, Moreira D, Swiderski P, Jozwiak A, Kowolik CM, Zhou J, Armstrong B, Raubitschek A, Rossi JJ, Kortylewski M.
J Control Release. 2013 Sep 28;170(3):307-15.
- TLR9-Targeted SiRNA Delivery In Vivo.
Hossain DM, Moreira D, Zhang Q, Nechaev S, Swiderski P, Kortylewski M.
Methods Mol Biol. 2016;1364:183-96.
- Targeted Delivery of miRNA Antagonists to Myeloid Cells In Vitro and In Vivo.
Su YL, Swiderski P, Marcucci G, Kortylewski M.
Methods Mol Biol. 2019;1974:141-150.
Legacy papers
- A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E.
Science. 2012 Aug 17;337(6096):816-21.
- Multiplex genome engineering using CRISPR/Cas systems.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Science. 2013 Feb 15;339(6121):819-23.
- RNA-guided human genome engineering via Cas9.
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. Science. 2013 Feb 15;339(6121):823-6.
- A Single Administration of CRISPR/Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing.
Finn JD, Smith AR, Patel MC, Shaw L, Youniss MR, van Heteren J, Dirstine T, Ciullo C, Lescarbeau R, Seitzer J, Shah RR, Shah A, Ling D, Growe J, Pink M, Rohde E, Wood KM, Salomon WE, Harrington WF, Dombrowski C, Strapps WR, Chang Y, Morrissey DV.
Cell Rep. 2018 Feb 27;22(9):2227-2235.
- Biological plasticity rescues target activity in CRISPR knock outs.
Smits AH, Ziebell F, Joberty G, Zinn N, Mueller WF, Clauder-Münster S, Eberhard D, Fälth Savitski M, Grandi P, Jakob P, Michon AM, Sun H, Tessmer K, Bürckstümmer T, Bantscheff M, Steinmetz LM, Drewes G, Huber W.
Nat Methods. 2019 Oct 28.
Base editor:
- Base editing: precision chemistry on the genome and transcriptome of living cells.
Rees HA, Liu DR.
Nat Rev Genet. 2018 Dec;19(12):770-788.
- Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity.
O’Reilly D, Kartje ZJ, Ageely EA, Malek-Adamian E, Habibian M, Schofield A, Barkau CL, Rohilla KJ, DeRossett LB, Weigle AT, Damha MJ, Gagnon KT. Nucleic Acids Res. 2019 Jan 25;47(2):546-558.
Protocols
Webinars & Educational videos
Prof. Keith T. Gagnon “An Overview of Chemical Modifications to CRISPR RNA”
Prof. Feng Zhang “Genome Editing Technologies and Beyond”
OTS 2018 Keynote presentation
Justin Barr “Getting started with CRISPR: A review of gene knockout and homology-directed repair”
Software & databases
- GPP sgRNA designer
- CHyMErA
- Cas13 Guide Design
- PrimeDesign
- Design tool for Prime editing
VBC-Score
Eteplirsen – Exondys 51
FDA Approves Eteplirsen for Duchenne Muscular Dystrophy: The Next Chapter in the Eteplirsen Saga.
Aartsma-Rus A, Krieg AM.
Nucleic Acid Ther. 2017 Feb;27(1):1-3.
Nusinersen – Spinraza
Nusinersen versus Sham Control in Infantile-Onset Spinal Muscular Atrophy.
Finkel RS, Mercuri E, Darras BT, Connolly AM, Kuntz NL, Kirschner J, Chiriboga CA, Saito K, Servais L, Tizzano E, Topaloglu H, Tulinius M, Montes J, Glanzman AM, Bishop K, Zhong ZJ, Gheuens S, Bennett CF, Schneider E, Farwell W, De Vivo DC; ENDEAR Study Group.
N Engl J Med. 2017 Nov 2;377(18):1723-1732.
Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy.
Mercuri E, Darras BT, Chiriboga CA, Day JW, Campbell C, Connolly AM, Iannaccone ST, Kirschner J, Kuntz NL, Saito K, Shieh PB, Tulinius M, Mazzone ES, Montes J, Bishop KM, Yang Q, Foster R, Gheuens S, Bennett CF, Farwell W, Schneider E, De Vivo DC, Finkel RS; CHERISH Study Group.
N Engl J Med. 2018 Feb 15;378(7):625-635.
Heplisav-B
(contains CpG oligo as adjuvants)
Patisiran – Onpattro
Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis.
Adams D, Gonzalez-Duarte A, O’Riordan WD, Yang CC, Ueda M, Kristen AV, Tournev I, Schmidt HH, Coelho T, Berk JL, Lin KP, Vita G, Attarian S, Planté-Bordeneuve V, Mezei MM, Campistol JM, Buades J, Brannagan TH 3rd, Kim BJ, Oh J, Parman Y, Sekijima Y, Hawkins PN, Solomon SD, Polydefkis M, Dyck PJ, Gandhi PJ, Goyal S, Chen J, Strahs AL, Nochur SV, Sweetser MT, Garg PP, Vaishnaw AK, Gollob JA, Suhr OB.
N Engl J Med. 2018 Jul 5;379(1):11-21.
Inotersen – Tegsedi
Inotersen Treatment for Patients with Hereditary Transthyretin Amyloidosis.
Benson MD, Waddington-Cruz M, Berk JL, Polydefkis M, Dyck PJ, Wang AK, Planté-Bordeneuve V, Barroso FA, Merlini G, Obici L, Scheinberg M, Brannagan TH 3rd, Litchy WJ, Whelan C, Drachman BM, Adams D, Heitner SB, Conceição I, Schmidt HH, Vita G, Campistol JM, Gamez J, Gorevic PD, Gane E, Shah AM, Solomon SD, Monia BP, Hughes SG, Kwoh TJ, McEvoy BW, Jung SW, Baker BF, Ackermann EJ, Gertz MA, Coelho T.
N Engl J Med. 2018 Jul 5;379(1):22-31.
Volanesorsen – Waylivra (EMA only)
Volanesorsen and Triglyceride Levels in Familial Chylomicronemia Syndrome.
Witztum JL, Gaudet D, Freedman SD, Alexander VJ, Digenio A, Williams KR, Yang Q, Hughes SG, Geary RS, Arca M, Stroes ESG, Bergeron J, Soran H, Civeira F, Hemphill L, Tsimikas S, Blom DJ, O’Dea L, Bruckert E.
N Engl J Med. 2019 Aug 8;381(6):531-542.
Golodirsen – Vyondys 53
Givosiran – Givlaari
Viltolarsen
Lumasiran
Legacy papers
Webinars & Educational videos
Ms. Mai Thayer “Quantification Methods for oligonucleotide therapeutics in serum and tissue”
Dr. Carl Amilon “Time matters! – Why PK/PD is important for oligo development”
Software & databases
Webinars & Educational videos
Dr Matthew McNeill “Tips for effective use of BLAST and other NCBI tools”
Software & databases
- Addgene – looking for plasmids?
- The fluorescent protein database
- The Human Protein Atlas
- Bio-GPS
- HUGO Gene Nomenclature Committee
- Sequence Manipulation Suite
- ApE – A plasmid Editor (free, donations welcomed)
- Mouse Genome Informatics
- Jax Mouse phenome database
- The Human Gene Mutation Database
- ClinVar
- GENCODE
- RefSeq
Webinars & Educational videos
Dr. Dan O’Reilly “Patient Representative Webinar”
Dr. Art Krieg “Oligonucleotide Therapeutics: New Drugs That Could Stop COVID-19”
Software & databases
List of recognized rare diseases
Reviews
- Understanding the basics of patenting.
Chitale S, Lawler C, Macfarlane S.
Nat Biotechnol. 2020 Mar;38(3):263-270.
- The alphabet soup of agreements.
Chitale S, Lawler C, Macfarlane S.
Nat Biotechnol. 2018 Mar 6;36(3):220-224.
- Closing the deal.
Chitale S, Lawler C, Macfarlane S.
Nat Biotechnol. 2016 Dec 7;34(12):1222-1225.
- Licensing lessons learned: if I knew then what I know now.
Chitale S, Lawler C, Macfarlane S.
Nat Biotechnol. 2013 Apr;31(4):362-3.
Webinars & Educational videos
- Dr. Laurence Gainey “Basics of intellectual property and patenting”
Embed //youtu.be/_XFm7R_0lt8
- Orphan Drug Development Guidebook Materials
//irdirc.org/orphan-drug-development-guidebook-materials/