Please click on the subheadings to see the Resource links.
Please email hotpapers@oligotherapeutics.org with additional resource link suggestions!

Essential Guidelines

Legacy papers

Reviews

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”

Software & databases

Scrambled oligo generators

(these say siRNA but are usable for ASO too)

Other general resources

Splicing switching oligonucleotides

Legacy papers

Reviews

Webinars & Educational videos

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

Regulatory perspective:

Legacy papers

Reviews

Webinars & Educational videos

  • 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

  • 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.

Quadruplex forming

Some guidelines at the end of this paper:

Legacy papers

Reviews

  • Aptamer chemistry.
    Röthlisberger P, Hollenstein M.
    Adv Drug Deliv Rev. 2018 Sep;134:3-21.

Recent papers of interest:

High-profile papers:

Webinars & Educational videos

  • Prof. Paloma Giangrande “Aptamers and SELEX: The Past, The Present, and The Future”

Software & databases

Fluorescent aptamers

Introduction

Reviews

Singh, A.S. Narang, et al. Subcellular fate and off-target effects of siRNA, shRNA, and miRNA. Pharmaceutical Research 28, 2996–3015 (2011).

  1. 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).
  2. E. Anderson, Q. Boese, et al. Identifying siRNA-induced off-targets by microarray analysis. Methods in Molecular Biology 442, 45–63 (2008).
  3. 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).
  4. 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).
  5. Federov, E.M. Anderson, et al. Off-targeting by siRNA can induce toxic phenotype. RNA 12(7), 1188–1196 (2006).
  6. 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).
  7. Fedorov, A. King, et al. Different delivery methods-different expression profiles. Nature Methods 2(4), 241 (2005).
  8. Reynolds, D. Leake, et al. Rational siRNA design for RNA interference. Nature Biotechnology 22(3), 326-330 (2004).
  9. L. Jackson, S.R. Bartz et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnology 21(6), 635–637 (2003).
  10. Khvorova, A. Reynolds, et al. Functional siRNAs and miRNAs exhibit strand bias. Cell 115 (2), 209–216 (2003).

Legacy papers

Reviews

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”

Embed //eu.idtdna.com/pages/videos/default-source/webinar-videos/functional-genomics/planning-and-executing-in-vivo-sirna-experiments.mp4?sfvrsn=65643207_14

  • Dr. Garrett Rettig “In vivo RNAi: Considerations and examples – a panel presentation”

Embed //eu.idtdna.com/pages/videos/default-source/webinar-videos/functional-genomics/in-vivo-rnai—-considerations-and-examples-a-panel-presentation.mp4?sfvrsn=8f643207_18

Software & databases

siRNA design

Remember to check if our siRNA design knocks down (all) your intended target splice isoform(s)

Other

RNAi phenotype database

siRNA off target

DO NOT use GFP siRNA as a control!

Legacy papers

Reviews

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

Design of efficient microRNA

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

Databases

Legacy papers

Reviews

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

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

Protocols

Webinars & Educational videos

Dr. Matthew Stanton “Messenger RNA as a Novel Therapeutic Approach”

Software & databases

Legacy papers

Reviews

Recent papers

  • 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”

Embed //eu.idtdna.com/pages/videos/default-source/webinar-videos/functional-genomics/knockdown-of-lncrnas-exploring-rnai-and-antisense-oligo-methods.mp4?sfvrsn=8c070c07_8

Software & databases

Legacy papers

Reviews

Protocols

Webinars & Educational videos

Software & databases

Legacy papers

Reviews

Guidelines for necessary experiments can be found here:

Protocols

Webinars & Educational videos

Embed //youtu.be/K3xwrfwCZDI

Software & databases

  • 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

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

with GalNAc

  • 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.

with TLR9

Legacy papers

Base editor:

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”

Embed //eu.idtdna.com/pages/videos/default-source/webinar-videos/crispr-genome-editing/getting-started-with-crispr-j-barr-031517.mp4?sfvrsn=9e123407_14

Software & databases

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

Webinars & Educational videos

Dr. Dan O’Reilly “Patient Representative Webinar

Dr. Art Krieg “Oligonucleotide Therapeutics: New Drugs That Could Stop COVID-19”

Software & databases

RARE List

List of recognized rare diseases

Reviews

  • Closing the deal.
    Chitale S, Lawler C, Macfarlane S.
    Nat Biotechnol. 2016 Dec 7;34(12):1222-1225.

Webinars & Educational videos