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Gapmers

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Toshifumi Yokota

    1. Department of Medical Genetics, University of Alberta, Edmonton, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Rika Maruyama

    1. Department of Medical Genetics, University of Alberta, Edmonton, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2176)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Basics and Introduction

    1. Front Matter

      Pages 1-1
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    2. Invention and Early History of Gapmers

      • Kenji Rowel Q. Lim, Toshifumi Yokota
      Pages 3-19

    3. Development and Clinical Applications of Antisense Oligonucleotide Gapmers

      • Leanna Chan, Toshifumi Yokota
      Pages 21-47

    4. Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers

      • Rika Maruyama, Toshifumi Yokota
      Pages 49-56

    5. Development of Antisense Oligonucleotide Gapmers for the Treatment of Huntington’s Disease

      • Tejal Aslesh, Toshifumi Yokota
      Pages 57-67

    6. Development of Antisense Oligonucleotide Gapmers for the Treatment of Dyslipidemia and Lipodystrophy

      • Tejal Aslesh, Toshifumi Yokota
      Pages 69-85

    7. Inotersen for the Treatment of Hereditary Transthyretin Amyloidosis

      • Maria Mahfouz, Rika Maruyama, Toshifumi Yokota
      Pages 87-98

    8. Degradation of Toxic RNA in Myotonic Dystrophy Using Gapmer Antisense Oligonucleotides

      • Quynh Nguyen, Toshifumi Yokota
      Pages 99-109

  3. Design of Gapmers and Strategies

    1. Front Matter

      Pages 111-111
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    2. DNA–RNA Heteroduplex Oligonucleotide for Highly Efficient Gene Silencing

      • Rintaro Iwata Hara, Kotaro Yoshioka, Takanori Yokota
      Pages 113-119

    3. Tips for Successful lncRNA Knockdown Using Gapmers

      • Kim A. Lennox, Mark A. Behlke
      Pages 121-140

    4. Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility

      • Fumito Wada, Shin-ichiro Hori, Satoshi Obika, Tsuyoshi Yamamoto
      Pages 141-154

    5. Evaluating the Knockdown Activity of MALAT1 ENA Gapmers In Vitro

      • Shinzo Iwashita, Takao Shoji, Makoto Koizumi
      Pages 155-161

    6. Albumin-Binding Fatty Acid–Modified Gapmer Antisense Oligonucleotides for Modulation of Pharmacokinetics

      • Yunpeng Cai, Chenguang Lou, Jesper Wengel, Kenneth A. Howard
      Pages 163-174

  4. In Vitro/In Vivo Evaluation of Gapmers

    1. Front Matter

      Pages 175-175
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    2. The Use of Gapmers for In Vivo Suppression of Hepatic mRNA Targets

      • David S. Greenberg, Yonat Tzur, Hermona Soreq
      Pages 177-184

    3. Development of LNA Gapmer Oligonucleotide-Based Therapy for ALS/FTD Caused by the C9orf72 Repeat Expansion

      • Chaitra Sathyaprakash, Raquel Manzano, Miguel A. Varela, Yasumasa Hashimoto, Matthew J. A. Wood, Kevin Talbot et al.
      Pages 185-208

    4. Targeted Gene Silencing in Malignant Hematolymphoid Cells Using GapmeR

      • Atish Kizhakeyil, Mobashar Hussain Urf Turabe Fazil, Navin Kumar Verma
      Pages 209-219

    5. Gapmer Antisense Oligonucleotides to Selectively Suppress the Mutant Allele in COL6A Genes in Dominant Ullrich Congenital Muscular Dystrophy

      • Sara Aguti, Elena Marrosu, Francesco Muntoni, Haiyan Zhou
      Pages 221-230
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Keywords

About this book

This volume presents a comprehensive collection of detailed state-of-the-art protocols for gapmer-mediated RNA knockdown from leaders in the field. Chapters detail a historical and contemporary perspective of RNase H-inducing antisense oligonucleotides called gapmers and gapmer-mediated RNA knockdown for basic research and therapies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Gapmers: Methods and Protocols aims to provide diverse applications of gapmers along with protocols that will assist readers in moving the frontier.

Editors and Affiliations

  • Department of Medical Genetics, University of Alberta, Edmonton, Canada

    Toshifumi Yokota, Rika Maruyama

Bibliographic Information

  • Book Title: Gapmers

  • Book Subtitle: Methods and Protocols

  • Editors: Toshifumi Yokota, Rika Maruyama

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0771-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0770-1Published: 01 September 2020

  • Softcover ISBN: 978-1-0716-0773-2Published: 01 September 2021

  • eBook ISBN: 978-1-0716-0771-8Published: 31 August 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 247

  • Number of Illustrations: 10 b/w illustrations, 29 illustrations in colour

  • Topics: Human Genetics

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