Main description:

This book provides a collection of comprehensive, up-to-date, and broadly applicable guides to the research and development fields of oligonucleotide (ON) therapeutics. Covering topics from the study of antisense and anti-gene effects to oligonucleotides in the context of drug discovery and development, the volume explores a wide-ranging and useful spectrum of methods and protocols needed to take full advantage of therapeutic applications involving ONs. Written for the highly successful Methods in Molecular Biology series, 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 practical, Oligonucleotide-Based Therapies: Methods and Protocols aims to be a great aid in the laboratory as well as an ideal reference guide when designing antisense and anti-gene oligonucleotides for therapeutic applications.

Contents:

Part I: Reviews

1. Chemical Development of Therapeutic Oligonucleotides

Karin E. Lundin, Olof Gissberg, C.I. Edvard Smith, and Rula Zain

2. Tissue-Specific Delivery of Oligonucleotides

Xin Xia, Nicolette Pollock, Jiehua Zhou, and John Rossi

Part II: Protocols and Strategies

3. Designing siRNA and Evaluating Its Effect on RNA Targets Using qPCR and Western Blot

Linda Vidarsdottir, Oksana Goroshchuk, Iryna Kolosenko, and Caroline Palm-Apergi

4. Antisense Oligonucleotides for Splice Modulation: Assessing Splice Switching Efficacy

Cristina S.J. Rocha

5. Assessing Oligonucleotide Binding to Double-Strand DNA

Negin Mozafari and Tea Umek

6. Modelling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy

Lennart Nilsson and Alessandra Villa

7. Characterization of Peptide/Oligonucleotide Complexes Using Electron Microscopy, Dynamic Light Scattering, and Protease Resistance Assay

Kart Padari, Ly Porosk, Piret Arukuusk, and Margus Pooga

8. Click-Shielded and Targeted Lipopolyplexes

Philipp Michael Klein and Ernst Wagner

9. Attachment of Peptides to Oligonucleotides on Solid Support Using Copper(I)-Catalyzed Huisgen 1,3-Dipolar Cycloaddition

Malgorzata Honcharenko, Dmytro Honcharenko, and Roger Stromberg

10. Characterizing Oligonucleotide Uptake in Cultured Cells: A Case Study Using AS1411 Aptamer

Elsa M. Reyes-Reyes and Paula J. Bates

11. Measuring the Action of Oligonucleotide Therapeutics in the Lung at the Cell Type-Specific Level by Tissue Disruption and Cell Sorting (TDCS)

Helen Graves, Steven Evans, Michael Fauler, Manfred Frick, and Sterghios A. Moschos

12. Delivery of Antisense Oligonucleotides Mediated by a Hydrogel System: In Vitro and In Vivo Application in the Context of Spinal Cord Injury

Pedro M.D. Moreno, Teresa Rodrigues, Marilia Torrado, Isabel F. Amaral, and Ana P. Pego

13. Evaluation of Cell-Penetrating Peptide Delivery of Antisense Oligonucleotides for Therapeutic Efficacy in Spinal Muscular Atrophy

Suzan M. Hammond, Frank Abendroth, Michael J. Gait, and Matthew J.A. Wood

14. Injection and Infusion of Compounds to the Central Nervous System

Margherita Zamboni

15. In Vitro Assessment of the Hepatotoxicity Potential of Therapeutic Oligonucleotides

Sabine Sewing, Tanja Minz, and Franziska Boess

16. Identifying Suitable Target Regions and Analyzing Off-Target Effects

Lykke Pedersen, Peter H. Hagedorn, and Troels Koch

17. RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting Therapeutics

Louise Usher, Pantazis I. Theotokis, and Sterghios A. Moschos

18. Studying the Biotransformation of Phosphorothioate-Containing Oligonucleotide Drugs by LC-MS

Christophe Husser, Erich Koller, Andreas Brink, and Simone Schadt

19. ADME: Assessing Pharmacokinetic-Pharmacodynamic Parameters of Oligonucleotides

Rasmus Jansson-Loefmark*, Christine Ahlstroem, and Peter Gennemark