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DNAzymes

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Gerhard Steger

    1. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

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  2. Hannah Rosenbach

    1. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

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  3. Ingrid Span

    1. Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

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  • 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 2439)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xvi
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  2. Systematic Evolution of Ligands by Exponential Enrichment (SELEX)

    1. Front Matter

      Pages 1-1
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    2. A Protocol for Gold Nanoparticle-Assisted Aptamer Selection for a Small Molecule Porphyrin to Develop DNAzyme

      • Wenjing Li, Yanwei Cao, Renjun Pei
      Pages 3-13

    3. Selection of Aptamer for N-Methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzyme

      • Luyan Yang, Yanwei Cao, Renjun Pei
      Pages 15-26

    4. PCR Methods for the Generation of Catalytic ssDNA

      • Deni Szokoli, Kristian K. Le Vay, Hannes Mutschler
      Pages 27-44

  3. Design: Kinetics, Performance, and Turnover

    1. Front Matter

      Pages 45-45
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    2. Design of a DNAzyme

      • Gerhard Steger, Julian Victor
      Pages 47-63

    3. Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes

      • Hannah Rosenbach, Gerhard Steger
      Pages 65-77

    4. Stability and Activity of the 10–23 DNAzyme Under Molecular Crowding Conditions

      • Nina Kirchgässler, Hannah Rosenbach, Ingrid Span
      Pages 79-89

    5. Quantifying the Number and Affinity of Mn2+-Binding Sites with EPR Spectroscopy

      • Christine Wuebben, Olav Schiemann
      Pages 91-101

  4. Biophysical Characterization of DNAzymes

    1. Front Matter

      Pages 103-103
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    2. Obtaining Crystals of Nucleic Acids in Complex with the Protein U1A Using the Soaking Method

      • Hannah Rosenbach, Ingrid Span
      Pages 105-115

    3. Crystallization and Structural Determination of 8–17 DNAzyme

      • Hehua Liu, Song Mao, Jia Sheng, Jianhua Gan
      Pages 117-130

    4. Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and Function

      • Jan Borggräfe, Manuel Etzkorn
      Pages 131-151

    5. Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System

      • Christoph G. W. Gertzen, Holger Gohlke
      Pages 153-170

  5. Further Biophysical Methods

    1. Front Matter

      Pages 171-171
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    2. Single-Molecule Kinetic Studies of Nucleic Acids by Förster Resonance Energy Transfer

      • Mélodie C. A. S. Hadzic, Roland K. O. Sigel, Richard Börner
      Pages 173-190

    3. Chemical Dual End-Labeling of Large Ribozymes

      • Esra Ahunbay, Fabio D. Steffen, Susann Zelger-Paulus, Roland K. O. Sigel
      Pages 191-204

    4. Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation

      • Maria Francesca Vicino, Christine Wuebben, Mark Kerzhner, Michael Famulok, Olav Schiemann
      Pages 205-221

    5. Preparation of Site-Specifically Spin-Labeled RNA by in Vitro Transcription Using an Expanded Genetic Alphabet

      • Lisa Bornewasser, Stephanie Kath-Schorr
      Pages 223-240
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Keywords

About this book

This volume explores a collection of different protocols for the analysis and characterization of DNAzymes and their functions. The topics covered in this book range from bioinformatics and molecular dynamics simulations for the study or modification of nucleic acids to the descriptions of spectroscopic, fluorescence-based, or crystallographic methods to understand the structure and function of DNAzymes. 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.

Cutting-edge and comprehensive, DNAzymes: Methods and Protocols is a valuable resource for scientists and researchers interested in learning more about this evolving field. 


Editors and Affiliations

  • Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

    Gerhard Steger, Hannah Rosenbach, Ingrid Span

Bibliographic Information

  • Book Title: DNAzymes

  • Book Subtitle: Methods and Protocols

  • Editors: Gerhard Steger, Hannah Rosenbach, Ingrid Span

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2047-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2046-5Published: 01 March 2022

  • Softcover ISBN: 978-1-0716-2049-6Published: 02 March 2022

  • eBook ISBN: 978-1-0716-2047-2Published: 28 February 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 312

  • Number of Illustrations: 18 b/w illustrations, 77 illustrations in colour

  • Topics: Enzymology, Genetics and Genomics

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