DNAzymes: Methods and Protocols

ISBN-13: 9781071620496 / Angielski / Miękka / 2022 / 312 str.

Gerhard Steger; Hannah Rosenbach; Ingrid Span

Opis

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. 

Spis treści

Acknowledgement...

Preface...

Table of Contents...

Contributing Authors...

Part I SELEX

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

Wenjing Li, Yanwei Cao, and Renjun Pei

2. Selection of Aptamer for N-methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzyme

Luyan Yang, Yanwei Cao, and Renjun Pei

3. PCR Methods for the Generation of Catalytic ssDNA

Deni Szokoli, Kristian K. Le Vay, and Hannes Mutschler

Part II Design – Kinetics/Performance/Turnover

4. Design of a DNAzyme: Prediction of mRNA Regions Accessible to a DNAzyme

Gerhard Steger and Julian Victor

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

Hannah Rosenbach and Gerhard Steger

6. Stability and Activity of the 10-23 DNAzyme under Molecular Crowding Conditions

Nina Kirchgässler, Hannah Rosenbach, and Ingrid Span

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

Christine Wuebben and Olav Schiemann

Part III Biophysical Characterization of DNAzymes

8. Obtaining Crystals of Nucleic Acids in Complex with the Protein U1A Using the Soaking Method

Hannah Rosenbach and Ingrid Span

9. Crystallization and Structural Determination of 8-17 DNAzyme

Hehua Liu, Song Mao, Jia Sheng, and Jianhua Gan

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

Jan Borggräfe and Manuel Etzkorn

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

Christoph G.W. Gertzen and Holger Gohlke

Part IV Further Biophysical Methods

12. Single-Molecule Kinetic Studies of Nucleic Acids by Förster Resonance Energy Transfer

Mélodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Börner

13. Chemical Dual End-Labeling of Large Ribozymes

Esra Ahunbay, Fabio D. Steffen, Susann Zelger-Paulus, and Roland K. O. Sigel

14. Spin Labeling of Long RNAs via Click Reaction and Enzymatic Ligation

Maria Francesca Vicino, Christine Wuebben, Mark Kerzhner, Michael Famulok, and Olav Schiemann

15. Preparation of Site-Specifically Spin-Labeled RNA by In Vitro Transcription using an Expanded Genetic Alphabet

Lisa Bornewasser and Stephanie Kath-Schorr

16. PELDOR Measurements on Nitroxide-Labelled Oligonucleotides

Tobias Hett and Olav Schiemann

Part V Use of DNAzymes

17. Sensing Metal Ions with Phosphorothioate-Modified DNAzymes

Po-Jung Jimmy Huang and Juewen Liu

18. Enhancement of Activity for Peroxidase-Mimicking DNAzyme by Covalent Attachment of Hemin to G-quadruplex-Forming Oligonucleotide Using Click Chemistry

Joanna Kosman

19. Generation of RNA with 2’, 3’-cyclic Phosphates by Deoxyribozyme Cleavage in Frozen Solutions

Kristian K. Le Vay and Hannes Mutschler

Subject Index List...