DNAzymes : methods and protocols
Author(s)
Bibliographic Information
DNAzymes : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2439）（Springer protocols）
Humana Press, c2022
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Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
Acknowledgement...Preface...Table of Contents...Contributing Authors...
Part I SELEX1. A Protocol for Gold Nanoparticle-Assisted Aptamer Selection for a Small Molecule Porphyrin to Develop DNAzymeWenjing Li, Yanwei Cao, and Renjun Pei
2. Selection of Aptamer for N-methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzymeLuyan Yang, Yanwei Cao, and Renjun Pei
3. PCR Methods for the Generation of Catalytic ssDNADeni 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 DNAzymeGerhard Steger and Julian Victor
5. Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymesHannah Rosenbach and Gerhard Steger
6. Stability and Activity of the 10-23 DNAzyme under Molecular Crowding ConditionsNina Kirchgassler, Hannah Rosenbach, and Ingrid Span
7. Quantifying the Number and Affinity of Mn2+-Binding Sites with EPR SpectroscopyChristine 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 MethodHannah Rosenbach and Ingrid Span
9. Crystallization and Structural Determination of 8-17 DNAzymeHehua Liu, Song Mao, Jia Sheng, and Jianhua Gan
10. Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and FunctionJan Borggrafe and Manuel Etzkorn
11. Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model SystemChristoph G.W. Gertzen and Holger Gohlke
Part IV Further Biophysical Methods
12. Single-Molecule Kinetic Studies of Nucleic Acids by Foerster Resonance Energy TransferMelodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Boerner
13. Chemical Dual End-Labeling of Large RibozymesEsra Ahunbay, Fabio D. Steffen, Susann Zelger-Paulus, and Roland K. O. Sigel
14. Spin Labeling of Long RNAs via Click Reaction and Enzymatic LigationMaria 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 AlphabetLisa Bornewasser and Stephanie Kath-Schorr
16. PELDOR Measurements on Nitroxide-Labelled OligonucleotidesTobias Hett and Olav Schiemann
Part V Use of DNAzymes
17. Sensing Metal Ions with Phosphorothioate-Modified DNAzymesPo-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 ChemistryJoanna Kosman
19. Generation of RNA with 2', 3'-cyclic Phosphates by Deoxyribozyme Cleavage in Frozen SolutionsKristian K. Le Vay and Hannes Mutschler
Subject Index List...
by "Nielsen BookData"