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Dnazymes: Methods and Protocols
Hardcover
Series: Methods in Molecular Biology, Book 2439
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ISBN10: 1071620460
ISBN13: 9781071620465
Publisher: Humana Pr
Published: Mar 1 2022
Pages: 312
Weight: 1.55
Height: 0.88 Width: 7.10 Depth: 10.00
Language: English
ISBN13: 9781071620465
Publisher: Humana Pr
Published: Mar 1 2022
Pages: 312
Weight: 1.55
Height: 0.88 Width: 7.10 Depth: 10.00
Language: English
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
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 Kirchgässler, 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 Borggräfe 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 Förster Resonance Energy TransferMélodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Börner
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...
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 Kirchgässler, 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 Borggräfe 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 Förster Resonance Energy TransferMélodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Börner
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...
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