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電子ブック

EB
Daniel Herschlag
出版情報: Elsevier ScienceDirect Books , Elsevier Science & Technology, 2009
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目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Chemical and Functional Probing of RNA Structure, Interactions, and Folding / Section I:
Nucleotide Analog Interference Mapping / Ian T. Suydam ; Scott A. Strobel1:
Introduction
Materials and Reagents / 2:
Methods / 3:
Properties of Analogs / 4:
Nucleotide Analog Interference Suppression / 5:
Conclusions / 6:
References
Hydroxyl-Radical Footprinting to Probe Equilibrium Changes in RNA Tertiary Structure / Inna Shcherbakova ; Somdeb Mitra
Sample Preparation
Equilibrium òOH Footprinting Based on Peroxidative Fenton Chemistry
Equilibrium òOH Footprinting Based on Oxidative Fenton Chemistry
Cleavage Product Separation
Quantitation of the Changes in the Reactivity and Data Analysis
Acknowledgments / 7:
Rapid Quantification and Analysis of Kinetic òOH Radical Footprinting Data Using SAFA / Katrina Simmons ; Joshua S. Martin ; Alain Laederach
Using SAFA
Data Normalization
Data Visualization
Conclusion
Acknowledgment
High-Throughput SHAPE and Hydroxyl Radical Analysis of RNA Structure and Ribonucleoprotein Assembly / Jennifer L. McGinnis ; Caia D. S. Duncan ; Kevin M. Weeks
Theory
Practice
Examples and Interpretation
Perspectives and Conclusion
Metal Ion-Based RNA Cleavage as a Structural Probe / Marcello Forconi ; Daniel Herschlag
Mechanisms of Metal Ion-Based Cleavage of Nucleic Acids
Metal Ion-Based Cleavage of RNA as a Structural Probe
Protocols
2'-Amino-Modified Ribonucleotides as Probes for Local Interactions Within RNA / James L. Hougland ; Joseph A. Piccirilli
2'-Amino-2'-Deoxynucleotide Synthesis and Incorporation
2'-Amino-2'-Deoxynucleotides as Sites for Covalent Modification
General Strategy for Investigating 2'-Hydroxyl Interactions Using 2'-Deoxy and 2'-Aminonucleotides
Studies of RNA Catalysis Using 2'-Amino-2'-Deoxynucleotides
Using 2'-Aminonucleotides to Investigate RNA Structure and Function: Case Studies
RNA Crosslinking Methods / Michael E. Harris ; Eric L Christian
Synthesis of Modified RNA Crosslinking Substrates
Generation of Crosslinked RNAs
Mapping of Crosslinked Nucleotides
Assessing the Validity of Crosslinking Data
Chemical Probing of RNA and RNA/Protein Complexes / Zhili Xu ; Gloria M. Culver8:
Materials
Handling of the Chemicals
Optimization of the Chemical Probing Reactions
Procedure of Chemical Probing
RNA Extraction
Normalization of the RNA Sample
Primer Extension Analysis
Data Evaluation / 9:
Summary / 10:
RNA Folding During Transcription: Protocols and Studies / Terrence N. Wong ; Tao Pan
Protocol 1: Determination of Transcriptional Pause Sites
Protocol 2: Structural Mapping of Paused Complexes
Protocol 3: Cotranscriptional RNA Folding as Measured via Oligohybridization
Protocol 4: Cotranscriptional RNA Folding Measured via P RNA Catalytic Activity
Protocol 5: The Folding of Self-Cleaving RNAs During Transcription
Additional Methodologies
Cotranscriptional Folding Studies from our Laboratory
Catalytic Activity as a Probe of Native RNA Folding / Yaqi Wan ; David Mitchell III ; Rick Russell
Preliminary Measurements of Catalytic Reaction
Following RNA Folding by Continuous Activity Assay
Following RNA Folding by Discontinuous Activity Assay
Other Applications of Catalytic Activity as a Probe of Folding
Probing RNA Structure Within Living Cells / Andreas Liebeg ; Christina Waldsich11:
Experimental Procedure
Application
Limitations
Structural Analysis of RNA in Living Cells by In Vivo Synchrotron X-Ray Footprinting / Tadepalli Adilakshmi ; Sarah F. C. Soper ; Sarah A. Woodson12:
Beamline Setup for In Vivo Footprinting
Preparation of Samples
Exposure of Cells to X-Ray Beam
Isolation of Total RNA from Irradiated Cells
Primer Extension
Analysis of X-Ray Footprinting Experiments
Results on E. coli RNAs
Future of Footprinting
Determination of Intracellular RNA Folding Rates Using Self-Cleaving RNAs / Peter Y. Watson ; Martha J. Fedor13:
Using RNA Turnover Rates as a "Clock" for Measuring RNA Assembly Kinetics
Applications
Identifying Metal Ion Interactions in RNA / Section II:
Separation of RNA Phosphorothioate Oligonucleotides by HPLC / John K. Frederiksen14:
Introduction: Phosphorothioate Oligonucleotides and the Need for Separation
HPLC Separation of Phosphorothioate Diastereomers
Materials and Methods
Examples of Phosphorothioate Oligonucleotide Separations
Use of Phosphorothioates to Identify Sites of Metal-Ion Binding in RNA / 15:
Use of Phosphorothioate-Containing Ribozymes to Identify Sites of Metal-Ion Binding
EPR Methods to Study Specific Metal-Ion Binding Sites in RNA / Laura Hunsicker-Wang ; Matthew Vogt ; Victoria J. DeRose16:
ENDOR Spectroscopy to Identify Metal Ligands
ESEEM Spectroscopy
RNA Thermodynamics / Section III:
Optical Melting Measurements of Nucleic Acid Thermodynamics / Susan J. Schroeder ; Douglas H. Turner17:
Instrumentation
Calibrations
Brief Theory of Optical Melting Experiments
Two-State Assumption
Experimental Design
Data Interpretation
Error Analysis
Analyzing RNA and DNA Folding Using Temperature Gradient Gel Electrophoresis (TGGE) with Application to In Vitro Selections / Durga M. Chadalavada ; Philip C. Bevilacqua18:
Temperature Gradient Gel Electrophoresis
Experimental Design and Application of TGGE to RNA and DNA
Studying RNA-DNA and RNA-Protein Interactions by Isothermal Titration Calorimetry / Andrew L. Feig19:
Required Materials
Sample Considerations and Preparation
Cleaning the Sample Cell and Titration Syringe
Collecting Titration Data
Data Processing and Analysis
Special Considerations
Author Index
Subject Index
Contributors
Preface
Volumes in Series
2.

電子ブック

EB
Daniel Herschlag
出版情報: Elsevier ScienceDirect Books , Elsevier Science, 2009
所蔵情報: loading…
目次情報: 続きを見る
A Chemical and Enzymatic Footprinting of RNA Structure
Equilibrium hydroxyl radical footprinting / 1:
Bench-top time-resolved hydroxyl radical footprinting / 2:
Analysis of hydroxyl radical footprinting gels 'SAFA' / 3:
Kinetic modeling of reaction pathways from hydroxyl radical data / 4:
"BABE" mapping of protein/RNA position / 5:
Multiplexed..(MOHCA) / 6:
SHAPE / 7:
"In-line Probing" / 8:
NAIM / 9:
Other NAIM / 10:
Purification of T7 RNA Polymerase / 11:
Purification of T4 RNA ligase / 12:
In vitro transcription of RNA / 13:
32P-labeling of RNA B. BIOPHYSICAL TECHNIQUES / 14:
Fluorescent labeling of RNAs / 15:
Assembly of complex RNAs by 'Moore-Sharp' ligations / 16:
General considerations for smFRET with RNA samples / 17:
Ion counting / 19:
ASAXS / 20:
NLPB / 21:
smNLPB / 22:
Gel mobility mapping of junction structure / 23:
Temperature gradient gels / 24:
Melting studies / 25:
Co-transcriptional folding studies / 26:
Activity assays to follow folding processes / 27:
2AP fluorescence / 28:
EPR measurements of RNA dynamics / 29:
FPA measurements of RNA dynamics / 30:
EPR methods to study specific metal ion binding sites in RNA / 32:
Thermodynamic study of site-specific metal ion binding sites in RNA / 33:
Oligonucleotide hybridization studies of RNA folding pathways / 34:
Native gel shifts / 35:
Tiling arrays to assess RNA structure / 36:
EPR distance measurements in RNA / 37:
RNA folding in vivo / 38:
Cleavage of RNAs with 'restriction DNAzymes' / 39:
A Chemical and Enzymatic Footprinting of RNA Structure
Equilibrium hydroxyl radical footprinting / 1:
Bench-top time-resolved hydroxyl radical footprinting / 2:
3.

電子ブック

EB
Daniel; Herschlag, Daniel Herschlag, Daniel Herschlag
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Chemical and Functional Probing of RNA Structure, Interactions, and Folding / Section I:
Nucleotide Analog Interference Mapping / Ian T. Suydam ; Scott A. Strobel1:
Introduction
Materials and Reagents / 2:
Methods / 3:
Properties of Analogs / 4:
Nucleotide Analog Interference Suppression / 5:
Conclusions / 6:
References
Hydroxyl-Radical Footprinting to Probe Equilibrium Changes in RNA Tertiary Structure / Inna Shcherbakova ; Somdeb Mitra
Sample Preparation
Equilibrium òOH Footprinting Based on Peroxidative Fenton Chemistry
Equilibrium òOH Footprinting Based on Oxidative Fenton Chemistry
Cleavage Product Separation
Quantitation of the Changes in the Reactivity and Data Analysis
Acknowledgments / 7:
Rapid Quantification and Analysis of Kinetic òOH Radical Footprinting Data Using SAFA / Katrina Simmons ; Joshua S. Martin ; Alain Laederach
Using SAFA
Data Normalization
Data Visualization
Conclusion
Acknowledgment
High-Throughput SHAPE and Hydroxyl Radical Analysis of RNA Structure and Ribonucleoprotein Assembly / Jennifer L. McGinnis ; Caia D. S. Duncan ; Kevin M. Weeks
Theory
Practice
Examples and Interpretation
Perspectives and Conclusion
Metal Ion-Based RNA Cleavage as a Structural Probe / Marcello Forconi ; Daniel Herschlag
Mechanisms of Metal Ion-Based Cleavage of Nucleic Acids
Metal Ion-Based Cleavage of RNA as a Structural Probe
Protocols
2'-Amino-Modified Ribonucleotides as Probes for Local Interactions Within RNA / James L. Hougland ; Joseph A. Piccirilli
2'-Amino-2'-Deoxynucleotide Synthesis and Incorporation
2'-Amino-2'-Deoxynucleotides as Sites for Covalent Modification
General Strategy for Investigating 2'-Hydroxyl Interactions Using 2'-Deoxy and 2'-Aminonucleotides
Studies of RNA Catalysis Using 2'-Amino-2'-Deoxynucleotides
Using 2'-Aminonucleotides to Investigate RNA Structure and Function: Case Studies
RNA Crosslinking Methods / Michael E. Harris ; Eric L Christian
Synthesis of Modified RNA Crosslinking Substrates
Generation of Crosslinked RNAs
Mapping of Crosslinked Nucleotides
Assessing the Validity of Crosslinking Data
Chemical Probing of RNA and RNA/Protein Complexes / Zhili Xu ; Gloria M. Culver8:
Materials
Handling of the Chemicals
Optimization of the Chemical Probing Reactions
Procedure of Chemical Probing
RNA Extraction
Normalization of the RNA Sample
Primer Extension Analysis
Data Evaluation / 9:
Summary / 10:
RNA Folding During Transcription: Protocols and Studies / Terrence N. Wong ; Tao Pan
Protocol 1: Determination of Transcriptional Pause Sites
Protocol 2: Structural Mapping of Paused Complexes
Protocol 3: Cotranscriptional RNA Folding as Measured via Oligohybridization
Protocol 4: Cotranscriptional RNA Folding Measured via P RNA Catalytic Activity
Protocol 5: The Folding of Self-Cleaving RNAs During Transcription
Additional Methodologies
Cotranscriptional Folding Studies from our Laboratory
Catalytic Activity as a Probe of Native RNA Folding / Yaqi Wan ; David Mitchell III ; Rick Russell
Preliminary Measurements of Catalytic Reaction
Following RNA Folding by Continuous Activity Assay
Following RNA Folding by Discontinuous Activity Assay
Other Applications of Catalytic Activity as a Probe of Folding
Probing RNA Structure Within Living Cells / Andreas Liebeg ; Christina Waldsich11:
Experimental Procedure
Application
Limitations
Structural Analysis of RNA in Living Cells by In Vivo Synchrotron X-Ray Footprinting / Tadepalli Adilakshmi ; Sarah F. C. Soper ; Sarah A. Woodson12:
Beamline Setup for In Vivo Footprinting
Preparation of Samples
Exposure of Cells to X-Ray Beam
Isolation of Total RNA from Irradiated Cells
Primer Extension
Analysis of X-Ray Footprinting Experiments
Results on E. coli RNAs
Future of Footprinting
Determination of Intracellular RNA Folding Rates Using Self-Cleaving RNAs / Peter Y. Watson ; Martha J. Fedor13:
Using RNA Turnover Rates as a "Clock" for Measuring RNA Assembly Kinetics
Applications
Identifying Metal Ion Interactions in RNA / Section II:
Separation of RNA Phosphorothioate Oligonucleotides by HPLC / John K. Frederiksen14:
Introduction: Phosphorothioate Oligonucleotides and the Need for Separation
HPLC Separation of Phosphorothioate Diastereomers
Materials and Methods
Examples of Phosphorothioate Oligonucleotide Separations
Use of Phosphorothioates to Identify Sites of Metal-Ion Binding in RNA / 15:
Use of Phosphorothioate-Containing Ribozymes to Identify Sites of Metal-Ion Binding
EPR Methods to Study Specific Metal-Ion Binding Sites in RNA / Laura Hunsicker-Wang ; Matthew Vogt ; Victoria J. DeRose16:
ENDOR Spectroscopy to Identify Metal Ligands
ESEEM Spectroscopy
RNA Thermodynamics / Section III:
Optical Melting Measurements of Nucleic Acid Thermodynamics / Susan J. Schroeder ; Douglas H. Turner17:
Instrumentation
Calibrations
Brief Theory of Optical Melting Experiments
Two-State Assumption
Experimental Design
Data Interpretation
Error Analysis
Analyzing RNA and DNA Folding Using Temperature Gradient Gel Electrophoresis (TGGE) with Application to In Vitro Selections / Durga M. Chadalavada ; Philip C. Bevilacqua18:
Temperature Gradient Gel Electrophoresis
Experimental Design and Application of TGGE to RNA and DNA
Studying RNA-DNA and RNA-Protein Interactions by Isothermal Titration Calorimetry / Andrew L. Feig19:
Required Materials
Sample Considerations and Preparation
Cleaning the Sample Cell and Titration Syringe
Collecting Titration Data
Data Processing and Analysis
Special Considerations
Author Index
Subject Index
Contributors
Preface
Volumes in Series
4.

電子ブック

EB
Herschlag, Daniel Herschlag
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
A Chemical and Enzymatic Footprinting of RNA Structure
Equilibrium hydroxyl radical footprinting / 1:
Bench-top time-resolved hydroxyl radical footprinting / 2:
Analysis of hydroxyl radical footprinting gels 'SAFA' / 3:
Kinetic modeling of reaction pathways from hydroxyl radical data / 4:
"BABE" mapping of protein/RNA position / 5:
Multiplexed..(MOHCA) / 6:
SHAPE / 7:
"In-line Probing" / 8:
NAIM / 9:
Other NAIM / 10:
Purification of T7 RNA Polymerase / 11:
Purification of T4 RNA ligase / 12:
In vitro transcription of RNA / 13:
32P-labeling of RNA B. BIOPHYSICAL TECHNIQUES / 14:
Fluorescent labeling of RNAs / 15:
Assembly of complex RNAs by 'Moore-Sharp' ligations / 16:
General considerations for smFRET with RNA samples / 17:
Ion counting / 19:
ASAXS / 20:
NLPB / 21:
smNLPB / 22:
Gel mobility mapping of junction structure / 23:
Temperature gradient gels / 24:
Melting studies / 25:
Co-transcriptional folding studies / 26:
Activity assays to follow folding processes / 27:
2AP fluorescence / 28:
EPR measurements of RNA dynamics / 29:
FPA measurements of RNA dynamics / 30:
EPR methods to study specific metal ion binding sites in RNA / 32:
Thermodynamic study of site-specific metal ion binding sites in RNA / 33:
Oligonucleotide hybridization studies of RNA folding pathways / 34:
Native gel shifts / 35:
Tiling arrays to assess RNA structure / 36:
EPR distance measurements in RNA / 37:
RNA folding in vivo / 38:
Cleavage of RNAs with 'restriction DNAzymes' / 39:
A Chemical and Enzymatic Footprinting of RNA Structure
Equilibrium hydroxyl radical footprinting / 1:
Bench-top time-resolved hydroxyl radical footprinting / 2:
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