| 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 |
ＥＢ
