RNA Recognition, Volume 623, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This updated volume covers a variety of topics, including The Preparation of cooperative RNA recognition complexes for crystallographic structural studies, Methods for thermal denaturation studies of fluorogenic aptamers, Dynamic combinatorial chemistry as a rapid, fragment-based approach to RNA-targeted compound discovery, Using a click chemistry assay to identify natural product ligands for pre-microRNAs, Lessons from exploration of chemical and structural small molecule:RNA space, Using ligand-observed NMR to study RNA-small molecule interactions, and much more.
1. Cover image - p. cover 2. Title page - p. cover 3. Table of Contents - p. cover 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface - p. xv 7. Chapter One: Preparation of cooperative RNA recognition complexes for crystallographic structural studies - p. xvii 8. Chapter Two: Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes - p. 22 9. Chapter Three: Identifying and validating small molecules interacting with RNA (SMIRNAs) - p. 43 10. Chapter Four: Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds - p. 66 11. Chapter Five: A click chemistry assay to identify natural product ligands for pre-microRNAs - p. 84 12. Chapter Six: Differentiation and classification of RNA motifs using small molecule-based pattern recognition - p. 99 13. Chapter Seven: Ligand-observed NMR techniques to probe RNA-small molecule interactions - p. 130 14. Chapter Eight: Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis - p. 149 15. Chapter Nine: Using Rosetta for RNA homology modeling - p. 175 16. Chapter Ten: Monitoring co-transcriptional folding of riboswitches through helicase unwinding - p. 207 17. Chapter Eleven: Strategies for understanding RNA recognition by X-ray crystallography and NMR methods - p. 227 18. Chapter Twelve: Sensitive detection of structural features and rearrangements in long, structured RNA molecules - p. 248 19. Chapter Thirteen: A fluorescent aminosugar to rapidly screen and study RNA binders - p. 289 20. Chapter Fourteen: The use of electrospray ionization mass spectrometry to monitor RNA-ligand interactions - p. 314 21. Chapter Fifteen: Design of RNA-targeting macrocyclic peptides - p. 337 22. Chapter Sixteen: Molecular recognition of HIV-1 RNAs with branched peptides - p. 372 23. Chapter Seventeen: Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids - p. 400 24. Chapter Eighteen: Evaluating riboswitch optimality - p. 416
RNA Recognition, Volume 623, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This updated volume covers a variety of topics, including The Preparation of cooperative RNA recognition complexes for crystallographic structural studies, Methods for thermal denaturation studies of fluorogenic aptamers, Dynamic combinatorial chemistry as a rapid, fragment-based approach to RNA-targeted compound discovery, Using a click chemistry assay to identify natural product ligands for pre-microRNAs, Lessons from exploration of chemical and structural small molecule:RNA space, Using ligand-observed NMR to study RNA-small molecule interactions, and much more.
1. Cover image - p. cover 2. Title page - p. cover 3. Table of Contents - p. cover 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface - p. xv 7. Chapter One: Preparation of cooperative RNA recognition complexes for crystallographic structural studies - p. xvii 8. Chapter Two: Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes - p. 22 9. Chapter Three: Identifying and validating small molecules interacting with RNA (SMIRNAs) - p. 43 10. Chapter Four: Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds - p. 66 11. Chapter Five: A click chemistry assay to identify natural product ligands for pre-microRNAs - p. 84 12. Chapter Six: Differentiation and classification of RNA motifs using small molecule-based pattern recognition - p. 99 13. Chapter Seven: Ligand-observed NMR techniques to probe RNA-small molecule interactions - p. 130 14. Chapter Eight: Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis - p. 149 15. Chapter Nine: Using Rosetta for RNA homology modeling - p. 175 16. Chapter Ten: Monitoring co-transcriptional folding of riboswitches through helicase unwinding - p. 207 17. Chapter Eleven: Strategies for understanding RNA recognition by X-ray crystallography and NMR methods - p. 227 18. Chapter Twelve: Sensitive detection of structural features and rearrangements in long, structured RNA molecules - p. 248 19. Chapter Thirteen: A fluorescent aminosugar to rapidly screen and study RNA binders - p. 289 20. Chapter Fourteen: The use of electrospray ionization mass spectrometry to monitor RNA-ligand interactions - p. 314 21. Chapter Fifteen: Design of RNA-targeting macrocyclic peptides - p. 337 22. Chapter Sixteen: Molecular recognition of HIV-1 RNAs with branched peptides - p. 372 23. Chapter Seventeen: Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids - p. 400 24. Chapter Eighteen: Evaluating riboswitch optimality - p. 416
