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.
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Table of Contents
1. Preparation of cooperative RNA recognition complexes for crystallographic structural studies Chen Qiu, Aaron C. Goldstrohm and Traci M. Tanaka Hall 2. Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes Lauren M. Aufdembrink, Tanner G. Hoog, Matthew R. Pawlak, Benjamin F. Bachan, Joseph M. Heili and Aaron E. Engelhart 3. Identifying and validating small molecules interacting with RNA (SMIRNAs) Matthew D. Disney, Sai Pradeep Velagapudi, Yue Li, Matthew G. Costales and Jessica L. Childs-Disney 4. Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds John D. McAnany and Benjamin L. Miller 5. A click chemistry assay to identify natural product ligands for pre-microRNAs Amanda L. Garner, Daniel A. Lorenz and Erin E. Gallagher 6. Differentiation and classification of RNA motifs using small molecule-based pattern recognition Giacomo Padroni, Christopher S. Eubanks and Amanda E. Hargrove 7. Ligand-observed NMR techniques to probe RNA-small molecule interactions David R. Calabrese, Colleen M. Connelly and John S. Schneekloth Jr. 8. Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis Yufeng Liang, Jie Mao and Dennis Bong 9. Using Rosetta for RNA homology modeling Andrew Watkins, Ramya Rangan and Rhiju Das 10. Monitoring co-transcriptional folding of riboswitches through helicase unwinding Christopher P. Jones, Subrata Panja, Sarah A. Woodson and Adrian R. Ferr�-D'Amar� 11. Strategies for understanding RNA recognition by X-ray and NMR methods Aiai Sun, Kaiyi Huang, Luqian Zheng and Aiming Ren 12. Sensitive detection of structural features and rearrangements in long, structured RNA molecules Rebecca L. Adams, Nicholas C. Huston, Rafael C.A. Tavares and Anna M. Pyle 13. A fluorescent aminosugar to rapidly screen and study RNA binders Nihar Ranjan and Dev P. Arya 14. The use of electrospray ionization mass spectrometry to monitor RNA-ligand interactions Danielle N. Dremann and Christine S. Chow 15. Design of RNA-targeting macrocyclic peptides Matthew J. Walker and Gabriele Varani 16. Molecular recognition of HIV-1 RNAs with branched peptides Ashley N. Peralta, Yumin Dai, Chringma Sherpa, Stuart F.J. Le Grice and Webster L. Santos 17. Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids Dziyana Hnedzko and Eriks Rozners 18. Evaluating riboswitch optimality Hannah Wayment-Steele, Michelle Wu, Michael Gotrik and Rhiju Das
