1. Structure Mapping Working Group

2. RNA Secondary Structure Experimental Constraints: Enzymatic Cleavage –Paired nucleotides –Unpaired nucleotides FMN Cleavage –U’s in GU pairs Chemical Modification (in vitro or in vivo) –Nucleotides that are unpaired, at the ends of helices, or in or adjacent to GU pairs. SHAPE Data –Probes backbone flexibility Microarray Data –Explores accessibility

3. Constrained Structure and P BP Prediction: E. coli 5S rRNA

4. Color Annotation: E. coli 5S rRNA

5. Immediate Goals: Can we standardize methods to archive and transmit experimental constraints? Can we agree on best practices for implementing constraints for secondary structure prediction? Can we learn from each other to improve experimental and computational methods?

6. Long-Term Goal: Can we use low-resolution mapping and sequence data to identify motifs? –Can this improve tertiary structure prediction? –Can we write an NIH P01 to do a large scale mapping project to compare methods?

7. Key Players Rob Knight Neocles Leontis Francois Major? Kevin Weeks Doug Turner Harry Noller or chemical modification mapper David Mathews