1. RNA Structure 1.RNA = DNA 2.Elements & Motifs : RNA :: Helices : DNA 3. Sequence Dependence ElementNo MotifYes /

2. RNA: Methods & History Methods X-ray diffraction Fiber Crystal NMR Chemical probing Mutation Modeling (constraints) History A-helix Ricin-Sarcin loop tRNA Self-splicing intron ribosomes

3. RNA: Constraints Electron density NMR nuclear interactions Chemical reactivities Evolutionary covariation Stability prediction

4. RNA Constraints: Covariation ACGTAATT GCGTAACA ACGTAATC ACGTAATG GCGTAGCG GCGTAGCA ACGTAATT GCGTAACA ACGTAATC ACGTAATG GCGTAGCG GCGTAGCA

5. RNA Constraints: RNA folding

6. Copyright restrictions may apply. Jossinet, F. et al. Bioinformatics 2005 21:3320-3321; doi:10.1093/bioinformatics/bti504 An S2S screenshot displaying the S2SViewer core tool (on the left), Rnalign (middle low), Rna3DViewer using PyMOL (middle up) and Rna2DViewer (on the right)

7. RNA Elements are recognized, commonly occurring features of RNA 3-D structure that are not dictated by the sequence. are principally assembled by Watson-Crick base pairing and stacking. A-helix Stems Coaxially stacked helices Cross-strand helices Pseudoknots Kissing loops Backbone zippers

8. RNA Element: A-Helix Figure 4.01a: A-DNA Protein Data Bank ID: 213D. Ramakrishnan, B., and Sundaralingam, M., Biophys. J. 69 (1995): 553-558 (top).

9. RNA Element: Stem

10. RNA Element: Coaxially Stacked Helices

11. RNA Element: Cross-strand Helices

12. RNA Element: Pseudoknot Image from Staple et al. Hepatitis Delta Virus (Image from Ke et al.).

13. RNA Element: Kissing Loops

14. RNA Element: Backbone Zipper

15. RNA Motifs are recognized, commonly occurring features of RNA 3-D structure that depend, in part, on the nucleotide sequence. often involve non-Watson-Crick pairings and higher order base interactions. Tetraloops Turns Interstrand structures Distant interactions

16. RNA Motifs: Tetraloops UNCG GNRA CUYG U-turn (YUNR)

17. RNA Motif: UNCG Tetraloop

18. RNA Motif: GNRA Tetraloop

19. RNA Motif: CUYG Tetraloop

20. U-turn

21. RNA Motifs: Turns K-turn Bulge-helix-bulge S-turn Hook turn

22. RNA Motif: K-turn

24. TERRY A. GOODY et al. RNA 2004; 10: 254-264 FIGURE 2. Anomalous electrophoretic migration of K-turn RNA is dependent on the presence of magnesium ions

25. RNA Motif: Bulge-helix-bulge

26. RNA Motif: S-turn

27. SZILVIA SZEP et al. RNA 2003; 9: 44-51 RNA Motif: Hook Turn

28. SZILVIA SZEP et al. RNA 2003; 9: 44-51 FIGURE 5. Stereodiagrams of some hook-turns found in rRNAs

29. RNA Motifs: Cross-strand Structures A-platforms bulged G T-loop

30. RNA Motif: A Platform

31. RNA Motif: Bulged G motif

32. RNA Motif: T-loop

33. RNA Motifs: Distant Interactions A-minor Receptor--GNRA Tetraloop

34. RNA Motif: A minor motif

35. RNA Motif: GNRA Tetraloop & Receptor

36. RNA Structure: Classification Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B., 2008. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. Journal of mathematical biology 56, 215- 52.

37. RNA Structure 1.RNA = DNA 2.Elements & Motifs : RNA :: Helices : DNA 3. Sequence Dependence ElementNo MotifYes / FUNCTION: next