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

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

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

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

RNA Constraints: RNA folding

Copyright restrictions may apply. Jossinet, F. et al. Bioinformatics : ; doi: /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)

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

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

RNA Element: Stem

RNA Element: Coaxially Stacked Helices

RNA Element: Cross-strand Helices

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

RNA Element: Kissing Loops

RNA Element: Backbone Zipper

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

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

RNA Motif: UNCG Tetraloop

RNA Motif: GNRA Tetraloop

RNA Motif: CUYG Tetraloop

U-turn

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

RNA Motif: K-turn

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

RNA Motif: Bulge-helix-bulge

RNA Motif: S-turn

SZILVIA SZEP et al. RNA 2003; 9: RNA Motif: Hook Turn

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

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

RNA Motif: A Platform

RNA Motif: Bulged G motif

RNA Motif: T-loop

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

RNA Motif: A minor motif

RNA Motif: GNRA Tetraloop & Receptor

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

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