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The Wonderful World of RNA

The Wonderful World of RNA. protein. DNA. RNA. Complexity of RNA Folding. 1 strand 4 building blocks Basic structural element: double helix. RNA folds back and forms Non-Watson Crick base pairs base triples Loop–loop, -single strand, -helix, helix - helix interactions.

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The Wonderful World of RNA

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  1. The Wonderful World of RNA protein DNA RNA

  2. Complexity of RNA Folding • 1 strand • 4 building blocks • Basic structural element: double helix • RNA folds backand forms • Non-Watson Crick base pairs • base triples • Loop–loop, -single strand, -helix, • helix - helix interactions The shape of an RNA molecule determines its function

  3. G C A U RNA Base Pairs G U G A G A

  4. I. RNA tetraloops Abundant in Nature Fullfill many structural and functional roles 16S rRNA: Of all loops > 50% are tetraloops Most are UNCG or GNRA Tetrahymena ribozyme

  5. II. Cis-regulating elements of poliovirus Single stranded RNA genome 7440 nt

  6. Poliovirus 5’-UTR Poliovirus 5´-UTR cloverleaf structure Aim: To characterize the stem-loop D - 3CD interaction by using in vivo SELEX.

  7. G C N N N N In vivo production of virus mutants U G N N N N U-G N-N N-N A-U N-N N-N U-A U-A U-A G-C G-C G-C G-C G-C G-C In vivo selection of randomly generated mutants polio wild type sequence random pool of 48 = 65536 possible sequences 22 different selected sequences

  8. A A C A G A U G C G U G anti anti syn anti U G G A Structures of UNCG and GNRA loops differ Du et al., 2003 Heus and Pardi, 1991

  9. A C U A C A G G A A U G C G U A U G GCUA loop adopts a YNMG tetraloop configuration UACG loop GAAA loop GCUA loop

  10. II. RNA pseudoknots •Occur in virtually all classes of RNA • Role in biological processes: - replication initiation - translational control - ribosomal frameshifting - core formation in larger RNAs

  11. RNA pseudoknot formation

  12. Ribosomal frameshifting SRV-1 genome overlapping region

  13. NMR-derived structure of SRV-1 RNA pseudoknot

  14. Guanine Riboswitch G ON OFF Guanine absent Guanine present Guanine

  15. Structural Differences P2-P3 interactionin both the free formand complex P3 arm P2 arm Disordered base pairsin free aptamer Base pairs in freeform and complex Flexible 5-residue “lid” P1 arm

  16. Importance for riboswitching

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