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RNA Structures

This study explores various aspects of RNA conformations, focusing on the A-form ribose ring structure and conformation angles in RNA oligonucleotides. It discusses the differences between crystal and solution states, including the role of internal loops and the involvement of water in mispairing. Key features such as stacking, hydrogen bonding, and their relationship to secondary and tertiary structures are examined. The discussion also highlights unique bases in tRNA and ribozymes, alongside references to crucial literature that enriches understanding of RNA's structural complexities and catalytic activity.

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RNA Structures

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  1. RNA Structures September 19, 21 2006

  2. Ribose ring

  3. A form conformation

  4. RNA conformation angles

  5. UpA

  6. UpA

  7. UpA

  8. UpA

  9. GpC

  10. RNA oligonucleotide A form

  11. Crystal vs solution conformation • Internal loopin xtal • Full loop in solution

  12. Schematic of internal loop

  13. Water involved in mispair

  14. tRNA

  15. L shaped

  16. H bonds between distant regions

  17. Many unusual bases

  18. Even more unusual bases

  19. Relationship between secondary and tertiary structure

  20. Conserved and semi conserved bases

  21. Different classes of tRNA

  22. Different types of hydrogen bonds between conserved bases

  23. Stacking is a key feature

  24. Ribozymes • RNA with catalytic activity

  25. Stacking

  26. Tertiary hydrogen bonds

  27. P4-P6

  28. Systematize unusual features: RNA ontology

  29. References “The Crystal Structure of an All-RNA Hammerhead Ribozyme: A Proposed Mechanism for RNA Catalytic Cleavage.” Cell, Vol. 81, June 30, 1995, pp. 992-993, 995. “Crystal Structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs”, Nature, Vol. 353, October 10, 1991, pp. 579, 581. Leontis and Westhof. RNA, Vol. 7, 2001, pp. 499-512 Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, pp. 140-142, 148. Neidle, Stephen, ed. Oxford Handbook of Nucleic Acid Structures. Oxford University Press, 1999, p. 610. Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, pp. 251, 332-333, 335.

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