Motifs


"Directed and ordered arrays of non-WC base pairs forming distinctive foldings of the phospodiester backbones of the interacting RNA strands."
Leontis and Westhof (Curr. Op. Str. Bio. 2003, 13:300-308)

The Leontis and Westhof definition of RNA Motifs refers to structural 3D motifs.

The Brenner group used to maintain the SCOR database where they proposed three grouping schemes for motifs, these are:

  • (STRUCTURE) Structural Motifs.
  • (FUNCTION) Function Based Motifs.
  • (INTERACTIONS) Tertiary Structure Interaction Motifs.

  • The main problem of SCOR, according to Westhof, is that there is no information regarding non-WC interactions for structural motifs, therefore ALL non-WC are represented by just one single dashed line, there is no differentiation. Holbrook 2005 classified structural motifs like:
  • Helices
  • Hairpin loops
  • Internal loops
  • Junction loops/multiloops
  • Binding motifs
  • Metal binding
  • Natural and selected aptamers
  • Tertiary interactions

  • One has to be careful when talking about RNA motifs since this can be very different concepts if one is thinking at the secondary structure level, or at the 3D level, for example Westhof 2006 states

    "At the level of secondary structure, the RNA double helix is the fundamental motif. Once helices are specified, other motifs become apparent, which, at the level of secondary structure, are classified as hairpin (or terminal) loops, internal loops (including bulges), and multihelix or junction loops. However, this description of RNA structure is incomplete, as it takes no account of non-WC"

    References:

  • P. B. Moore 1999. Structural Motifs in RNA. Annual Reviews in Biochemistry. 68:287-300 [EBSCO]
  • Neocles B. Leontis and Eric Westhof 2003. Analysis of RNA motifs. Current Opinion in Structural Biology. 13:300-308 [Current Opinion]
  • Donna K. Hendrix and Steven E. Brenner and Stephen R. Holbrook 2005. RNA Structural Motifs: Building Blocks of a Modular Biomolecule. Quarterly Reviews of Biophysics. 38:221-243 [Quarterly Reviews of Biophysics]