RNA 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.
Brenner group mantains the SCOR database
where they propose 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]