Theory and Application of a Novel RNA Folding Approach Based on Nucleotide Cyclic Motifs

Wednesday, October 31, 2007 - 11:00am - 11:30am
EE/CS 3-180
Francois Major (University of Montreal)
Joint work with Marc Parisien (Institute for Research in Immunology and Cancer,
Department of Computer Science,
University of Montreal).

We change the classical rationale underlying RNA structure prediction by
incorporating the contributions of the non-Watson-Crick base pairs. To do
so, we define a new first-order object for representing nucleotide
relationships in structured RNAs, which we call nucleotide cyclic motif
(NCM) (1). In comparison to the classical stacks of Watson‑Crick base pairs,
the properties that make NCMs appealing for structure determination are the
facts that: i) the same algorithm can be employed for predicting secondary,
tertiary, and 3-D structures; ii) the RNA structural motifs are either made
of one or more NCMs (2); iii) the NCMs embrace indistinctly both canonical
and non‑canonical base pairs; and, iv) the NCMs precisely designate how any
nucleotide in a sequence relates to the others. A structure generator and
scoring function has been developed: MC-Fold. We show how MC-Fold, combined
to MC-Sym (3), builds RNA 3-D structures from sequence data and, combined to
MC-Cons, clusters and aligns RNA family sequences. We show how
low-resolution data can be incorporated in the modeling to reach
conformational states that are difficult to access by sequence data alone.

1. Lemieux, S. and Major, F. (2006) Automated extraction and classification
of RNA tertiary structure cyclic motifs. Nucleic Acids Res., 34, 2340-2346.

2. St-Onge, K., Thibault, P., Hamel, S. and Major, F. (2007) Modeling RNA
tertiary structure motifs by graph-grammars. Nucleic Acids Res, 35,

3. Major, F. (2003) Building Three-Dimensional Ribonucleic Acid Structures.
IEEE Comp Science Eng 5:44-53.