| Speaker | Caroline Thurner |
| Title | Konservierte und Konsensus RNA Strukturen |
The function of a biomolecule is closely related to its structure, thus even in very different species, molecules with the same function exhibit very similar structure. For RNA molecules secondary structures are a useful coarse graining of the spatial structure, since they cover most of the free energy of folding, they are conserved during evolution and have been used successfully to interpret RNA function. Moreover they are computationally easy to handle, because only discrete base pair patterns (no coordinates) are considered.
We combined phylogenetic and thermodynamic information to search for evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This family consists of the three genera Flavivirus, Pestivirus, Hepacivirus, and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. The main findings of our survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C, as it has been proposed previously for the members of the genus Flaviviruses, a surprisingly large number of conserved RNA motifs in the coding regions, and a lower level of detailed structural conservation of the motifs in the Internal Ribosomal Entry Sites and 3' untranslated regions than reported in the literature.
Pseudoknots are normally excluded from secondary structure by definition, yet they are occasionally functionally important. Therefore, in the second part of this thesis the secondary structure detection algorithm was extended to allow for prediction of some restricted kinds of pseudoknots. The algorithm is tested on three kinds of RNAs which are known to contain pseudoknots. These are Signal recognition particle RNA, ribonuclease P RNA and tmRNA.