Module 7: Molecular Computing with RNA Sequences
RNA Structure, Ribosomal and Transfer RNA
- Secondary structures of RNA: RNA is single-stranded in its native state. It can hybridize intramolecularly
through hydrogen bonds between A and U residues and C and G residues resulting in stem and loop type of structures.
An excellent site for RNA secondary structure prediction is operated by Michael Zuker at Rensselaer Palytechnic Institute
(Mfold Server - DNA input and
Mfold Server - RNA input)
- Transfer RNA: (Figure of tRNA Bound to ATP) One can
search for tRNA genes in genomic DNA or RNA sequences by using the
- Ribosomal RNA: A compilation of ribosomal RNA's (rRNA) from both prokaryotic and eukaryotic organisms can
be found at the lsu rRNA Database (large
sub units) and the ssu rRNA Database
(small sub units). The Ribosomal Database
Project (RDP) provides ribosome related data services to the scientific community, including online data
analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. Also, 5S rRNA sequences can be
accessed from the 5S rRNA Database either through a
listing of prokaryotes and eukaryotes and/or based on a taxonomic classification.
- RNA Genie: This program
locates novel RNA genes based on the premise that all stable, functional RNAs share common structural elements and
that sequences corresponding to these elements would occur preferentially in RNA genes. It employs six structural
parameters unique to RNA genes such as the calculated free energy of intramolecular folding etc.