| Abstract |
Recent discoveries have demonstrated that RNA serves many important
cellular functions that were previously
unknown. For example, it is RNA in the ribosome that catalyzes peptide
bond formation and RNA is important in
post-transcription gene regulation through RNAi. Given the recent
awareness that RNA serves many important,
previously unknown functions, there is interest in the discovery of novel
functional RNA sequences, called
non-coding RNA (ncRNA), in genomes. On the basis of predicted secondary
structure formation free energy change,
we have developed a sensitive and specific method for ncRNA discovery in
crudely aligned genomes.
For RNA to function, structures must be flexible. Conformational changes
have been shown to be important for
ribosome function and for RNA self-splicing. We have implemented the
nudged elastic band (NEB) methodology in the
AMBER molecular dynamics software package to determine low energy pathways
for conformational changes. NEB can be
used to quantitatively determine pathways of any timescale. We have
modeled the conformation change of a GG
non-canonical pair. Our results demonstrate the plasticity of RNA helices
and that NEB can be used to find
complex pathways for conformational changes.
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