Regensburg 2007 – scientific programme

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BP: Fachverband Biologische Physik

BP 9: Regulation and Signaling

BP 9.10: Talk

Tuesday, March 27, 2007, 12:30–12:45, H43

Detection of functional RNA in genomic sequences — •Bernd Burghardt and Alexander Hartmann — Institut für Theoretische Physik, Universität Göttingen

Some ten years ago it was believed that RNA mainly acts by transferring genetic information, i.e. essentially its primary structure is relevant. However, many RNAs provide functionality by its secondary and tertiary structure. Such non-coding RNA (ncRNA) is coded in genomic DNA sequences and includes well known types, e.g. tRNA and rRNA as well as recently discovered ones, e.g. miRNA. An important issue is, how to detect regions in the DNA which code for such functional RNAs, i.e. to distinguish it from gene-coding and other parts.

We present here a efficient numerical method to detect such functional RNAs in long RNA (or DNA) sequences. The method is based on the ground-state calculations of RNA secondary structures for all subsequences up to a certain length. By analysing the average ground-state energy one gets strong evidence where such such functional RNA fragments are embedded.