Berlin 2005 – wissenschaftliches Programm

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DY: Dynamik und Statistische Physik

DY 21: Statistical Physics in Biological Systems

DY 21.3: Vortrag

Samstag, 5. März 2005, 09:00–09:15, TU H2032

Designability of RNA secondary structures — •Bernd Burghardt and Alexander K. Hartmann — Institut für Theoretische Physik, Universität Göttingen

Some RNA, e.g. ribozyme, provides by its secondary and tertiary structure enzymatic functionality. For a biologically relevant structure of an RNA sequence it is required that it is the most stable one, i.e. ground state, and that the ground state is unique, otherwise no definite functionality could be assigned to the sequence.

Given a RNA secondary structure the answer whether there is a RNA sequence which has this structure as its ground state structure or not, depends on the chosen energy model: for energy models with only pair contributions always such a sequence exits, while for energy models with stacking contributions there are structures that are not ground state of any RNA sequence. We numerically investigate whether this structures appear quite regularly in the space of all structures or are exceptional cases with an algorithm that exactly calculates the ground states in polynomial time. Because stacking contributions are always present in real RNA, this might have consequence for possible structures, and therefore functionality, of RNA structures.