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Figure 2 | Algorithms for Molecular Biology

Figure 2

From: Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

Figure 2

Relation between graph-distance distribution and smFRET data. (A) The graph-distance distribution of a Diels-Alderase (DAse) ribozyme at temperature 37°C. Structures (a), (b) and (c) are the top three secondary structures considering their free energy: the minimum free energy structure is shown in (a), (c) is the experimentally determined secondary structure, which is ranked as the 3rd best sub-optimal structure with RNAsubopt -e. The graphic representations of these structures are produced with VARNA[20]. (B) The corresponding smFRET efficiency (E fret ) histograms are reported in [12]. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. (C) The graph-distance distribution in the ensemble which is approximated with RNAsubopt -p at temperature 50°C.

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