EXAMPLE 3

Here we present some results from the folding of an RNA that is related to a Human adenovirus pre-terminal protein (U52533). This RNA exhibits both ``well-defined'' and ``poorly-defined'' folding regions, as shown in Figure 17. A total of 7 foldings were computed using the default parameters.

  

Figure 17: The energy dot plot for the ``Example 3'' sequence, with $\Delta G$ = -196.3 kcal/mole and $\Delta \Delta G$ = 9.8 kcal.mole. The region from bases 180 to 295 shows a great deal of uncertainty in its folding. This may be interpreted as a large ensemble of different foldings, or simply an ``unstructured'' region. In contrast, the long stem pairing bases 160-178 with 316-298, respectively, is extremely well determined. Also well-determined is a stem loop region that stretches from 37-81 and 322-365.