Compatible Structure

In order to have any enzymatic activity the molecule should fold into the structure of the ribozyme. Here a number of alternative structures can also be considered.

A sequence is said to be compatible with a structure if for every base pair (i j) in the structure the bases at the ith and jth positions in the sequence can form one of the allowed base pairs (that is, A:U, U:A, G:C, C:G, U:C, G:U). Enforcing strict compatibility might result in an overestimation of the negative effects of mispair mutations. Some mispair mutants retain relatively high level of activity; for example the C662G mispair mutation in the VS ribozyme decreases activity to 23% of the wild type (Beattie et al., 1995). Thus, even sequences with partial compatibility should be considered compatible in this step. The negative effect of mispairs is taken into account in the next step.

If a sequence is not compatible - even when considering the possibility of mis-pairs - with any of the possible structures, then it has no activity and its fitness is set to 0. The activity factor for this step (A;tmcture) is the activity associated with the structure to which the sequence can fold. The activities of the various possible structures can be different.

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