Home Tutorials Modeling of Pool Synthesis Use of RNA Pool Designer

Starting Sequences

The starting structure allows exploration of the structural neighbors of that structure via mutations. For example, the starting sequences with distinct tree structures are 70S (chain F) (80-nt), tRNA (81-nt), P5abc domain of group I intron (56-nt), GTP-binding aptamer (69-nt), modified P5abc domain (51-nt) and modified GTP-binding aptamer (54-nt).

As shown, distinct tree structures are represented as graphs by converting stems to edges and other structural elements (e.g., loop, bulge, etc) to vertices according to tree graph rules. We generate pools with all possible combinations of mixing matrices and starting sequences for the target structural distributions.
We use 30 starting sequences classified by the shape, length range, and function as shown below: