Here we discuss four important questions (1) how can we be sure that the thermodynamically most-probable folding-pathway yields the minimum free energy for secondary structure using the dynamic programming algorithm (DPA) approach, (2) what are its limitations, (3) how can we extend the DPA to find the minimum free energy with pseudoknots, and finally (4) what limitations can we expect to find in a DPA approach for pseudoknots. It is our supposition that some structures cannot be fit uniquely by the DPA, but may exist in real biology situations when disordered regions in the biomolecule are necessary. These regions would be identifiable by using suboptimal structure analysis. This grants us some qualitative tools to identify truly random RNA sequences, because such are likely to have greater degeneracy in their thermodynamically most-probable folding-pathway.
RNA folding; Entropy; Dynamic programming algorithm; RNA structure; functional RNA; bioinformatics