Open AccessA new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP)
Author(s) -
Wayne Dawson,
Gota Kawai
Publication year - 2015
Publication title -
journal of nucleic acids investigation
Language(s) - English
Resource type - Journals
eISSN - 2035-6005
pISSN - 2036-7996
DOI - 10.4081/jnai.2015.2653
Subject(s) - folding (dsp implementation) , degeneracy (biology) , rna , computer science , entropy (arrow of time) , nucleic acid secondary structure , statistical physics , algorithm , computational biology , physics , theoretical computer science , bioinformatics , biology , thermodynamics , engineering , gene , genetics , electrical engineering
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