A physical origin for functional domain structure in nucleic acids as evidenced by cross-linking entropy: II

In Part I, cross-linking entropy (CLE) was proposed as a mechanism that limits the size of functional domains of RNA. To test this hypothesis, the theory is developed into an RNA secondary structure prediction filter which is applied to nearest-neighbor secondary structure (NNSS) algorithms that utilize a free energy (FE) minimization strategy. (The NNSS strategies are also referred to as the dynamic programming algorithm in the literature.) The cross-linking entropy for RNA is derived from a generalized Gaussian polymer chain model where the entropic contributions caused by the formation of base pairs (stacking) in RNA are analysed globally. Local entropic contributions are associated with the freezing out of degrees of freedom in the links. Both global and local entropic effects are strongly influenced by the persistence length. The cross-linking entropy provides a physical origin for the size of functional domains in long nucleic acid sequences and may go further to explain as to why the majority of the domain regions in typical sequences tend to be less than 600 nucleotides in length. In addition, improvements were observed in the "best guess" predictive capacity over NNSS prediction strategies. The thermodynamic distribution is more representative of the expected structures and is strongly governed by such physical parameters as the persistence length and the excluded volume. The CLE appears to generalize the tabulated penalties used in NNSS algorithms. The principal parameter influencing this entropy is the persistence length. The model is shown to accomodate a variable persistence length and is capable of describing the folding dynamics of RNA. A two-state kinetic model based on the CLE principle is used to help elucidate the folding kinetics of functional domains in the group I introns.