A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations

Abstract

In previous work, we have shown that the entropy of a folded RNA molecule can be divided into local and global contributions using the cross-linking entropy (CLE) model, where, in the case of RNA, the crosslinks are the base-pair stacking interactions. The local contribution to the CLE is revealed in the Kuhn length (a measure of the stiffness of the RNA). The Kuhn length acts as a scaling parameter. When the size of the system is rescaled, the relationship between local and global free energy must be renormalized to reflect this rescaling. In this renormalization process, the Kuhn length increases, the local entropy also increases due to freezing out of the local conformational degrees of freedom. At the same time, as the number of degrees of freedom decrease, there is a significant reduction in the global entropy. Here we present a method, based on the concepts of renormalization theory, to quantitatively estimate the size of the contribution from the local entropy as a function of the Kuhn length. The local entropy correction is used to predict the current empirically derived constant in the JacobsonStockmayer equation. The variation in the Kuhn length is shown to be largely influenced by the length of the double-stranded RNA stems formed in the secondary structure of folded RNA. This result is used to test the resulting entropy under a variable Kuhn length in stem-loop structures. Comparisons between a variable Kuhn length and a static Kuhn length on a short stem-loop of RNA are also examined. The model is quite general and is also directly applicable to protein structure and folding problems.

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

“…The Tm of G-C double-stranded oligonucleotides was calculated using the Crosslinking Entropy (CLE) Method [45,46]. According to this method the Tm of these molecules at the concentration here used of 1.3 M is, when fully paired, 86 °C.…”

Theoretical Search for RNA Folding Nuclei

“…Upon protein structure modeling we have shown that the term responsible for the persistent length does not make a large contribution to the calculations of the loop entropy (the persistent length 20 Å) [6]. The persistence length for RNA molecules is ~10-20 Å [43], and therefore here we ignore this parameter (the term itself is not so strict and can be largely treated as a constant in the first approximation [44]). …”