A Physical Origin for Functional Domain Structure in Nucleic Acids as Evidenced by Cross-linking Entropy: II

A new entropy model for RNA: part I. A critique of the standard Jacobson-Stockmayer model applied to multiple cross links

“…[23][24][25][26][27][28] In the first part of this Series, we examine the use of the standard entropy model that is based on the Jacobson-Stockmayer equation. 1 The objective is to look at the subtle role of this long range entropy effect that arises in polymers and to show why it is a misconception to equate the entropy evaluation of interactions between two independent strands in dsRNA structures with apparently similar single-stranded RNA secondary structure and likewise for other polymers such as dsDNA and protein topologies.…”

“…The focus is mainly on RNA secondary structure where the JS-model has been used with considerable success in the development of prediction algorithms that employ thermodynamic evaluation methods. [2][3][4] To understand the presentation in this work, the reader needs to be familiar with the basic concept of the Gaussian polymer chain (GPC), 30,31 the CLE model, [23][24][25][26][27][28] and the basic concepts of the thermodynamics of RNA secondary structure calculations. [32][33][34][35][36][37][38] The standard model: the loop penalty model (LP-model)…”

“…Moreover, corrections for any such details are independent of the stacking free energy and, at most, influence the Kuhn length; a measure of the stiffness of a polymer and typically short in single-stranded RNA: about 5 nt for poly(A) and 3 nt for poly(U). 27,28 The Kuhn length is not an explicit property used in evaluating the loop penalty model either. Because these uncertainties are largely local in character, they are not likely in most cases to overcome the global issues discussed here.…”

“…The right hand side of Equation (25) can be modified to the following form (26) where (27) and we obtain an expression resembling Equation (15) , with (28) In general, the parameters r1 and r2 in Equations (24) and (25) correspond to states in thermodynamic equilibrium. Assuming r1>r2 for the given polymer, this would usually be a denatured state (r1 2 =x Nb 2 ) and a bound state r2>rb.…”

“…The domain is then subdivided into these separate stems, and the entropy evaluated as in Equation (31) for different stems. In such cases, in previous work, [23][24][25]28 we have identified such objects with a tilde notation:…”