THEORY FOR THE CONFORMATIONAL-CHANGES OF DOUBLE-STRANDED CHAIN MOLECULES

We develop statistical mechanical theory to predict the thermodynamic properties of chain molecules having noncovalent double-stranded confo rmations, as in RNA molecules and beta-sheets in proteins. Sequence de pendence and excluded volume interactions are explicitly taken into ac count. We classify conformations by their polymer graphs and enumerate all the conformations corresponding to each graph by a recently devel oped matrix method [S-J. Chen and K. A. Dill, J. Chem. Phys. 103, 5802 (1995)]. All such graphs are summed by a recursive method. Tests agai nst exact: computer enumeration for short chains on a 2D lattice show that the density of states and partition function are given quite accu rately. So far, we have explored two classes of conformations; hairpin s, which model small beta-sheets, and RNA secondary structures. The ma in folding transition is predicted to be quite different for these two conformational classes: the hairpin transition is two-state while the RNA secondary structure transition is one-state for homopolymeric cha ins. (C) 1998 American Institute of Physics.