Combinatorics of locally optimal RNA secondary structures (Q2436594)

This paper is devoted to the asymptotic enumeration of RNA secondary structures. The authors consider the base stacking energy model, where each stacked base pair contributes \(-1\) toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. The enumeration of such structures was studied earlier in the context of a dynamic programming algorithm. In this present paper, the authors determine the asymptotic number of these structures using generating functions and enumerative combinatorics methods. Analogous combinatorial problems for secondary structures with annotated single-standed, stacking nucleotides (dangles) are also studied.