An infinite class of unsaturated rooted trees corresponding to designable RNA secondary structures

TL;DR

This paper introduces an infinite class of rooted trees with unpaired nucleotides at maximum depth, proving their corresponding RNA secondary structures are designable, thus expanding understanding of RNA designability.

Contribution

It presents a new infinite class of rooted trees with unpaired nucleotides at maximum depth, demonstrating their structures are designable, advancing the combinatorial RNA design theory.

Findings

Identified an infinite class of rooted trees with unpaired nucleotides at maximum depth

Proved that the corresponding RNA secondary structures are designable

Complemented previous results in the RNA designability classification

Abstract

An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to determine whether or not a given RNA secondary structure is designable. Hale\v{s} et al. identified certain classes of designable and non-designable secondary structures by reference to their corresponding rooted trees. We introduce an infinite class of rooted trees containing unpaired nucleotides at the greatest depth, and prove constructively that their corresponding secondary structures are designable. This complements previous results for the combinatorial RNA design problem.