Posets and spaces of k-noncrossing RNA structures

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Abstract

RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modeled combinatorially in terms of a certain type of graph called an RNA diagram. In this paper we introduce a new poset of RNA diagrams ${\mathcal B}^r_{f,k}$, $r\ge 0$, $k \ge 1$, and $f \ge 3$, which we call the Penner--Waterman poset, and, using results from the theory of multitriangulations, we show that this is a pure poset of rank $k(2f-2k+1)+r-f-1$, whose geometric realization is the join of a simplicial sphere of dimension $k(f-2k)-1$ and an $\left((f+1)(k-1)-1\right)$-simplex in case $r=0$. As a corollary for the special case $k=1$, we obtain a result due to Penner and Waterman concerning the topology of the space of RNA secondary structures. These results could eventually lead to new ways to study landscapes of RNA $k$-noncrossing structures.
Original languageEnglish
Pages (from-to)1586-1611
Number of pages26
JournalSIAM Journal on Discrete Mathematics
Volume36
Issue number3
DOIs
Publication statusPublished - 7 Jul 2022

Keywords

  • RNA structures
  • k-noncrossing pseudoknots
  • multitriangulations
  • poset topology

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