Bulletin of Mathematical Biology

, Volume 70, Issue 4, pp 951–970 | Cite as

Asymptotic Enumeration of RNA Structures with Pseudoknots

  • Emma Y. Jin
  • Christian M. Reidys
Original Article


In this paper, we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the asymptotic expansion for the numbers of k-noncrossing RNA structures. Our results are based on the generating function for the number of k-noncrossing RNA pseudoknot structures, \({\mathsf{S}}_{k}(n)\) , derived in Bull. Math. Biol. (2008), where k−1 denotes the maximal size of sets of mutually intersecting bonds. We prove a functional equation for the generating function \(\sum_{n\ge 0}{\mathsf{S}}_{k}(n)z^{n}\) and obtain for k=2 and k=3, the analytic continuation and singular expansions, respectively. It is implicit in our results that for arbitrary k singular expansions exist and via transfer theorems of analytic combinatorics, we obtain asymptotic expression for the coefficients. We explicitly derive the asymptotic expressions for 2- and 3-noncrossing RNA structures. Our main result is the derivation of the formula \({\mathsf{S}}_{3}(n)\sim \frac{10.4724\cdot4!}{n(n-1)\cdots(n-4)}(\frac{5+\sqrt{21}}{2})^{n}\) .


Asymptotic enumeration RNA secondary structure k-noncrossing RNA structure Pseudoknot Generating function Transfer theorem Hankel contour Singular expansion 


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Copyright information

© Society for Mathematical Biology 2008

Authors and Affiliations

  1. 1.Center for Combinatorics, LPMC-TJKLCNankai UniversityTianjinPeople’s Republic of China

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