title: Combinatorics of saturated secondary structures of RNA.
abstract: Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated secondary structures are local minima in the energy landscape, hence form kinetic traps during the folding process. Here we present recurrence relations and closed form asymptotic limits for combinatorial problems related to the number of saturated secondary structures. In addition, Python source code to compute the number of saturated secondary structures having k base pairs can be found at the web servers link of bioinformatics.bc.edu/clotelab/.
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA. clote@bc.edu
authors.forename: P
authors.initials: P
authors.lastname: Clote
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001699:Biometry; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012313:RNA