منابع مشابه
Canonical RNA Pseudoknot Structures
In this paper, we study k-noncrossing, sigma-canonical RNA pseudoknot structures with minimum arc-length greater or equal to four. Let T(k, sigma)([4])(n) denote the number of these structures. We derive exact enumeration results by computing the generating function T(k, sigma)([4])(z) = summation operator(n) T(k, sigma)([4])(n)z(n) and derive the asymptotic formulas T(k, 3)([4])(n) approximate...
متن کاملRNA-LEGO: Combinatorial Design of Pseudoknot RNA
In this paper we enumerate k-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of k-noncrossing structures without isolated base pairs are significantly smaller than the number of all k-noncrossing structures. In particular we prove that the number of 3and 4-noncrossing RNA structures with stack-length ≥ 2 is for large n given by 311.2470 4! n(n−1)....
متن کاملShapes of RNA Pseudoknot Structures
In this article, we study abstract shapes of k-noncrossing, σ-canonical RNA pseudoknot structures. We consider lv1k- and lv5k-shapes, which represent a generalization of the abstract π'- and π-shapes of RNA secondary structures introduced by Giegerich et al. Using a novel approach, we compute the generating functions of lv1k- and lv5k-shapes as well as the generating functions of all lv1k- and ...
متن کاملCrowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA.
Formation of a pseudoknot (PK) in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the PK is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that cr...
متن کاملPredicting RNA pseudoknot folding thermodynamics
Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequen...
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ژورنال
عنوان ژورنال: Journal of Molecular Biology
سال: 1990
ISSN: 0022-2836
DOI: 10.1016/0022-2836(90)90192-o