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The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. [2] Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots . These structures are categorized as cross (X) topology within the circuit topology framework, which, in contrast to knot theory, is a contact-based approach.
Shape abstraction retains adjacency and nesting of structural features, but disregards helix lengths, thus reduces the number of suboptimal solutions without losing significant information. Furthermore, shapes represent classes of structures for which probabilities based on Boltzmann-weighted energies can be computed.
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots .
formation of a pseudoknot with coaxial stacking of the two helices. Two common motifs involving coaxial stacking are kissing loops and pseudoknots. In kissing loop interactions, the single-stranded loop regions of two hairpins interact through base pairing, forming a composite, coaxially stacked helix.
Secondary structure in pistol ribozyme was observed to be highly conserved. There are 3 Watson-Crick base-paired stems: P1, P2, and P3, which are all connected by loops. A pseudoknot interaction exists between the loop of P1 and the junction connecting P2 and P3. [2]
The Influenza virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome. [1] Pseudoknots are commonly found in viral genomes , especially RNA viruses , where they incorporate an RNA splice site and can have a wide range of functions. [ 2 ]
Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits.
The 3' splice site region used to produce M2 was experimentally probed with structure-sensitive chemicals and enzymes and was found to adopt both the hairpin and pseudoknot conformations in solution. Each conformation places important splicing regulatory sites in different structural environments, which has implications for the modulation of ...