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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.
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 .
A long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control. A long range pseudoknot is thought to negatively regulate the translation of the IF3-L35-L20 operon in E. coli. This operon encodes the translation initiation factor IF-3 and ribosomal proteins L35 and L20.
Functional RNAs are often folded, stable molecules with three-dimensional shapes rather than floppy, linear strands. [50] Cations are essential for thermodynamic stabilization of RNA tertiary structures. Metal cations that bind RNA can be monovalent, divalent or trivalent. Potassium (K +) is a common monovalent ion that binds RNA.
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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 fast-spreading wildfire that erupted this week about 45 miles northwest of Los Angeles roared from nothing to nearly 10,000 acres − in a matter of hours.