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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. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. [ 2 ]
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 .
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
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.
The stability of the loop also influences the formation of the stem-loop structure. Optimal loop length tends to be about 4-8 bases long; loops that are fewer than three bases long are sterically impossible and thus do not form, and large loops with no secondary structure of their own (such as pseudoknot pairing) are unstable.
Lists of shapes cover different types of geometric shape and related topics. They include mathematics topics and other lists of shapes, such as shapes used by drawing ...
An example of an RNA stem-loop. If now a second RNA stem-loop has complementary base-sequence, the two loops can base pair resulting in a kissing loop.
In SAM-IV, the P4 stem is located downstream of the P1 stem and interacts, by a second pseudoknot, with P3, while the kink turn is absent. SAM-I/IV variant riboswitches [8] combine features of SAM-I and SAM-IV riboswitches. For example, they have the P4 outside of the multistem junction, like SAM-IV riboswitches, but also often have a SAM-I ...