Pseudoknot

This example of a naturally occurring pseudoknot can be found in the RNA component of human telomerase . Sequence off.

Spatial representation of a pseudoknot of a human telomerase RNA. (A): stick model. (B) RNA backbone. Both figures are based on the PDB  1YMO pdb file and the ribonucleic acid color scheme .

A pseudoknot is an RNA - secondary structure consisting of two hairpin structures , wherein the loop of a strain forming part of the second. Pseudoknots were first discovered in 1982 in a mosaic virus (TYMV, turnip yellow mosaic virus ). Pseudo knots fold into knot-shaped three-dimensional structures, but these do not represent real topological knots .

Prediction and detection

Common prediction methods for secondary structures such as Mfold and Pfold cannot always recognize pseudoknots as such, since the positions of the base pairings in the sequence can overlap. The standard methods of dynamic programming recognize paired hairpin structure stems by means of recursive evaluation systems and can consequently only recognize correctly nested, overlap-free base pairings. Even with the new methods of stochastic context-free grammars , recognition is impossible. They only recognize the more stable of the two pseudo-node stems.

It is possible that in some situations methods similar to dynamic programming can detect pseudo nodes, but these are generally very inefficient. The general problem of pseudoknot prediction has been shown to be NP-complete .

Biological importance

Some important biological processes are based on RNA molecules that form pseudoknots. For example, the human telomerase contains a pseudoknot which is essential for the activity of the enzyme.

credentials

1. ↑ ^{a b} Chen, JL. and Greiger, CW. (2005): Functional analysis of the pseudoknot structure in human telomerase RNA . In: Proc Natl Acad Sci USA 102 (23); 8080-8085; PMID 15849264 ; PDF (free full text access)
2. ^ Staple, DW. and Butcher, SE. (2005): Pseudoknots: RNA structures with diverse functions . In: PLoS Biol 3 (6); e213; PMID 15941360 ; PMC 1149493 (free full text).
3. ↑ Archived copy ( memento of the original from April 26, 2006 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. 
4. ↑ Archived copy ( Memento of the original from May 10, 2012 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. 
5. ↑ Rivas, E. and Eddy, SR. (1999): A dynamic programming algorithm for RNA structure prediction including pseudoknots. In: J Mol Biol , 285 (5); 2053-2068; PMID 9925784 ; doi : 10.1006 / jmbi.1998.2436
6. ↑ Lyngsø, RB. and Pedersen, CN. (2000): RNA pseudoknot prediction in energy-based models . In: J Comput Biol 7 (3-4): 409-427; PMID 11108471 ; PDF (free full text access)