Pseudoknot

A pseudoknot is an RNA secondary structure consisting of two hairpin structures, the loop of a strain forming part of the second. Were pseudo- node for the first time in 1982 in a mosaic virus ( TYMV, turnip yellow mosaic virus ) was discovered. Pseudoknot fold into three-dimensional nodular structures that are not actually real topological node.

Forecasting and detection

Pseudoknot can not always be recognized as such by conventional prediction methods for secondary structures such as Mfold and PFOLD, since the positions of the base pairs may overlap in the sequence. The standard methods of dynamic programming recognize paired hairpin structure strains using recursive evaluation systems, and thus can only detect correctly nested, überlappfreie base pairings. Even with the new methods of stochastic context-free grammars is a recognition impossible. They merely recognize the more stable of the two pseudoknot stems.

It is possible that in some situations the dynamic programming methods can detect pseudoknot similar, but they are generally very inefficient. For the general problem of pseudoknot prediction has been proved that it is NP -complete.

Biological Significance

A number of important biological processes are based on the RNA molecules which form the pseudo node. For example, the human Telomerase contains a pseudoknot which is essential for the activity of the enzyme.

Credentials

• Biochemistry
• Nucleic acid
• Genetics