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.  The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of general pseudoknots in nucleic acid sequences impossible to predict by the standard method of dynamic programming, which uses a recursive scoring system to identify paired stems and consequently cannot detect non-nested base pairs with common algorithms. However, limited subclasses of pseudoknots can be predicted using modified dynamic programs.
Newer structure prediction techniques such as stochastic context-free grammars are also unable to consider pseudoknots.
Pseudoknots can form a variety of structures with catalytic activity and several important biological processes rely on RNA molecules that form pseudoknots. For example, the RNA component of the human telomerase contains a pseudoknot that is critical for its activity. The hepatitis delta virus ribozyme is a well known example of a catalytic RNA with a pseudoknot in its active site. Though DNA can also form pseudoknots, they are generally not present in standard physiological conditions.