A pseudoknot is a knotlike structure formed by an RNA molecule when pairs of nucleotides from the endpoints of overlapping intervals in the RNA strand base pair with each other. The overlapping intervals can range in length from a single nucleotide to much longer regions. An example of a pseudoknot is illustrated in the figure below.
To bar pseudoknots when modeling RNA mathematically secondary structures, we demand that the matching of basepair edges in the bonding graph of the RNA string in question must be noncrossing.
