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PSEUDOKNOTS

    As noted in the help topic STEM/REGION_STACKING, two stems can form a pseudoknot
when  a strand of each is part of the hairpin or branching loop
of the other stem in such a manner that one stem can be regarded
as a coaxial extension of the other by stacking their tops together.
Such stacking results in increased conformation stability.

    The pseudoknot motif is interesting not only as a means of
increasing conformation stability, but also in the fact that it
can lead to a variety of base-pairing topologies, the two principal
cases of which result from two pseudoknots occuring in tandem
or of one being nested within the other.  The RNA_2D3D program is 
designed to handle all the known cases.  But because of the complexity
of some of the topologies, there is usually required some careful
editing and post refinement to obtain satisfactory structures.

    Samples of pseudoknots exemplifying  actual and imagined
structures are provided in the "sample BPL" data base.
As will be noticed in looking at any of these sample structures,
the stems forming a pseudoknot are colored: one red and the
other yelllow.  This coloring is for readily distinguishing a
pseudoknot from stems which do not participate in pseudoknot
formation.  The stem colored red is at the 5' end of the knot
and the yellow at the 3' end.

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