The RNA single-stranded polynucleotide
chain folds in on itself in complex ways, forming hydrogen-bonded segments
(e.g., A-U and G-C), imperfect with stems, loops, bulge loops, and junctions.
The most stable fold for any particular RNA structure is the base paired
structure that results in the minimum amount of free energy.
RNA folds form both secondary and
tertiary structures. An RNA secondary structure shows how the bases
pair to each other to produce stems, loops, and other secondary-structure
motifs. The tertiary structure is considerably more complex; it is
a representation of how the secondary structural elements interact with
each other in three dimensional space. For example, a single strand RNA,
that is identified by the Nucleic
Acid Database as PR0021, has the following sequence of bases along
its single strand:
RNA Sequence:
G G C U C U G U U U A C C A G G U C A G G U C C G A A A G G A A G C
A G C C A A G G C A G A G C CCC
This sequence folds into the following secondary structure:
Image of PR0021 created using Zuker's mFold
Using the method described in the RNA
Tree Graph Tutorial section of our website on how to create a secondary
graph from a secondary structure, the secondary tree graph structure for
this single strand RNA would appear as follows:
A pictoral view of the tertiary structure (complexed with a protein,
purple) is provided in the Nucleic
Acid Database, and it appears as follows: