Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures

Random graph theory is used to model relationships between sequences and secondary structures of RNA molecules. Sequences folding into identical structures form neutral networks which percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value. The networks of any two different structures almost touch each other, and sequences folding into almost all “common” structures can be found in a small ball of an arbitrary location in sequence space. The results from random graph theory are compared with data obtained by folding large samples of RNA sequences. Differences are explained in terms of RNA molecular structures.