An RNA folding rule.

The folding of single-stranded RNA into its secondary structure is postulated to be equivalent to the simple rule that the next double-helical region (stem) to form is the one with the largest equilibrium constant. The rule is tested and shown to give results consistent with the enzyme cleavage data of several sequences. Computational time complexity is of order NxN for a sequence of N bases. A modification of the rule provides for the probabilistic choice of the next stem among those having an equilibrium constant within a specified range of the largest. Populations of competing structures are thus generated for detecting common characteristics and for assessing the applicability of the simple rule.