Abundance of pseudoknots in the RNA world

The pseudoknot fold is often seen in auto-catalytic RNA and in viruses. A recent polymer physics model and statistical-mechanical theory predicts relative probabilities of different pseudoknot folds consonant with a database of known folds. Now we extend that theory for a preliminary estimate of the abundance of pseudoknot folds in RNA sequences, finding approximately 1 per 40,000 nucleotides. This theoretical probability density compares favorably to what we infer from structure databases and has implications for genome organization, RNA folding algorithms, and the RNA World.