Statistical significance of DNA sequence symmetries

Abstract

SOME regions of DNA involved in regulatory or catalytic interactions with proteins have sites with twofold rotation symmetry in the primary nucleotide sequence^1–3. It would be worthwhile to determine whether certain of these symmetries occur so rarely by chance that they probably have a function, for example, as recognition sites for symmetric protein complexes. Likewise, it would be useful to be able to dismiss other apparent symmetries as probable statistical accidents of no functional importance. The following quantitative method can be used to evaluate the statistical significance of hyphenated (that is, incomplete) symmetries, where a more intuitive approach may be misleading. Since the probability of random occurrence of a given subsequence increases in almost direct proportion to the length of the sequence considered, a rigorous approach will become increasingly important in the evaluation of the significance of subsequence anomalies occurring in the much longer DNA sequences that will be determined in the future.