Homonyms, synonyms and mutations of the sequence/structure vocabulary

Calladine (1982) proposed that steric repulsion between adjacent purines on opposite helix backbones accounts for the local variation seen in four helical parameters. By defining simple sum functions based on Calladine's proposal, Dickerson (1983) has taken what he terms "the first step in establishing a sequence/structure vocabulary". In this letter we analyze the implications of the Calladine-Dickerson model with regard to "homonyms", "synonyms" and mutations. Specifically, we (1) show that because of the number of adjacent helical positions affected by one transversion, two purine-pyrimidine sequences may be similar at the sequence level yet be very different structurally (homonyms); (2) list all sequences which, though different at the sequence level, share adjacent structural parameter values (synonyms); and (3) use two simple statistical measures to show that transversion mutations occurring between a purine and a pyrimidine (5′ → 3′ on the same strand) are in general less disruptive of local helical structure than transversions occurring between a pyrimidine and purine. On the assumption that they are not inconsistent with experimental findings, we discuss the significance of these implications.