An intramolecular DNA triplex is disrupted by point mutations associated with hereditary persistence of fetal hemoglobin

Several investigators have suggested that secondary structures in DNA may be involved with physiologic gene regulatory processes in higher organisms. This hypothesis has been difficult to prove, however, since naturally occurring mutations that alter secondary DNA structures have not yet been identified. In this report, we describe a secondary DNA structure upstream from the human γ-globin genes; this structure is formed in a homopyrimidine-homopurine tract and is stabilized by acidic pH and negative supercoiling of plasmid DNA. Since this structure is asymmetrically cleaved by S1 nuclease, it probably contains a single-stranded region and an intramolecular triplex. The single-stranded region is actually accessible for Watson-Crick base pairing with exogenous oligomers, a characteristic that permitted us to directly map the secondary DNA structure without additional chemical modifications of the supercoiled DNA. Five different point mutations just downstream from the single-stranded region are associated with hereditary persistence of fetal hemoglobin; four of these mutations dramatically reduce the stability of the secondary DNA structure, suggesting that these mutations alter formation of the intramolecular triplex by destabilizing critical Hoogsteen (triple-stranded) base pairs. These mutations may therefore represent a novel class of genetic defects that alter gene expression by changing the interaction of a critical regulatory molecule with a secondary DNA structure.