Intramolecular quadruplex formation of the G-rich strand of the mouse hypervariable minisatellite Pc-1

The minisatellite Pc-1, isolated from the mouse genome consisting of a tand em repeat of d(GGCAG), is hypervariable with a mutation rate of 0.15/genera tion. Here we describe a structural characterization of the G-rich strand o f Pc-1 by biochemical and physicochemical methods. It was found to be compa ratively resistant to both single-stranded DNA-binding protein binding and digestion by single-stranded DNA-specific nuclease and to cause arrest of D NA synthesis. The guanine imino proton NMR signals observed on the Pc-1 G-r ich strand and their slow H-1/H-2 exchange profiles pointed to a quadruplex structure with guanine quartets. The melting temperature of the quadruplex determined by CD was not dependent on DNA concentration. These results ind icate that the G-rich strand of Pc-1 forms an intramolecular folded-back qu adruplex structure under physiological conditions. Possible mechanisms of t he Pc-1 mutations implicated with the formation of the quadruplex structure are discussed. (C) 1999 Academic Press.