An intramolecular triplex structure from non-mirror repeated sequence containing both Py:Pu.Py and Pu:Pu.Py triads.

A plasmid insert containing the (TA)7GATC(TA)7 inverted repeat and an adjacent (AG)7 tract adopts a cruciform structure at neutral pH. However, under acidic conditions the cruciform becomes readily disrupted in favor of a triplex. The (AG)7.(CT)7 duplex and one strand of the (TA)7GATC(TA)7 element are engaged in the three-stranded DNA formation, as determined using single-stranded DNA specific probes. The structure extrudes by displacing the (TA)7 strand adjacent to the (AG)7, and folding it back into the major groove of the (AG)7.(CT)7 duplex. This new variant of H-DNA is supercoil and pH dependent, requiring pH 6.1 or lower to form. The triplex is stabilized by T:A.T and A+:G.C triads. This unusual triad composition (50% of T:A.T and 50% of A+:G>C), that has not previously been observed in intramolecular triplexes, violates both the widely accepted division of triplexes into Py:Pu.Py or Pu:Pu.Py types and the requirement for mirror repeat symmetry.