A Stable Interaction between Separated Pyrimidine·Purine Tracts in Circular DNA

Abstract

Pyrimidine·purine tracts are widespread in eukaryotic genomes and have the potential to form a number of unusual structures including triplexes. Two such tracts, which could form triplexes with each other but not with themselves, were cloned into a plasmid at separate sites. Upon lowering the pH, linear, open circular and relaxed plasmid molecules formed a number of novel structures that were observed on agarose gels and directly by electron microscopy. In open circles a stable join was formed between the two Pyr·Pur tracts giving rise to molecules resembling dumbells, trefoils and tetrafoils, which collectively are termed T-loops. THe structure was stable at pH 8 and contains a single-stranded region that was sensitive to P 1nuclease. Thus, there is no apparent topological impediment to the formation of triplex-mediated loops in circular molecules. These structures may be important for gene regulation and chromosome condensation.