Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded

(Pyrimidine)n . (purine)n DNAs of repeating sequences form a distinctive complex on lowering the pH below 6. Previously this complex was thought to be tetra-stranded. The present work is inconsistent with this view, and four lines of evidence show that the complex consists of a triplex together with a poly d(purine) possessing secondary structure. Formula: (see text). (a) S1 nuclease digestion leads to degradation of 50% of the poly d(purine) content of the pH 5-induced complex. (b) Buoyant density studies demonstrate that there is no interaction between the triplex and added free poly d(purine) and also that the complex formed from duplex DNA contained poly d(purine) which is free to form a triplex on addition of an appropriate poly d(pyrimidine) in the correct stoichiometry. (c) The hyperchromic shifts of the triplex and poly d(purine), upon melting, are mutually independent. (d) The circular dichroism spectrum of the complex is simply the weighted average of a triplex together with a free poly d(purine). The triplexes have tm's approximately 20 degrees higher than the corresponding duplexes under comparable conditions and they are extremely resistant to various deoxyribonucleases; properties which may prove useful for their isolation from natural sources.