Triple Helix Formation and Homologous Strand Exchange in Pyrene-Labeled Oligonucleotides

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Abstract
The orientations of the symmetrical third strands (G3A4G3) and (G3T4G3) within the triplexes (C3T4C3)−(G3A4G3)×(G3A4G3) and (C3T4C3)−(G3A4G3)×(G3T4G3) were investigated by fluorescence spectroscopy and thermal denaturation using pyrene-labeled oligodeoxynucleotides. In the two triplex structures, both parallel and antiparallel orientations of the third strand with respects to the purine Watson−Crick one were identified by means of pyrene excimer formation. The pyrene labels do not modify the melting temperature of the (C3T4C3)−(G3A4G3)×(G3T4G3) triplex but somewhat stabilize the corresponding duplex against thermal denaturation. The absorption melting profiles of the (C3T4C3)−(G3A4G3)×(G3A4G3) triplex are monophasic in agreement with previous reports. In contrast, the melting of this structure, when monitored by the pyrene excimer band, reveals a biphasic behavior. These data, together with kinetics measurements, strongly suggest exchange mechanisms between the homologous oligomers (G3A4G3), Hoogsteen, and Watson−Crick strands.