Structural heterogeneity in intramolecular DNA triple helices

Oligodeoxynucleotides designed to form intramolecular triple helices are wi dely used as model systems in thermodynamic and structural studies. We now report results from UV, Raman and NMR experiments demonstrating that the st rand polarity, which also determines the orientation of the connecting loop s, has a considerable impact on the formation and stability of pyr pur pyr triple helices, Them are two types of monomolecular triplexes that can be d efined by the location of their purine tract at either the 5'- or 3'-end of the sequence. We have examined four pairs of oligonucleotides with the sam e base composition but with reversed polarity that can fold into intramolec ular triple helices with seven base triplets and two T-4 loops under approp riate conditions, UV spectroscopic monitoring of thermal denaturation indic ates a consistently higher thermal stability for the 5'-sequences at pH 5.0 in the absence of Mg2+ ions, Raman spectra provide evidence for the format ion of triple helices at pH 5 for oligomers with purine tracts located at e ither the 5'- or 3'-end of the sequence. However, NMR measurements reveal c onsiderable differences in the secondary structures formed by the two types of oligonucleotides, Thus, at acidic pH significant structural heterogenei ty is observed for the 3'-sequences, Employing selectively N-15-labeled oli gomers, NMR experiments indicate a folding pattern for the competing struct ures that at least partially changes both Hoogsteen and Watson-Crick base-b ase interactions.