Thermodynamic and kinetic studies of the formation of triple helices between purine-rich deoxyribo-oligonucleotides and the promoter region of the human c-src proto-oncogene

The thermodynamic and kinetic parameters of tripler formation between four purine-rich oligonucleotides and a 22 bp pyrimidine purine tract in the promoter region of the c-src gene were determined by fluorescence polarization studies. Three of these four oligonucleotides were 11 nt in length, corresponding to the left, central or right portion of the tract, while the fourth was a 22mer covering the whole tract. Binding constants (K-a) were measured as a function of Mg2+ concentration (0-10 mM) and temperature (0-41 degrees C), In 10 mM Mg2+, K-a for the left, central and right 11mers were 0.26, 0.75 and 1.4 x 10(8)/M, respectively, while for the 22mer the value was 1.8 x 10(8)/M at 22 degrees C. Under the same conditions, K-a was estimated by an electrophoretic band shift technique. The agreement between the two methods was acceptable for the 22mer but not for the 11mers, Kinetic measurements demonstrated that the rate of dissociation of the 22mer from the tripler was significantly slower than that of the 11mers, providing an explanation for the observed discrepancy. The entropy and enthalpy of tripler formation were calculated from van't Hoff plots. In all cases the entropy was favourable, especially for the 22mer and for the 11mer with the lowest guanine content. The enthalpy was unfavourable for the 22mer and most favourable for the 11mer with the highest guanine content, These results provide a thermodynamic explanation for length and sequence effects on the formation of purine pyrimidine purine triplexes.