Energetics of strand-displacement reactions in triple helices: a spectroscopic study

DNA triple helices offer exciting new perspectives toward oligonucleotide-d irected inhibition of gene expression. Purine and GT triplexes appear to be the most promising motifs for stable binding under physiological condition s compared to the pyrimidine motif, which forms at relatively low pH. There are, however, very little data available for comparison of the relative st abilities of the different classes of triplexes under identical conditions. We, therefore, designed a model system which allowed us to set up a compet ition between the oligonucleotides of the purine and pyrimidine motifs targ eting the same Watson-Crick duplex. Several conclusions may be drawn: (i) a weak hypochromism at 260 nm is associated with purine tripler formation; ( ii) Delta H degrees of GA, GT and TC tripler formation (at pH 7.0) was calc ulated as -0.1, -2.5 and -6.1 kcal/mol per base triplet, respectively. This unexpectedly low Delta H degrees for the purine triple helix formation imp lies that its Delta G degrees is nearly temperature-independent and it expl ains why these triplexes may still be observed at high temperatures. In con trast, the pyrimidine tripler is strongly favoured at lower temperatures; ( iii) as a consequence, in a system where two third-strands compete for trip ler formation, displacement of the GA or GT strand by a pyrimidine strand m ay be observed at neutral pH upon lowering the temperature. This original p urine-to pyrimidine tripler conversion shows a significant hypochromism at 260 nm and a hyperchromism at 295 nm which is similar to the duplex-to-trip ler conversion in the pyrimidine motif. Further evidence for this tripler-t o-tripler conversion is provided by mung bean-nuclease footprinting assay. (C) 1999 Academic Press.