Kinetic discrimination in the folding of intramolecular triple helices

We report a study of the physical properties of oligonucleotide intramolecular Pyr.Pur.Pyr triplexes modeled after H-form DNA. The experiments utilized a set of palindromic pyrimidine strands which form triplexes when combined with complementary purine strands. Triplexes of this nature have two possible isomers, one where the 3' half of the pyrimidine strand acts as the third strand (Y3) or one where the 5' end does (Y5). Kinetic studies of these triplexes revealed that the Y3 isomer folded 10 to 50 times faster than the corresponding Y5 isomer. Despite these kinetic differences, the complexes display relatively similar equilibrium stabilities, with seven of eight falling within a 1.1 kcal range. Addition of non-pairing sequence to the ends of the purine strand both reverses the kinetic bias (slowing Y3 formation > 200 fold) and destabilizes the Y3 isomer 1.4 kcal/mol relative to Y5. Three features appear to lie at the source of both the kinetic and thermodynamic variability seen: (1) the prenucleation geometry of the triplexes prior to formation; (2) the accessibility of the major groove to the third strand; and (3) the nature of the triplex loop formed. Based on the data we propose a model for formation of H-form DNA that explains the biases observed for one isomer over the other in different situations. The conclusions have general implications for the tertiary folding of nucleic acids.