Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2′-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine

Abstract

We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2′-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both the number and location of the modifications. BAU-containing oligonucleotides generate triplexes with extremely slow kinetics, as evidenced by 14 °C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 °C min⁻¹. The association kinetics were measured by analysis of the hysteresis profiles, temperature-jump relaxation and DNase I footprinting. We find that the slow kinetics are largely due to the decreased rate of dissociation; BAU modification has little effect on the association reaction. The sequence selectivity is also due to the slower dissociation of BAU from AT than other base pairs.