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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 degrees C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 degrees 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.

Original publication

DOI

10.1039/b713088k

Type

Journal article

Journal

Org Biomol Chem

Publication Date

07/01/2008

Volume

6

Pages

122 - 129

Keywords

Base Pair Mismatch, Base Sequence, DNA, Deoxyribonuclease I, Fluorescence, Kinetics, Oligonucleotides, Peptide Mapping, Temperature, Time Factors, Transition Temperature, Uridine