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

Journal article

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.

Authors: Rusling, D; Broughton-Head, V; Tuck, A; Khairallah, H; Osborne, S

• Publication status: Published
• Journal: Organic and biomolecular chemistry
• Volume: 6
• Issue: 1
• Pages: 122-129
• Publication date: 2008-01-01
• DOI: 10.1039/b713088k
• EISSN: 1477-0539
• ISSN: 1477-0520
• Language: English
• Keywords: Temperature; Base Sequence; Time Factors; Uridine; Oligonucleotides; DNA; Fluorescence; Peptide Mapping; Kinetics; Deoxyribonuclease I; Base Pair Mismatch; Transition Temperature