Effect of a Triplex-Binding Ligand on Parallel and Antiparallel DNA Triple Helices Using Short Unmodified and Acridine-Linked Oligonucleotides

Cassidy, Sarah A., Strekowski, Lucjan, Wilson, W. David and Fox, Keith R. (1994) Effect of a Triplex-Binding Ligand on Parallel and Antiparallel DNA Triple Helices Using Short Unmodified and Acridine-Linked Oligonucleotides. Biochemistry, 33 (51), 15338-15347. (doi:10.1021/bi00255a015).

Abstract

We have used DNase I footprinting to investigate the effect of a triplex-binding ligand on the formation of intermolecular DNA triple helices at target sites that have been cloned into longer DNA fragments. In the presence of a triplex-binding ligand (N-[2-(dimethylamino)ethyl]-2-(2-naphthyl)quinolin-4-ylamine), the concentrations of T₅C₅ and C₅T₅ required to generate DNase I footprints at the target sites A₆G₆·C₆T₆ and G₆A₆·T₆C₆, respectively, are reduced by at least 100-fold. Complexes with the acridinelinked oligonucleotides Acr-T₅C₅ and Acr-C₅T₅ are stabilized to a much lesser extent and produce footprints at concentrations similar to those of the unmodified oligonucleotides in the presence of the ligand. The stabilizing effects of acridine modification or the addition of a triplex-binding ligand are not additive. The position and length of the footprints produced by Acr-T₅C₅ and T₅C₅ at the target sequence A₆G₆·C₆T₆ are unaffected by the ligand. In contrast, footprints at the target site G₆A₆·T₆C₆ appear 3–4 bases shorter in the presence of the ligand, when viewed from the pyrimidine strand, and 1–2 bases longer on the purine strand. These results are explained by suggesting that the compound binds at T·AT triplets and prevents the transmission of any DNA structural changes into the flanking duplex. The compound has a smaller stabilizing effect on short antiparallel triplexes consisting of G·GC and T·AT triplets. Binding of Acr-G₅T₅ to A₆G₆·C₆T₆ is enhanced slightly by the compound, which increases the apparent footprinting site, probably by preventing fraying at the 3′-end of the third strand. The compound does not promote the binding of G₅T₅ to A₆G₆·C₆T₆, or that of Acr-T₅G₅ and T₅G₅ to G₆A₆·T₆C₆.

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Contributors

Author: Keith R. Fox

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