EFFECT OF A TRIPLER-BINDING LIGAND ON PARALLEL AND ANTIPARALLEL DNA TRIPLE HELICES USING SHORT UNMODIFIED AND ACRIDINE-LINKED OLIGONUCLEOTIDES

We have used DNase I footprinting to investigate the effect of a tripl er-binding ligand on the formation of intermolecular DNA triple helice s at target sites that have been cloned into longer DNA fragments. In the presence of a triplex-binding ligand hylamino)ethyl]-2-(2-naphthyl )quinolin-4-ylamine), the concentrations of T5C5 and C5T5 required to generate DNase I footprints at the target sites A(6)G(6)C(6)T(6) and G (6)A(6)T(6)C(6), respectively, are reduced by at least 100-fold. Compl exes with the acridine-linked oligonucleotides Acr-T5C5 and Acr-C5T5 a re stabilized to a much lesser extent and produce footprints at concen trations similar to those of the unmodified oligonucleotides in the pr esence of the ligand. The stabilizing effects of acridine modification or the addition of a tripler-binding ligand are not additive. The pos ition and length of the footprints produced by Acr-T5C5 and T5C5 at th e target sequence A(6)G(6)C(6)T(6) are unaffected by the ligand. In co ntrast, footprints at the target site G(6)A(6)T(6)C(6) appear 3-4 base s shorter in the presence of the ligand, when viewed from the pyrimidi ne strand, and 1-2 bases longer on the purine strand. These results ar e explained by suggesting that the compound binds at T.AT triplets and prevents the transmission of any DNA structural changes into the flan king duplex. The compound has a smaller stabilizing effect on short an tiparallel triplexes consisting of G GC and T AT triplets. Binding of Acr-G(5)T(5) to A(6)G(6)C(6)T(6) is enhanced slightly by the compound, which increases the apparent footprinting site, probably by preventin g fraying at the 3'-end of the third strand. The compound does not pro mote the binding of G(5)T(5) to A(6)G(6)C(6)T(6) or that of Acr-T(5)G( 5) and T(5)G(5) to G(6)A(6)T(6)C(6).