DNA-SEQUENCE SPECIFICITY OF A NAPHTHYLQUINOLINE TRIPLE HELIX-BINDING LIGAND

We have examined the effect of a naphthylquinoline tripler-binding lig and on the formation of intermolecular triplexes on DNA fragments cont aining the target sites A(6)G(6) . C6T6 and G(6)A(6) . T6C6. The ligan d enhances the binding of T6C2, but not T2C6, to A(6)G(6) . C6T6 sugge sting that it has a greater effect on T AT than C+. GC triplets. The c omplex with T6C2 is only stable below pH 6.0, confirming the requireme nt for protonation of the third strand cytosines, Antiparallel triplex es with GT-containing oligonucleotides are also stabilised by the liga nd. The complex between G(5)T(5) and A(6)G(6) . C6T6 is stabilised by lower ligand concentrations than that between T(5)G(5) and G(6)A(6) . C6T6. The ligand does not promote the interaction with CT-containing o ligonucleotides which have been designed to bind in a parallel orienta tion. Although the formation of antiparallel triplexes is pH independe nt, we find that the ligand has a greater stabilising effect at lower pH, suggesting that the active species is protonated. The ligand does not promote the binding of antiparallel GA-containing oligonucleotides at pH 7.5 but induces the interaction between A(5)G(5) and G(6)A(6) . T6C6 at pH 5.5. Ethidium bromide does not promote the formation of an y of these triplexes and destabilises the interaction of acridine-link ed pyrimidine-containing third strands with these target sites.