Spectrophotometric binding studies of a series of the naphthalene diimide derivatives, 1-7, carrying different chains with a human telomere oligonucleotide, d(TTAGG)(4) was carried out in 0.1 M AcOK-AcOH buffer (pH 5.6) and 0.1 M KCl. Under this condition, this DNA could exist as the mixture of two-type tetraplex structures and these derivatives could bind to this DNA with strong affinity of 10(6) M(-1). The effect of the linker chain is not so large in those binding affinity, but the ligand 5 having piperazine skeleton in the linker chain had relative higher affinity for this tetraplex DNA than other derivatives. Large hypochromic effect of these derivatives upon binding to the tetraplex DNA suggested that the binding mode of these derivatives might contribute the stacking interaction between the naphthalene diimide and guanine tetraplex planes.