The DNA binding properties of cationic salen-type Ni(II) complexes (Fig. 1) have been studied by CD and NMR measurements. The binding constants estimated for poly(dA-dT)2 and poly(dA)poly(dT) revealed that (1) binds more preferentially to poly(dA)poly(dT) than to poly(dA-dT)2, and vice versa for (2). The intermolecular NOE and chemical shift change of the oligonucleotides, d(CGCGAATTCGCG)2 (ODN1) and d(CGCGTATACGCG)2 (ODN2) indicated that the two complexes bound to the minor grooves at AT-rich site of the ODNs from the "en" bridging side. The difference in the sequence specificity between (1) and (2) was attributed to the difference in the width of the minor groove; (2) recognized the wider minor groove of ODN2 'TATA' region. In contrast to (1) and (2), the asymmetric complex (3) bound to the major groove at terminal GC-rich site of ODN1. In this study, we could reveal that hydrophobic interaction is an important factor for base sequence recognition and an appropriate modification of the salen could switch the binding site from minor to major groove of DNA.