We here report our studies on the conjugation of photoreactive Ru 2+ complex to oligonucleotides (ODNs), which give stable duplex with the complementary target DNA strand. These functionalized DNA duplexes bearing photoreactive Ru 2+ complex can be specifically photolyzed to give the reactive aqua derivative, [Ru(tpy)(dppz)(H 2 O)] 2+ -ODN, in situ, which successfully cross-links to give photoproduct(s) with the target DNA strand in a sequence specific manner. Thus, the stable precursor of aqua-ruthenium complex, monofunctional polypyridyl ruthenium complex:[Ru(tpy)(dppz)(CH 3 CN)] 2+ (tpy = 2,2':6',2''-terpyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine), has been site-specifically tethered to ODN, for the first time, both by solid phase synthesis and post- Table 1). This shows that with the rigidly packed structure, as in the duplex with middle-Ru 2+ ODN, the metal center flexibility is considerably reduced, and consequently the accessibility of target G residue by the aquaruthunium moiety becomes severely restricted, which results in a poor yield in the cross-coupling reaction. The crosslinked product was characterized by PAGE, followed by MALDI-TOF MS.