We have investigated the recognition of nucleic acid derivatives by organometallic ruthenium(II) arene anticancer complexes of the type [(eta(6)-arene)Ru(II)(en)X] where en = ethylenediamine, arene = biphenyl (Bip), tetrahydroanthracene (THA), dihydroanthracene (DHA), p-cymene (Cym) or benzene (Ben), X = Cl(-) or H(2)O using (1)H, (31)P and (15)N ((15)N-en) NMR spectroscopy. For mononucleosides, [(eta(6)-Bip)Ru(en)](2+) binds only to N7 of guanosine, to N7 and N1 of inosine, and to N3 of thymidine. Binding to N3 of cytidine was weak, and almost no binding to adenosine was observed. The reactivity of the various binding sites of nucleobases toward Ru at neutral pH decreased in the order G(N7) > I(N7) > I(N1), T(N3) > C(N3) > A(N7), A(N1). Therefore, pseudo-octahedral diamino Ru(II) arene complexes are much more highly discriminatory between G and A bases than square-planar Pt(II) complexes. Such site-selectivity appears to be controlled by the en NH(2) groups, which H-bond with exocyclic oxygens but are nonbonding and repulsive toward exocyclic amino groups of the nucleobases. For reactions with mononucleotides, the same pattern of site selectivity was observed, but, in addition, significant amounts of the 5'-phosphate-bound species (40-60%) were present at equilibrium for 5'-TMP, 5'-CMP and 5'-AMP. In contrast, no binding to the phosphodiester groups of 3', 5'-cyclic-GMP (cGMP) or cAMP was detected. Reactions with nucleotides proceeded via aquation of [(eta(6)-arene)Ru(en)Cl](+), followed by rapid binding to the 5'-phosphate, and then rearrangement to give N7, N1, or N3-bound products. Small amounts of the dinuclear species, e.g., Ru-O(PO(3))GMPN7-Ru, Ru-O(PO(3))IMPN1-Ru, Ru-O(PO(3))TMPN3-Ru, Ru-N7IMPN1-Ru, and Ru-N7InoN1-Ru were also detected. In competitive binding experiments for [(eta(6)-Bip)Ru(en)Cl](+) with 5'-GMP versus 5'-AMP or 5'-CMP or 5'-TMP, the only final adduct was [(eta(6)-Bip)Ru(en)(N7-GMP)]. Ru-H(2)O species were more reactive than Ru-OH species. The presence of Cl(-) or phosphate in neutral solution significantly decreased the rates of Ru-N7 binding through competitive coordination to Ru. In kinetic studies (pH 7.0, 298 K, 100 mM NaClO(4)), the rates of reaction of cGMP with [(eta(6)-arene)Ru(II)(en)X](n+) (X = Cl(-) or H(2)O) decreased in the order: THA > Bip > DHA >> Cym > Ben, suggesting that N7-binding is promoted by favorable arene-purine hydrophobic interactions in the associative transition state. These findings have revealed that the diamine NH(2) groups, the hydrophobic arene, and the chloride leaving group have important roles in the novel mechanism of recognition of nucleic acids by Ru arene complexes, and will aid the design of more effective anticancer complexes, as well as new site-specific DNA reagents.