JBIC (1999) 4 : 325–340 Q SBIC 1999 ORIGINAL PAPER Ming Zhao 7 M. J. Clarke Effects of trans-pyridine ligands on the interactions of Ru II and Ru III ammine complexes N7-coordinated to purine nucleosides and DNA Received: 11 November 1998 / Accepted: 3 March 1999 M. Zhao 7 M. J. Clarke (Y) Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA e-mail: clarke6bc.edu, Fax: c1-617-5522705 Supplementary material Additional information is available as Tables S1–S9 on Springer Verlag’s server at http://link.springer.de/journals/jbic/. Abstract DNA binding by trans-[(H 2 O)(Pyr)- (NH 3 ) 4 Ru II ] 2c (Pyrppy, 3-phpy, 4-phpy, 3-bnpy, 4- bnpy) is highly selective for G 7 with K G p1.1!10 4 to 2.8!10 4 , with the more hydrophobic Pyr ligands exhi- biting slightly higher binding. A strong dependence on ionic strength indicates that ion-pairing with DNA oc- curs prior to binding. At mp0.05, d[Ru II -DNA]/ dtpk[Ru II ][DNA], where kp0.17–0.21 M –1 s –1 with the various Pyr ligands. The air oxidation of [(py)(NH 3 ) 4 Ru II ] n -DNA to [(py)(NH 3 ) 4 Ru III ] n -DNA at pH 6 occurs with a pseudo-first-order rate constant of k obs p5.6!10 –4 s –1 at mp0.1, Tp25 7C. Strand cleav- age of plasmid DNA appears to occur by both Fenton/ Haber-Weiss chemistry and by base-catalyzed routes, some of which are independent of oxygen. Base-cata- lyzed cleavage is more efficient than O 2 activation at neutral pH and involves the disproportionation of cov- alently bound Ru III and, in the presence of O 2 , Ru- facilitated autoxidation to 8-oxoguanine. Dispropor- tionation of [py(NH 3 ) 4 Ru III ] n -DNA occurs according to the rate law: d[Ru II –G DNA ]/dtpk 0 [Ru III - –G DNA ]ck 1 [Ru III –G DNA ][OH – ], where k 0 p5.4!10 –4 s –1 and k 1 p8.8 M –1 s –1 at 25 7C, mp0.1. The appearance of [(Gua)(py)(NH 3 ) 4 Ru III ] under ar- gon, which occurs according to the rate law: d[Ru III –G]/dtpk 0 [Ru III –G DNA ]ck 1 [OH – ][Ru III - –G DNA ] (k 0 p5.74!10 –5 s –1 , k 1 p1.93!10 –2 M –1 s –1 at Tp25 7C, mp0.1), is consistent with lysis of the N-gly- cosidic bond by Ru IV -induced general acid hydrolysis. In air, the ratio of [Ru-8-OG]/[Ru-G] and their net rates of appearance are 1.7 at pH 11, 25 7C. Small amounts of phosphate glycolate indicate a minor oxida- tive pathway involving C4b of the sugar. In air, a dy- namic steady-state system arises in which reduction of Ru IV produces additional Ru II . Key words Ruthenium 7 DNA 7 N-glycolysis 7 Disproportionation 7 Cleavage Abbreviations Pyr: a generic pyridine ligand 7 py: pyridine 7 3-bnpy: 3-benzylpyridine 7 4-bnpy: 4-benzylpyridine 7 3-phpy: 3-phenylpyridine 7 4-phpy: 4-phenylpyridine 7 L: a purine ligand 7 G 7 : N7 of guanine 7 Guo: guanosine 7 Ino: inosine 7 dGuo: 2b-deoxyguanosine 7 Gua: guanine 7 9-MeGua: 9-methylguanine 7 8-OGua: 8-oxoguanine 7 Ino: inosine 7 Cyt: cytosine 7 Uri: uridine 7 Ado: adenosine 7 CT-DNA: calf thymus DNA 7 Tris: tris(hydroxymethyl)aminomethane 7 DTT: dithiothreitol 7 EDTA: ethylenediaminetetraacetic acid 7 BSTFA: bis(N,N-trimethylsilyl)- trifluoroacetamide Introduction Studies in a number of laboratories have produced a variety of ruthenium complexes that interact with nu- cleic acids in a number of ways [1, 2, 3, 4, 5]. Much of this research has focused on the antitumor activity of ruthenium amine and aromatic imine complexes that often bind fairly selectively to the N7 of guanine (G 7 ) on DNA [3, 6, 7, 8, 9, 10, 11, 12]. The presence of (NH 3 ) 5 Ru III at the N7 of purine nu- cleosides (Guo, dGuo, Ino) has long been known to lead to cleavage of the N-glycosidic bond by a general acid route [13]. Ruthenium(III) also assists autoxida- tion to 8-oxo nucleosides, in which the N-glycosidic bond would be expected to be susceptible to piperidine base hydrolysis and strand cleavage [14]. However, neither of these reactions is efficient at cleaving DNA