Chromomycin dimer-DNA oligomer complexes. Sequence selectivity and divalent cation specificity

This paper reports on a solution NMR characterization of the sequence selectivity and metal ion specificity in chromomycin-DNA oligomer complexes in the presence of divalent cations. The sequence selectivity studies have focused on chromomycin complexes with the self-complementary d(A1-A2-G3-G4-C5-C6-T7-T8) duplex containing a pair of adjacent (G3-G4)·(C5-C6) steps and the self-complementary d(A1-G2-G3-A4-T5-C6-C7-T8) duplex containing a pair of separated (G2-G3)·(C6-C7) steps in aqueous solution. The observed intermolecular NOEs establish that chromomycin binds as a Mg(II)-coordinated dimer [1 Mg(II) per complex] and contacts the minor-groove edge with retention of 2-fold symmetry centered about the (G3-G4-C5-C6)·(G3-G4-C5-C6) segment of the d(A2G2C2T2) duplex. By contrast, complex formation is centered about the (G2-G3-A4-T5)·(A4-T5-C6-C7) segment and results in removal of the two fold symmetry of the d(AG2ATC2T) duplex. These observations suggest a hierarchy of chromomycin binding sites, with a strong site detected at the (G-G) step due to the hydrogen-bonding potential of acceptor N3 and donor NH2 groups of guanosine that line the minor groove. The authors have measured the real-time proton to deuterium exchange kinetics of the aglycon C8-hydroxyl proton in the symmetric chromomycin-d-(A2G2C2T2) complex after dissolution in D2O solution. The hydrogen exchange lifetimes in the absence of added catalysts decreases in the order NI(II) much-gt Mg(II) > Zn(II) > Cd(II) complexes. These results establish that the divalent cation exchange does not occur through direct penetration of the cation into the complex but rather following dissociation of the divalent cation coordinated chromomycin dimer from its duplex binding site