A series of 9,lO-phenanthrenequinone diimine (phi) complexes of rhodium have been prepared so as to systematically explore contributions of hydrogen bonding and van der Waals interactions to DNA site specificity. The novel, synthetic complexes A-and A-[Rh(en)2phiI3+ (2), as well as the analogs [Rh(NH3)4phi]3+ (l), [Rh( [ 12]aneN4)-phi]3+ (3), and [Rh ([ 12]aneS4)phiI3+ (4) (en = ethylenediamine, [ 12]aneN4 = 1,4,7,1O-tetraazacyclodcdecane, [ 121-aneS4 = 1,4,7,1O-tetrathiacyclododecane) bind in the major groove of DNA via intercalation and promote DNA strand cleavage upon activation with UV light. Complexes 1, A-2, and 3, all of which contain axial amines, display a high sequence preference for 5'-GC-3' steps which is not observed for 4. The 5'-GC-3' preference is attributed to the hydrogen-bonding interactions between the amine ligands and the guanine 0 6 atoms in the major groove. Complex 4, which lacks hydrogen bond donating groups in the axial positions, shows instead a high degree of specificity for a S-ATG-3'site which is best explained by shape selection. 8-2 cleaves DNA with lower sequence selectivity but cleaves enantioselectively at 5'-TX-3' steps. Photocleavage of an oligonucleotide containing the substitution of 5'-UA-3' for 5'-TA-3' shows no similar enantioselectivity, and hence chiral recognition of the 5'-TA-3' step is attributed to van der Waals interactions between the methylene groups of the A-isomer and the thymine methyl groups in the major groove of DNA. These results provide a first example of binding and photoactivated cleavage using saturated amines and macrocyclic thioethers as ancillary ligands in DNA recognition by metallointercalators and illustrate how discrete elements of molecular recognition may direct specificity for a DNA site.
Molybdocenes form monomeric and dimeric complexes upon dissolution in water. The solution structures of the molybdocenes at neutral pH are inferred as the monomeric [(CpR) 2 Mo(OH 2 )(OH)] + and the dimeric [(CpR) 2 Mo(µ-OH) 2 Mo(CpR) 2 ] 2+ . The equilibrium constants for the monomer-dimer equilibria were obtained from 1 H NMR dilution studies as K′ eq ) (7.9 × 10 -2 ) ( (1.0 × 10 -3 ) M for R ) CH 3 at pD 7 and as K eq ) (3.5 × 10 -2 ) ( (1.3 × 10 -3 ) M for R ) H at pD 3.5. Qualitatively, the monomer of the CpMe molybdocene is more favored than the Cp analogue, compared to their respective dimers.
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