Monday, June 30, 2008 - 1:30 PM
Diamond I (Sheraton Burlington Hotel and Conference Center)
116

Chemical Models of DNA Binding Based on Ruthenium Compounds with Organic Side Chains

Samantha Glazier, Stephanie Walter, and Kristin Berretta. St. Lawrence University, Canton, NY

Charge, extended pi structures, shape, size, and water solubility are examples of the chemical features affecting the properties of DNA binding important to drug design. A new series of model complexes, [Ru(phen)2bpy-L-R]2+ where phen= 1,10-phenanthroline, bpy= 2,2'-bipyridine, L = organic chain of variable length, and R = conjugated ring, possess chemical features correlated with effective interactions with DNA. The ligands, bpy-L-R = 4-(4-butyl ether-methylnaphthal)-4'-methyl-bpy and 4-methoxy methylnaphthal-4'-methyl-bpy, were obtained. Two synthetic approaches were employed. First, an indirect synthetic method introduced an acetal protecting group on the end of a hydrocarbon chain during a LDA reaction, a subsequent deprotection step to an aldehyde, and finally a reduction 4-(4-hydroxybutyl)-4'-methyl-bpy with NaBH4 in 55% yield. Second, 4,4'-dimethyl-2,2'-bipyridine is reacted with SeO2 to yield an aldehyde, 4-formyl-4'-methyl-bpy, which was reduced as before to obtain the bpy-alcohol, 4-hydroxymethyl-4'methyl-bpy in 38% yield. The indirect and selenium approaches both employed a Williamson ether synthesis to attach a naphthalene R group. The reaction is initiated by reaction of the alcohol and sodium metal to create an alkoxide, which then attacks an aromatic alkyl halide to form the final substituted bipyridine product. Naphthalene was chosen because it is commercially available and has a planar, aromatic structure important for intercalative DNA binding. Initial DNA binding studies using a fluorescence titration method of CT DNA with [Ru(phen)2(4-methoxy methylnaphthal-4'-methyl-bpy)](PF6)2 showed that the complex binds to DNA non-cooperatively with a binding constant of 1.64x106 M-1 and a binding site size of 2.76. The phenanthroline co-ligand was chosen to promote initial groove binding of the complex, so that the organic side chain will be in close proximity to the hydrophobic base pair region of DNA. The control, [Ru(phen)3](H2O), proved that the tethered ligand participates in the binding mechanism. Modifications to the organic side chain and R group are the immediate targets of future work.