Transition metal complexes as probes of DNA sequence-dependent structure

Citation

Campisi, Donna (1996) Transition metal complexes as probes of DNA sequence-dependent structure. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/kay4-sz63. https://resolver.caltech.edu/CaltechETD:etd-09082006-114255

Abstract

Different transition metal complexes have been applied in probing variations in the structure of double helical DNA. The following probes, which all bind DNA noncovalently, have been utilized: Ru(phen)3(2)+, Ru(TMP)3(2)+, Rh(phen)2phi3+, Rh(TMP)2phi3+, Rh(dmbpy)2phi3+, Ru(phen)2dppz2+, Ru(bpy)2dppz2+, and Rh(bpy)2dppz3+ (phen = 1,10 phenanthroline; TMP = 3,4,7,8,-tetramethyl- 1,10-phenanthroline; phi = 9,10-phenanthrenequinone diimine; dmbpy = 5,5'-dimethylbipyridyl; bpy = bipyridyl; dppz = dipyrido[3,2-a;2',3'-c]phenazine). The local structure recognized by [Delta]-Rh(phen)2phi3+ has been defined by comparisons of photocleavage data on crystallographically characterized oligonucleotides with their structural parameters. A quantitative correlation has been determined between [Delta]-Rh(phen)2phi3+ photocleavage and extent of openness in the major groove due to differential propeller twisting, or interpurine angle. Therefore, [Delta]-Rh(phen)2phi3+ has been developed as a probe of DNA propeller twisting in solution. Differences in reaction pathway partitioning between enantiomers of Rh(phen)2phi3+ are attributed to differing extent of shape complementarity with DNA binding sites. Rh(TMP)2phi3+ has been explored in probing DNA mismatches in solution. Both [Delta]-Rh(phen)2phi3+ and Rh(TMP)2phi3+ sensitively mark local structural perturbations in an oligonucleotide, arising from substitution of a CG base pair with TG and AG mismatches. Rh(phen)2phi3+ and Ru(TMP)3(2) have also been applied in probing structural variations in the context of a long DNA strand. A C7 stretch is targeted by Ru(TMP)3(2), an A DNA probe and Rh(phen)2phi3+, a B DNA probe. These results indicate this sequence is heteronomous, containing wide major and minor grooves. [Delta]- and [Lambda]-Rh(phen)2phi3+ also discriminate structural differences between bent and nonbent DNA fragments. Variations in metal complex-DNA interactions have also been examined by a gel electrophoretic mobility assay. Intercalator size, hydrophobicity of ancillary ligands, metal complex charge, and chirality all influence the extent of DNA retardation. Taken together, these studies demonstrate that transition metal complexes can be profitably and uniquely applied towards exploring DNA structural heterogeneity.

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