Recognition of Base Mismatches in DNA by Chrysenequinone Diimine Intercalators of Rhodium (III)

Author: Jackson, Brian Anthony

Year: 1999

Degree: Dissertation (Ph.D.)

Advisor: Barton, Jacqueline K.

Committee Members: Parker, Carl Stevens; Barton, Jacqueline K.; Bercaw, John E.; Imperiali, Barbara

Option: Chemistry

DOI: 10.7907/xkpd-qa72

Abstract

The ability to recognize base mismatches in DNA is of interest both for application to the molecular diagnosis of genetic mutations and for the design of chemotherapeutic agents for diseases associated with failure of cellular mismatch repair. The design and synthesis of a family of transition metal complexes containing the novel chrysenequinone diimine (chrysi) intercalating ligand is described. This sterically bulky intercalating ligand was designed to preferentially bind to the destabilized regions of DNA introduced by most base mismatches. One such compound, bis 2,2'-bipyridine chrysenequinone diimine rhodium(III) ([Rh(bpy)2(chrysi)]3+), has been shown to be a broadly specific mismatch recognition agent which binds and, upon photo-activation, cleaves DNA at or near 82% of the 128 possible three base pair DNA sequences containing a central mismatched base. The cleavage of DNA at individual sites has been shown to be broadly correlated with the helix destabilization caused by the mismatch although it is clear that many factors can affect both the binding affinity and efficiency of its photocleavage chemistry from site to site.

[Rh(bpy)2(chrysi)]3+ has also been demonstrated to be exquisitely specific. Binding constants at some mismatch sites were found to be as high as 2 x 107 M-1 compared to an association constant of 4 x 104 M-1 to B-form DNA. This level of specificity was sufficient to allow discrimination of a single base mismatch in a 2725 base pair plasmid heteroduplex. The study of these compounds also led to the discovery that some mono-quinone diimine complexes of rhodium(III) can photocatalytically cleave DNA when irradiated with visible light. Such a property could be advantageous in the design of photodynamic therapy agents based on these compounds. Preliminary experiments and progress towards the elucidation of the mechanism of this photocatalytic cleavage is also described.

In addition to the application of chrysi complexes to mismatch recognition, novel methods for the synthesis of these compounds based on the condensation of aromatic quinones with ammine ligands on rhodium(III) are also reported. Methodology for the quantitative measurement of thermodynamic binding constants for molecules which bind and cleave nucleic acids are also discussed.

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