Title

Recognition, binding, and cleavage of DNA by anthracene derivatives and heme proteins

Date of Completion

January 2000

Keywords

Chemistry, Biochemistry

Degree

Ph.D.

Abstract

The design of molecules that can bind to specific sites or sequences of DNA is important in the area of drug development, molecular biology, and biotechnology. Understanding how specific functional groups on these molecules affect their DNA recognition and binding is a crucial step in the development of these. The interactions of several substituted anthracenes with calf thymus DNA and deoxypolynucleotides were investigated using various spectroscopic techniques. Branching and cationic substitutions on the 9 and 10 positions of anthracene affect the binding affinity and orientation of the probes to DNA. As the substitutions become more branched on both the 9 and 10 positions of anthracene, intercalation into the DNA helix becomes less favored. ^ The anthracene derivatives can be activated by light and induce cleavage of DNA. Irradiation of a mixture of plasmid pUC18 and the anthracene derivatives at 350–400 nm converts supercoiled pUC18 to nicked circular form indicating the cleavage of the sugar-phosphate backbone. Addition of cobalt(III) hexammine chloride (CoHA) improves the efficiency of DNA cleavage by 9-anthryl methyl ammonium chloride (AMAC). Sequencing studies reveal that DNA cleavage by AMAC and CoHA prefer a 5-TCC-3 sites. This preference may be due to the longer lifetime of the anthracene chromophore in AT sequences and the more favored oxidation at 5-GG-3 sequences. Laser flash photolysis studies of a mixture of AMAC and CoHA indicate the formation of a cation radical and this may be responsible for the DNA cleavage. ^ The study is extended to examine the interaction of larger molecules such as heme proteins with DNA. Myoglobin, hemoglobin, and cytochrome c show an affinity for DNA. The Fe(III) in the heme group of these proteins can be oxidized to the reactive Fe(IV)-oxo form by the addition of hydrogen peroxide and in the presence of DNA is reduced back to Fe(III). The cleavage of supercoiled pUC18 by these heme proteins are revealed in gel electrophoresis experiments. The cleavage mechanism may involve a combination of hydroxyl radical chemistry and the oxidative chemistry involving the high oxidation state iron. ^