Chemical Snapshots of DNA
Chemical probes of DNA structure have proved to be complementary to high-resolution structural methods, like X-ray crystallography and NMR spectroscopy, for determining details of DNA structure in solution. I will discuss in this lecture our use of the hydroxyl radical to acquire structural information on DNA and DNA-protein complexes. The hydroxyl radical has the advantages of small size, high reactivity, and ease of generation by simple metal-based redox chemistry. These advantages have led to its use in a wide variety of experimental systems. Recent deuterium kinetic isotope effect experiments from my laboratory1 have begun to give us a clearer idea of how to interpret the "chemical images" of DNA structure that are embodied in hydroxyl radical cleavage patterns. We concluded from these experiments that the solvent-accessible surface area of a hydrogen atom in a deoxyribose residue in the backbone of DNA governs its reactivity with the hydroxyl radical. Our picture is therefore of a "reactive water molecule" (the hydroxyl radical) which by its ability to cleave the DNA strand gives us information on the shape of the surface of DNA in solution. We have found that the hydroxyl radical cleavage pattern is distinctive for different local structural features in DNA, and is particularly striking for bent A-tract DNA2. In my lecture I will summarize our recent mechanistic studies on hydroxyl radical reactivity with DNA, and then show how we can use these results and ideas to develop a chemical picture of the structure of DNA and DNA-protein complexes in solution.
1. B. Balasubramanian, W. K. Pogozelski and T. D. Tullius, "DNA Strand Breaking by the Hydroxyl Radical is Governed by the Accessible Surface Areas of the Hydrogen Atoms of the DNA Backbone," Proc. Natl. Acad. Sci. (USA) 95, 9738-9743 (1998).
Department of Chemistry, Boston University,