DNA Footprinting with the Hydroxyl Radical

Abstract

The Fenton reaction of iron(II) EDTA with hydrgen peroxide, performed in the presence of ascorbateion. has proven to be useful as a probe of structure in DNA systems. Two aspects of this chemistry are discussed: the identity of the active DNA cleaving agent produced by this reagent, and the application of the Fenton reaction to the determination of the structure of the Holliday junction, the four-stranded DNA molecule that is a key intermediate in recombination. The cleavage pattern of the Holliday junction has pseudo-twofold symmetry, putting important constraints on possible structures.

Key Words:

• Iron(II) EDTA
• DNA structure
• gamma radiation
• Holliday junction
• hydroxyl radical.