Free radicals and DNA structural analysis

For a variety of purposes, procedures have been described to ascertain the nature of the complexes between regulatory proteins and DNA. An early approach was to form a complex between the DNA and the protein and then to subject this complex to digestion with deoxyribonuclease I. The particular region of DNA in specific contact with the protein is protected by the latter from enzymic digestion (see Kadona- 

These footprinting analyses, based on enzymic and chemical digestion, are now widely used to define DNA (and RNA) and their complexes with various ligands. Recently active radical probes have been used as footprinting agents in protection assays in a variety of systems (e.g., Tullius and Dombroski, 1986 Chalepakis and Beato, 1989 Hayes and Tullius, 1989 Schickor et al., 1990). Such probes rely on active radical intermediates, most likely hydroxyl radicals, released by Fe(II) in the presence of an electron donor, probably via a Fenton reaction. In addition, hydroxyl radicals also appear to react with DNA in a conformation-specific manner which may allow some prediction of DNA secondary structure (see Burkhoft and Tullius, 1987 Zorbas et al., 1989 Lu et al., 1990). 

5 -dithiobis(2-nitrobenzoic acid) (DTNB) (Sigma Chemical Co.) 

Altex Analytic columns (Hichrom) Carbohydrate Analysis Column (Waters Associates) 

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