A correlation between the secondary structure of DNA and the reactivity of adenine residues with chloroacetaldehyde

Abstract

The rate of reaction of chloroacetaldehyde (0.039 M) with the "free" adenine residue in deoxyadenosine-5'-phosphate (dAMP) at pH 6.5 has been found to be nearly equal to that at pH 4.5. Practically 100% of the adenine is converted to a fluorescent product (epsilon-adenine residue) on incubation for 60 h at 37 degrees C and pH 6.5. Of the adenine residues in "single-stranded" DNA, however, only 14% react with chloroacetaldehyde (0.039 M) under the same incubation conditions. The reaction rate of this 14% is nearly equal to that of dAMP, but the fluorescence of the product is appreciably quenched; the quantum yield is only 0.45 times that of the "free" adenine residue. In "double-helical" DNA, on the other hand, no adenine residue has been found to react with chloracetaldehyde. Possible application of these findings to structural studies of DNA is suggested.