Isolation and identification of cross-links from formaldehyde-treated nucleic acids

Cross-linked nucleosides have been isolated from formaldehyde-treated ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) by using reverse-phase high-pressure liquid chromatography. Methylene-bridged products containing cytosine, as well as the purines, have been isolated. A combination of ultraviolet and nuclear magnetic resonance (NMR) spectra, pKa values, hydrolysis, and reduction has been used to establish that the cross-links connect the amino groups of the nucleosides involved. For example, the 6-amino functions of two adenosine residues are linked by a methylene bridge to produce a compound which, when dissolved in deuterated dimethyl sulfoxide, displays 11 unsplit resonances in its proton-decoupled 13C NMR spectrum. The procedure reported here is more rapid and less laborious than an earlier one recommended by us for the isolation of cross-linked products from DNA [Dubelman, S., & Shapiro, R. (1977) Nucleic Acids Res. 4, 1815-1827]. This new approach may be of value in the study of other types of cross-linking reactions involving nucleic acids.