Synthesis of DNA Duplexes Containing Site-Specific Interstrand Cross-Links via Sequential Reductive Amination Reactions Involving Diamine Linkers and Abasic Sites on Complementary Oligodeoxynucleotides

Interstrand DNA cross-links are important in biology, medicinal chemistry, and materials science. Methods for the targeted installation of interstrand cross-links in DNA duplexes may be useful in diverse fields including studies of DNA repair, materials science, and structural biology. Here a simple procedure is reported for the preparation of DNA duplexes containing site-specific, chemically-defined interstrand cross-links. The approach involves sequential reductive amination reactions between diamine linkers and two abasic (apurinic/apyrimidinic, AP) sites on complementary oligodeoxynucleotides. Use of the symmetrical triamine, tris(2-aminoethyl)amine, in this reaction sequence enabled preparation of a cross-linked DNA duplex bearing a derivatizable aminoethyl group.