Full details of the template-directed covalent cross-linking of duplex oligodeoxynucleotides are presented. 4-Thio-2'-deoxyuridine was incorporated synthetically into a 17mer oligodeoxynucleotide, and the thiocarbonyl group of the modified base was alkylated with a variety of alpha-bromoacetyl-derivatized diamines. Covalent cross-linking was initiated by annealing the electrophilic probe oligomers with their complementary sequences, where a dG base was targeted at the position complementary to the modified 4-thio-2'-deoxyuridine. The sequence selectivity of cross-link formation as a function of tether topology and rigidity was examined, and the thermal stability of the modified duplexes was measured by UV melting experiments.

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A method for the introduction of depurinated lesions in DNA is described, and is based on the formation of a covalent cross-link between an antisense oligonucleotide probe and the target DNA sequence followed by an unexpectedly mild thermal depurination.

Irradiation of 2‐ethyl‐3‐methyl‐4‐pyrone 3 in aqueous solution led to the formation of trans‐4‐ethyl‐5‐methy‐4,5‐dihydroxycyclopent‐2‐enone 4 and trans‐2‐methyl‐3‐ethyl‐4,5‐dihydroxycyclopent‐2‐enone 5. In the latter case 1H nmr analysis confirmed the trans‐configuration at C4 and C5. These results are consistent with trapping of a photochemically generated oxabicyclohexenyl zwitterion by nucleophilic attack of both sides of the oxyally system along a path anti to the epoxide ring.