Site-Specific Photomodification of Single-Stranded DNA Targets by Arylazide and Perfluoroarylazide Derivatives of Oligonucleotides

Abstract

Highly efficient site-specific photomodification of single-stranded DNA targets was achieved with oligonucleotide reagents bearing aromatic azido groups (R (R¹ = p-azidotetrafluorobenzoyl, R² = 2-nitro-5-azidobenzoyl, R³ = p-azidobenzoyl) at either the terminal phosphate or at the C5 position of deoxyuridine at the end or inside of the oligonucleotide chain. The extent of modification strongly depends on the reagent type. It does not exceed 5% in the case of the reagent with R³. It was 25%–50% and 60%–70% for the reagents with R2 and R1 depending on the target structure. The reagent with perfluoroarylazido group R¹ appeared to be most efficient. The extent of covalent adduct formation amounts to 70% for all reagents bearing a perfluoroarylazide group at the end of the oligonucleotide chain, independently of whether it was attached to the 3‵- or 5‵-phosphate or to the C5 of deoxyuridine. The reagents with the reactive group within the chain provided fewer cross-links (50%–55%). The reagents with R¹ and R² were found to be sensitive to the nucleotide structure of the target. Guanine and cytosine residues were modified preferentially when adjacent to the R¹ or R² group of the reagent, respectively.