Sequence-Specific Photomodification of Single-Stranded and Double-Stranded DNA Fragments by Oligonucleotide Perfluoroarylazide Derivative

Abstract

A highly efficient, sequence-specific photomodification of single-stranded (ss) and double-stranded (ds) DNA fragments was carried out with a hexadecathymidilate derivative, R ~ p(T)₁₆ (R-perfluoroarylazido group), using 27-base pair DNA fragments as a target. The main points of modification were G7 and G24 of the A-rich strand of the ss target and G7 and G22 of the A-rich and T-rich strands, respectively, for the ds target. The extent of photomodification was 60%–77% for ss DNA and 10%–53% for ds DNA depending on the reaction conditions. Photomodification increased in buffer with a high ionic strength (1.0 M) and at low temperature (4°C) when presumably the triplexes were more stable.