Synthesis of oligonucleotides containing a new azobenzene fragment with efficient photoisomerizability

The azobenzene derivatives possessing substituents of ROCH2CH2O- and-CH2CH2OR' or -CONHCH2CH2OR' at p,p'-positions, where R and R' are 4,4'-dimethoxytrityl and 2-cyanoethyl-N,N'-diisopropylphophoramidite, have been synthesized for linking two oligonucelotide segments. It has been found that the azobenzene linkers efficiently undergo trans-cis isomerization by exposing to UV light. The conversion efficiency showed slight dependence on structure or conformation of oligonucleotides attached to the azobenzene chromophore. The cis-form of the azobenzene in oligonucleotides was sufficiently stable at low temperature under dark. The present findings would open the way for light switch of nucleic acid structures.