Method for Preparing New Flavin Derivatives:  Synthesis of Flavin−Thymine Nucleotides and Flavin−Oligonucleotide Adducts

In order to link to the 5‘-end of oligonucleotides the flavin analogs 9a,b possessing only one terminal hydroxy group on the side chain, the phosphoramidite and the H-phosphonate coupling methods were developed. Surprisingly, after reaction of compounds 9a,b with 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, the flavin phosphoramidates 11a,b were isolated instead of the expected phosphoramidite derivatives 10a,b. A very efficient photooxidation process occurred probably during the isolation of the products. From the prepared flavin H-phosphonates 12a,b, flavin−thymine nucleotides and flavin−oligonucleotide adducts were synthesized for the first time. The versatility of the method was demonstrated in the oxidation step with the synthesis of the flavin−thymine nucleotides 1517 possessing a phosphodiester, a phosphorothioate, and a methyl phosphate linkage, respectively. This method is of general interest with regard to the extensive research developed for preparing flavin analogs and modified oligonucleotides possessing interesting biological or/and catalytic properties.