Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides

Abstract Pyrrolo-dC ( 1a , 6-methyl-3-(2-deoxy-β- d -ribofuranosyl)-3 H -pyrrolo[2,3- d ]pyrimidin-2-one) and its cyanoethyl phosphoramidite 2a were synthesized. The latter was incorporated into oligodeoxyribonucleotides by standard automated synthesis techniques, where pyrrolo-dC was found to serve as a fluorescent analog of deoxycytidine. The cyanoethylphosphoramidite ( 2b ) of pyrrolo-C ( 2a , 6-methyl-3-(β- d -ribofuranosyl)-3 H -pyrrolo[2,3- d ]pyrimidin-2-one) was also synthesized and may find use for the site-specific incorporation of a fluorescent cytidine analog into oligoribonucleotides.