RNA containing pyrrolocytidine base analogs: good binding affinity and fluorescence that responds to hybridization

Abstract

6-Phenylpyrrolocytidine and 6-methoxymethylene-pyrrolocytidine are base-modified nucleosides with remarkable fluorescence properties. When incorporated into RNA, these analogs enhance binding affinity towards RNA and DNA targets with a concomitant change in their fluorescence upon duplex formation. The fluorescence response depends on the nature of the 6-substituent and the sequence position of the modified nucleoside. The fluorescence response of these structurally conservative, well-tolerated fluorescent nucleosides may be exploited as probes in the study of nucleic acid processing enzymes.