Pyrene derivatives as fluorescent probes of conformation near the 3′ termini of polyribonucleotides

When pyrene butyric acid hydrazide or pyrene acetic acid hydrazide is attached to single‐strand RNA 3′ termini a red shift in absorbance and substantial hypochromicity are observed. A strong induced CD is seen and the fluorescence intensity is quenched by an order of magnitude. In double‐stranded samples, a further 10‐fold quenching of fluorescence is seen. Several lines of evidence suggest that the residual fluorescence of pyrene butyric acid hydrazide‐duplex conjugates arises from a minor species. The most likely possibility is dye reacted at a site other than the 3′ end. Some indication exists that 3′‐attached pyrene may perturb the relative stability of nearby duplex. Within the limits of this reservation, it appears that 3′‐pyrene conjugates may be rather useful for detecting the existence of duplex regions accessible to a dye at the 3′ end of complex RNAs.