Study of RNA structure by pyrene-labeled oligonucleotides.

Fluorescent-labeled oligonucleotides containing 2'-(1-pyrenylmethyl) uridine (Upy) that have G or C adjacent to 3'-site of Upy, I and II, respectively, showed a remarkable increase in the emission intensity when they hybridized with the complementary oligoribonucleotides (ORN). However such change was not observed when they hybridized with the complementary oligodeoxyribonucleotides(ODN). Tm values derived from the UV melting curves for I-ORN and II-ORN duplexes were 5 degrees C and 10 degrees C lower than the normal duplexes without Upy, respectively. The intensity of induced CD based on the pyrene groups for the I-ORN and II-ORN duplexes were a half of that for the corresponding I-ODN and II-ODN duplexes. These results suggest that pyrene groups were released from the stacking interaction upon duplex formation and that the remarkable change of emission intensity was then occurred. Based on these properties, it is suggested that Upy-probes that have G or C adjacent to 3'-site of Upy can be useful to search the single strand region of RNA.