Efficient quenching of the excimer fluorescence derived from pyrene arrays on RNA duplexes

We studied the RNA oligomers having pyrenylmethyl substituents at the 2'-O-sugar residues. It has been shown that the pyrene-modified RNAs can form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism spectra revealed that the multiply incorporated pyrenes are projected toward the outside of RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence. In the present work, we carried out the fluorescence quenching of the excimer derived from the pyrene-arrays assembled on RNA duplexes in order to evaluate the mobility of the exciton along the pyrene array.