5'-AMINO PYRENE PROVIDES A SENSITIVE, NONPERTURBING FLUORESCENT-PROBE OF RNA SECONDARY AND TERTIARY STRUCTURE FORMATION

Blocked phosphoramidites of 5'-amino-5'-deoxycytidine and 5'-amino-5'-deoxyuridine have been prepared and coupled to the 5'-end of oligoribonucleotides. These 5'-amino RNA oligomers may be readily conjugated to a variety of commercially available amine reactive fluorescent dyes, including succinimidyl ester derivatives. The synthesis, purification, and properties of 5'-pyrene-labeled RNA oligomers are described. These oligomers are shown to be unusually attractive probes for studies of oligomer-oligomer and oligomer-ribozyme interactions. In particular, 5'-pyrene oligomers are stable and very sensitive to environment while having minimal perturbations on the thermodynamics of secondary and tertiary structure formation in RNA. Thus the 5'-positioning of pyrene with a short linker appears to provide an ideal probe for the binding and dynamics of RNA substrates.