R. Kierzek et al., 5'-AMINO PYRENE PROVIDES A SENSITIVE, NONPERTURBING FLUORESCENT-PROBEOF RNA SECONDARY AND TERTIARY STRUCTURE FORMATION, Journal of the American Chemical Society, 115(12), 1993, pp. 4985-4992
Blocked phosphoramidites of 5'-amino-5'-deoxycytidine and 5'-amino-5'-
deoxyuridine have been prepared and coupled to the 5'-end of oligoribo
nucleotides. 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. Thes
e 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 t
ertiary 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.