Dimerization of Double-Stranded RNA Possessing a 3′-Overhanging Single-Stranded End

Abstract

A simple system derived from the acceptor stem of tRNA^Ala is presented which undergoes a pH-dependent dimerization. This is brought about by formation of C⁺-G-C base triples of the pyrimidine motif type between protonated cytidines of the 3′ single-stranded end and regularly paired G-C pairs in the double-helical stem. In addition, an unusual interaction between a protonated adenine and a regular G-C pair is suggested. The equilibrium between monomer and dimer forms can be monitored via NMR spectroscopy and UV melting curve analysis. A dimerization enthalpy of 159 kJ mol⁻¹ was found at pH 5.0. The system could serve as a model for inter- and intra-molecular association, repectively, of single-stranded and double-helical regions to enable optimal packing of large RNA molecules.