Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker

A GAAA tetraloop domain and receptor domain are connected by a single-strander A7 linker to investigate the metal ion dependence, kinetics and thermodynamics for the isolated tertiary interaction in RNA of the GAAA-tetraloop motif. Studies of docking induced using a variety of metal ions show that the single-stranded region functions primarily as a flexible tether and inhibition of docking by oligonucleotides complementary to the linker is investigated.