Conformational comparisons among homologous bony fish 5S ribosomal RNAs

The reversible thermal melting of homologous 5S ribosomal RNAs of three bony fishes, rainbow trout (Salmo gairdneri), carp (Cyprinus carpio), and dog salmon (Onchorhynchus keta), were compared in aqueous salts (sodium chloride and/or divalent metal chlorides) by means of differential optical absorption at 260 and 280 nm, and c.d. at 265 nm. The melting parameters of the multiphasic melting process were conserved among the homologous RNAs, and it was shown that they did not depend on the methods of measurement but on concentrations of [Na+] and of [metal2+]. Other physicochemical methods, such as FT-IR absorption, gave the same melting profiles as the u.v. methods. The c.d. spectrum was homologous among the ribosomal RNAs. The melting is explained by changes in local structures in the 'consensus secondary structure model'. Also, stabilization of the secondary and tertiary structures by binding of Mg2+ and Ca2+, and the catalysed hydrolysis of the main chains by various divalent ions are discussed.