Abstract Band splitting and/or bands shifting in opposite directions due to coupling of vibrations of neighboring groups observed in the infrared spectra of tRNA Phe and 23 S RNA give information on the secondary structure. The base pairing, dependent on temperature, is investigated, discussing coupling effects with the base residues' vibrations in the region 1700-1500 cm −1. The secondary structure of the backbone is studied, discussing coupling effects with vibrations in the region 1300-1000 cm −1. The 2′OH groups are cross-linked with the O atoms of the neighboring ribose residues via hydrogen bonds. Probably the >PO − 2 groups are turned inward at the backbone, i.e. towards the base residues. The base pairs as well as the secondary structure of the backbone melt with increasing temperature and with dialysis against distilled water. The comparison of the Mg 2+ and the K + salts of the tRNA Phe shows that the changes of base pairing due to Mg 2+ are small. At the backbone, however, Mg 2+ favor somewhat more the discussed secondary structure than K + does. All Mg 2+ effects on secondary structure are, however, too small to explain the considerable increase in melting temperature due to Mg 2+. Thus it is supposed that the rise in the melting temperature due to Mg 2+ is not caused by a change in secondary but in the tertiary structure of tRNA Phe. Furthermore, the influence of Mg 2+ on the secondary structure of 23 S RNA is studied. The following results are obtained: (1) The double helical regions become more compact and probably increase due to the influence of Mg 2+. (2) At the backbone, Mg 2+ induces strong hydrogen bonding between the 2′OH groups and the ether O atoms of neighboring ribose residues. Probably they turn the >PO − 2 groups toward the base residues, i.e., inward at the backbone. Schulte, Morrison and Garrett found that a critical level of Mg 2+ is required for binding certain proteins to rRNA (Biochemistry (1974) 13, 1032). Thus the observed conformation is probably necessary for binding these proteins.