Conserved unpaired adenine residues are important for ordered structures of 5S ribosomal RNA. An infrared study of the secondary and tertiary structure of <em>Thermus thermophilus</em> 5S rRNA.

An improved set of infrared calibration spectra for the determination of G · C and A · U base pairs leads to 32 ± 3 G · C (+G · U) and 4 ± 1 A · U base pairs for Thermus thermophilus 5S RNA in the presence and absence of Mg²⁺. These results give further support for the consensus secondary structure of 5S RNA recently proposed by several groups. T thermophilus 5S RNA shows, in the presence of Mg²⁺, a distinct two-step thermal melting of its ordered structure. Based on new data about the stacking dependence of infrared intensities of unpaired ribonucleotides the spectral changes of the low-temperature transition should be explained by melting of stacked arrangements of unpaired bases and/or non-standard base pairs. Striking is the reduction in A stacking, which is not related to the melting of A · U base pairs, indicating the importance of the mostly conserved unpaired adenines for the Mg²⁺ stabilized higher-order structures especially within internal loops of 5S RNA. [ABSTRACT FROM AUTHOR]