Ribosomal 5.85 RNA is a component of the large (605) ribosomal subunit in eucaryotes. Studies of 5.85 rRNA in solution have shown that under certain conditions, including standard isolation procedures, the molecule complexes with itself to form dimers and higher multimers. Two models have been proposed in the literature to explain the intermolecular interactions responsible for 5.85 rRNA dimer formation. The terminal interaction model of Sitz et al. (Biochem. 17, 5811-5815, 1978) proposes that the dimer forms through base-pairing of the 5' and 3' terminal sequences of two 5.85 rRNA molecules. Pavlakis et al. (Nucl. Acids Res. 7, 2213-2237, 1978) showed that 5.85 rRNA lacking the 3' terminal region was capable of forming dimer. They proposed an alternative model for 5.85 rRNA dimer formation in which an entirely different part of the molecule interacts to form a double-stranded palindrome.

In this study, enzymatic probing techniques and stability measurements (both experimental and theoretical) were used to determine which model most accurately describes the intermolecular interactions of the 5.88 rRNA dimer. The methods used for determining stability were not able to discriminate between the models for 5.88 rRNA dimer formation. Results from the structural probing studies, however, support the terminal interaction model and indicate that the palindrome interaction does not occur in 5.88 rRNA dimer formed from the intact molecule.