= RNA dimer
{c}
An <RNA dimer> is a complex containing two associated <RNA> molecules. The two strands can have identical or different <nucleotide sequences>, and they need not form one completely paired duplex. Association joins molecular partners; it is different from joining their backbones into one longer covalent <RNA> strand.
For an original count, two 27-<nucleotide> strands contain 54 residues altogether. They remain two <RNA> molecules in a dimer even if much of their <base pairing> is intermolecular. One continuous 54-residue strand with an intramolecular <stem-loop> has the same total residue count but a different connectivity. Strand count and <RNA secondary structure> are separate specifications.
A primary experiment used a 79-<nucleotide> <RNA> that gave two bands in native <polyacrylamide gel electrophoresis> but one band under denaturing conditions. That observation suggested alternative assemblies, but a second method was needed to test their molecular sizes. <Sedimentation equilibrium> measurements at 20,000 rpm used <DNA> standards of known size. Samples containing two native-gel bands had an apparent average molecular mass $1.6\pm0.15$ times the monomer mass, compared with $1.1\pm0.1$ for a preparation giving one native band. The combined evidence supported monomer and dimer assignments.<Conversion of stable RNA hairpin to a metastable dimer in frozen solution by Xueguang Sun and others>[Results, native gels and Sedimentation equilibrium studies.]{ref}
The study also located an important 21-residue association segment and showed preparation-history effects. Heating and cooling could change the observed assembly, and some dimer states were kinetically trapped.<Conversion of stable RNA hairpin to a metastable dimer in frozen solution by Xueguang Sun and others>[Abstract and Results,21-nucleotide segment and transition reversibility.]{ref} Thus two bands are not automatically two sequence lengths, and one predicted low-energy duplex is not sufficient experimental proof of an <RNA dimer>.
For a reversible self-complementary duplex, <self-complementary RNA duplex population> provides a quantitative two-species model. More complicated contacts, competing folds or <RNA melting hysteresis> require corresponding experimental and kinetic tests.
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