RNA dimer

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 $1.6\pm 0.15$ times the monomer mass, compared with $1.1\pm 0.1$ for a preparation giving one native band. The combined evidence supported monomer and dimer assignments.^[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.^[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.