Chapter 7: The Structure and Folding of Helical Junctions in RNA

Helical junctions are discontinuities in a double-stranded nucleic acid, where a number of helices are connected through the covalent continuity of their strands. RNA can be viewed as double-helical segments that are connected by junctions. Junctions are very common structural elements in natural RNA species, affecting the trajectory of helices, mediating long range tertiary interactions and stabilizing medium-sized RNA species. Most natural junctions have formally-single stranded regions that connect the helical segments. Perfect four-way junctions (4H) exist, but many four-way junctions have single-stranded connecting sections. Three-way junctions almost always have at least one single-stranded section between helices. Pairwise coaxial stacking is a major driving force for the folding of helical junctions, and occurs in the majority of cases. Most have at least one pair of stacked helices; in the case of four-way junctions there are usually two stacked pairs. Two or more stacking conformers are usually possible, but the lowest free energy form normally places the fewest connecting nucleotides onto continuous strands. Single molecule experiments reveal interconversion of conformers. Other interconversions are also observed, such as between antiparallel and parallel conformations of 4H RNA junctions. These processes may provide flexibility during the biogenesis and assembly of complex RNA-based cellular species.