THE GLOBAL FOLDING OF 4-WAY HELICAL JUNCTIONS IN RNA, INCLUDING THAT IN U1 SNRNA

Helical junctions are important elements in the architecture of folded RNA molecules. The global geometry of fully base-paired four-way junc tions between RNA helices has been analyzed by comparative gel electro phoresis. Junctions appear to fold by pairwise coaxial helical stackin g in one of two possible stereochemically equivalent isomers based upo n alternative selections of stacking partners. In the presence of 1 mM Mg2+, the two continuous helical axes are approximately at right angl es to each other for all junctions studied, but the RNA junctions exhi bit significant sequence-dependent differences in their structures as a function of ionic conditions. The four-way junction found in the U1 snRNA folded by coaxial helical stacking. It retained the 90 degrees c rossed stacked structure under all ionic conditions tested, despite th e presence of a G . A mismatch at the point of strand exchange.