The Chirality of a Four-Way Helical Junction in RNA

摘要

Helical junctions are commonly occurring elements in RNA structure. They play a key role in small autonomously folding RNA molecules. Four-way junctions in DNA and RNA exhibit a strong propensity to undergo pairwise coaxial stacking of helical arms1 and a dependence of the structure on metal ions. A four-helix junction in DNA with no unpaired bases (4H)~2 adopts a right-handed, antiparallel stacked structure in the presence of Mg~(2+) ions in solution, and in the crystal. 4H RNA junctions tend to adopt an antiparallel structure in the presence of divalent metal ions of unknown handedness. The hairpin ribozyme consists of a 4H junction on which two adjacent arms have unpaired internal loops that interact to create the active site. The junction is antiparallel and left-handed in the crystal. However, it is not known if this is the natural propensity of the junction alone or if it is forced by the interaction between the loops. We have therefore used the ribozyme as a basis for analyzing the handedness of the simple four-way junction derived from it, using electrophoretic experiments.