GLOBAL STRUCTURE OF 4-WAY RNA JUNCTIONS STUDIED USING FLUORESCENCE RESONANCE ENERGY-TRANSFER

Four-way helical junctions are found widely in natural RNA species. In this study, we have studied the conformation of two junctions by fluo rescence resonance energy transfer. We show that the junctions are fol ded by pairwise coaxial helical stacking, forming one predominant stac king conformer in both examples studied. At tow magnesium ion concentr ations, the helical axes of both junctions are approximately perpendic ular. One junction undergoes a rotation into a distorted antiparallel structure induced by the binding of a single magnesium ion. By contras t, the axes of the four-way junction of the U1 snRNA remain approximat ely perpendicular under all conditions examined, and we have determine d the stacking conformer adopted.