X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr2+ ions at subatomic resolution (0.61 angstrom)

Four-stranded guanine tetraplexes in RNA have been identified to be involve d in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 Angstro m). The space group is P42(1)2, and cell constants are a = b = 36.16 Angstr om and c = 74.09 Angstrom. The structure was solved by the multiple-wavelen gth anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative b,UGGGGU and refined to 0.61-Angstrom resolut ion. Each of the four strands in the asymmetric unit forms a parallel tetra plex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tall) to form a pseud ocontinuous column. All of the 5'-end uridines rotate around the backbone o f G2, swing out, and form unique octaplexes with the neighboring G tetraple xes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. A ll of the bases are anti, and the riboses are in the mixed C2'- and C3'-puc kering mode. Strontium ions are observed in every other guanine tetrad plan e, sitting on the fourfold axis and associated to the eight O6 atoms of nei ghboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens a re clearly observed in the structure.