Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G center dot G/U center dot U tandem wobble base pairs: comparison with other tandem G center dot U pairs

We have determined the crystal structure of the RNA octamer duplex r(guguuu ac)/r(guaggcac) with a tandem wobble pair, G.G/U.U (motif III), to compare it with U.G/G.U (motif I) and G.U/U.G (motif II) and to better understand t heir relative stabilities. The crystal belongs to the rhombohedral space gr oup R3. The hexagonal unit cell dimensions are a = b = 41.92 Angstrom, c = 56.41 Angstrom, and gamma = 120 degrees, with one duplex in the asymmetric unit, The structure was solved by the molecular replacement method at 1.9 A ngstrom resolution and refined to a final R factor of 19.9% and R-free of 2 3.3% for 2862 reflections in the resolution range 10.0-1.9 Angstrom with F greater than or equal to 2 sigma (F). The final model contains 335 atoms fo r the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar h ead-to-tail fashion forming a pseudo-continuous helix. The uridine bases of the tandem U.G pairs have slipped towards the minor groove relative to the guanine bases and the uridine O2 atoms form bifurcated hydrogen bonds with the N1 and N2 of guanines. The N2 of guanine and O2 of uridine do not brid ge the 'locked' water molecule in the minor groove, as in motifs I and II, but are bridged by water molecules in the major groove. A comparison of bas e stacking stabilities of motif III with motifs I and II confirms the resul t of thermodynamic studies, motif I > motif III > motif II.