Nucleic Acids Research, 2000, Vol. 28, No. 21 4376-4381
© 2000 Oxford University Press
Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G·G/U·U tandem wobble base pairs: comparison with other tandem G·U pairs
Department of Chemistry and Department of Biochemistry, Biological Macromolecular Structure Center, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210-1002, USA
We have determined the crystal structure of the RNA octamer duplex r(guguuuac)/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 their relative stabilities. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 41.92 Å, c = 56.41 Å, and 
= 120°, with one duplex in the asymmetric unit. The structure was solved by the molecular replacement method at 1.9 Å resolution and refined to a final R factor of 19.9% and Rfree of 23.3% for 2862 reflections in the resolution range 10.0–1.9 Å with F 
2
(F). The final model contains 335 atoms for the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar head-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 bridge 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 base stacking stabilities of motif III with motifs I and II confirms the result of thermodynamic studies, motif I > motif III > motif II.
* To whom correspondence should be addressed. Tel: +1 614 292 2925; Fax: +1 614 292 2524; Email: sundaral@chemistry.ohio-state.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Xu, T. Landon, N. L. Greenbaum, and M. O. Fenley The electrostatic characteristics of G{middle dot}U wobble base pairs Nucleic Acids Res., June 28, 2007; 35(11): 3836 - 3847. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.-M. LANCHY, J. D. IVANOVITCH, and J. S. LODMELL A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA RNA, August 1, 2003; 9(8): 1007 - 1018. [Abstract] [Full Text] [PDF]
|
|