The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs.
The crystal structure of the RNA octamer, 5'-GGCGUGCC-3' has been determined from x-ray diffraction data to 1.5 angstroms resolution. In the crystal, this oligonucleotide forms five self-complementary double-helices in the asymmetric unit. Tandem 5'GU/3'UG basepairs comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation among the five crystallographic duplexes and the solution structure. The G.U pairs in the five duplexes of the crystal form two direct hydrogen bonds and are stabilized by water molecules that bridge between the base of guanine (N2) and the sugar (O2') of uracil. This contrasts with the NMR structure in which only one direct hydrogen bond is observed for the G.U pairs. The reduced stability of the r(CGUG)2 motif relative to the r(GGUC)2 motif may be explained by the lack of stacking of the uracil bases between the Watson-Crick and G.U pairs as observed in the crystal structure.
Jang
Se Bok
SB
Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Keumjeong-gu, Busan, Korea. sbjang@pusan.ac.kr
Hung
Li-Wei
LW
Jeong
Mi Suk
MS
Holbrook
Elizabeth L
EL
Chen
Xiaoying
X
Turner
Douglas H
DH
Holbrook
Stephen R
SR
D020029:Base Pairing; D003198:Computer Simulation; D003461:Crystallography; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D020080:Tandem Repeat Sequences
D015226:Dinucleoside Phosphates; C018310:guanylyl-(3'-5')-uridine; D012313:RNA