This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.106.081018v1 90/12/4530    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Jang, S. B. Articles by Holbrook, S. R. Search for Related Content PubMed PubMed Citation Articles by Jang, S. B. Articles by Holbrook, S. R.

The Crystal Structure at 1.5 Å Resolution of an RNA Octamer Duplex Containing Tandem G·U Basepairs

Se Bok Jang ^*, Li-Wei Hung , Mi Suk Jeong ^*, Elizabeth L. Holbrook , Xiaoying Chen , Douglas H. Turner  and Stephen R. Holbrook 

^* Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Keumjeong-gu, Busan, Korea; Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California; and Department of Chemistry, University of Rochester, Rochester, New York

Correspondence: Address reprint requests to S. B. Jang, Tel.: 82-51-510-2523; E-mail: sbjang{at}pusan.ac.kr; or S. R. Holbrook, Tel.: 1-510-486-6059; E-mail: srholbrook{at}lbl.gov.

The crystal structure of the RNA octamer, 5'-GGCGUGCC-3' has been determined from x-ray diffraction data to 1.5 Å 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.