Published in: Structure, Vol 11, no. 11, pp. 1423-1430 (November, 2003).
http://www.structure.org/content/article/abstract?uid=PIIS0969212603002181

"Crystal Structure of a Bulged RNA Tetraplex at 1.1 Å Resolution: Implications for a Novel Binding Site in RNA Tetraplex".

Baocheng Pan 1, Yong Xiong 2, Ke Shi 1, and Muttaiya Sundaralingam 1, *

1 Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Lab, 176 West 19th Avenue, Columbus, OH USA
2 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA

* Correspondence: Muttaiya Sundaralingam
(614) 292-2925 (phone);  (614) 292-2524 (fax)
E-mail:   sundaral@chemistry.ohio-state.edu


Abstract:

Bulges are an important structural motif in RNA and can be used as recognition and interaction sites in
RNA-protein interaction and RNA-RNA interaction. Here we report the first crystal structure of a bulged RNA tetraplex at 1.1 Å resolution. The hexamer r(U)(BrdG)r(UGGU) forms a parallel tetraplex with the uridine sandwiched by guanines bulging out. The bulged uridine adopts the syn glycosidic conformation and its O2 and N3 atoms face outwards, serving as an effective recognition and interaction site. The bulge formation both widens the groove width and changes the groove hydrogen-bonding pattern on its 5' side. However, the bulge does not make any bends or kinks in the tetraplex structure. The present study demonstrates the dramatic difference between uridine and guanine in forming tetraplex structure. In addition, both G(syn) tetrad and G(anti) tetrad have been observed. They display the same base-pairing pattern and similar C1'-C1' distance but different hydrogen-bonding patterns in the groove.


Additional References:

1. Berglund JA, "Expanding the Structural Repertoire of G-Quadruplexes", Structure, 2003, vol. 11, no. 11, pp. 1315-1316 (November, 2003).
http://www.structure.org/content/article/abstract?uid=PIIS0969212603002417

Preview: "Expanding the Structural Repertoire of G-Quadruplexes".
J. Andrew Berglund *
Department of Chemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 94703 USA
*Correspondence: (541) 346-5097 (phone);  (541) 346-5891 (fax)
E-mail:  aberglund@molbio.uoregon.edu


Abstract:
A crystal structure in this issue by Pan and colleagues adds a new dimension to nucleic acid quadruplex
structural biology by revealing an RNA quadruplex with bulged uridines.

2. Hershkovitz E, Tannenbaum E, Howerton SB, Sheth A, Tannenbaum A,  and Williams LD, "Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA", Nucleic Acids Research, vol. 31, no. 21, pp. 6249-6257 (November 1, 2003).

3. Doudna JA, "Structural Genomics of RNA", Nature Structural Biology, vol. 7, no. 11, supp,  pp. 954-956 (November, 2000).

4. Frenster JH, "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
 


Top of Page - Euchromatin Network - Current Research - Forums - Other Sites - Future Events -
For Further Information and Feedback:
E-mail: frenster@euchromatin.net
Phone: +1 650 367 6483

euchromatin: "the most active portion of the genome within the cell nucleus".