title: Stable triplet of uracil-uracil basepairs in a small antisense RNA.
abstract: The interaction between ant (antirepressor) mRNA and its antisense RNA, sar (small antisense RNA), is important in regulation of the development of bacteriophage P22. Sar is 68-69 nucleotides in length and is believed to consist of two hairpin structures separated by a small inter-hairpin region, followed by a short 3' tail [Schaefer and McClure RNA 1997, 3, 141-156]. A novel feature of the proposed secondary structure of the first hairpin is a extremely rare triple U:U base stack. Heteronuclear NMR studies presented here show that the first hairpin does not possess a unique structure in the absence of the second hairpin. However, it acquires a well-defined structure within full length sar. Remarkably, the triple U:U stack appears to be a stable feature of the first hairpin, regardless of the presence or absence of the second hairpin.
authors.affiliation: Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Zhan
authors.forename: Gordon S
authors.initials: GS
authors.lastname: Rule
mesh_terms: D020029:Base Pairing; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016372:RNA, Antisense / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry; D014498:Uracil / Q000737:chemistry*
chemical_list: D016372:RNA, Antisense; D012333:RNA, Messenger; D014498:Uracil