J Am Chem Soc. 2005 Nov 16;127(45):15714-5.

Stable triplet of uracil-uracil basepairs in a small antisense RNA.

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Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.

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.

PMID:: 16277508; [PubMed - indexed for MEDLINE]

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