Structure of an unusually stable RNA hairpin
- Univ. of California, Berkeley (USA)
The structure of a very common RNA hairpin, 5{prime}GGAC(UUCG)GUCC, has been determined in solution by NMR spectroscopy. The loop sequence, UUCG, occurs exceptionally often in ribosomal and other RNAs, and may serve as a nucleation site for RNA folding and as a protein recognition site. Reverse transcriptase cannot read through this loop, although it normally transcribes RNA secondary structure motifs. A hairpin with that loop displays unusually high thermodynamic stability; its stability decreases when conserved nucleotides are mutated. The three-dimensional structure for the hairpin was derived from interproton distances and scalar coupling constants determined by NMR using distance geometry, followed by restrained energy minimization. The structure was well-defined despite the conservative use of interproton distances, by constraining the backbone conformation by means of scalar coupling measurements. A mismatch G{center dot}U base pair, with syn-guanosine, closes the stem. This hairpin has a loop of only two nucleotides; both adopt C{sub 2{prime}}-endo sugar pucker. A sharp turn in the phosphodiester backbone is stabilized by a specific cytosine-phosphate contact, probably a hydrogen bond, and by stacking of the cytosine nucleotide on the G{center dot}U base pair. The structural features of the loop can explain the unusual thermodynamic stability of this hairpin and its sensitivity to mutations of loop nucleotides.
- DOE Contract Number:
- FG03-86ER60406
- OSTI ID:
- 5398100
- Journal Information:
- Biochemistry; (United States), Vol. 30:13; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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