Characterization of the structure and melting behavior of the loop i fragment of cole1 rna i

Ta Hsien Lin, Horng Dar Lin, Jeng Ling Yang, Vladimir R. Kaberdin, Sue Lin-Chao, Tai Huang Huang

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Abstract

We have synthesized two RNA fragments: a 42-mer corresponding to the full loop I sequence of the loop I region of ColE1 antisense RNA (RNA I), plus three additional Gs at the 5′-end, and a 31-mer which has 11 5′-end nucleotides (G(-2)-U9) deleted. The secondary structure of the 42-mer, deduced from one- and two-dimensional NMR spectra, consists of a stem of 11 base-pairs which contains a U-U base-pair and a bulged C base, a 7 nucleotide loop, and a single-stranded 5′ end of 12 nucleotides. The UV-melting study of the 42-mer further revealed a multi-step melting behavior with transition temperatures 32°C and 71°C clearly discernible. In conjunction with NMR melting study the major transition at 71°C is assigned to the overall melting of the stem region and the 32°C transition is assigned to the opening of the loop region. The deduced secondary structure agrees with that proposed for the intact RNA I and provides structural bases for understanding the specificity of RNase E.

Original languageEnglish
Pages (from-to)677-685
Number of pages9
JournalJournal of Biomolecular Structure and Dynamics
Volume13
Issue number4
DOIs
Publication statusPublished - 1996 Feb

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ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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