A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.

No abstract is available for this paper.

• Publication year

  1998

• Venue

  Journal of Molecular Biology

• Publication date

  1998-10-30

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1006/JMBI.1998.2106PMID 9784367
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  1998cited by this paper
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  1998cited by this paper
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  1998cited by this paper
• Database on the structure of large ribosomal subunit RNA

  1997cited by this paper
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  1997cited by this paper
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  1997cited by this paper
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  1997cited by this paper
• The RDP (Ribosomal Database Project)

  1997cited by this paper
• A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA.

  1997influential reference
• Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core.

  1997cited by this paper
• Structural Analysis and Modifications of the Hairpin Ribozyme

  1996cited by this paper
• Database on the structure of large ribosomal subunit RNA

  1996cited by this paper
• RNA Tertiary Structure Mediation by Adenosine Platforms

  1996cited by this paper
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  1996cited by this paper
• Hairpin ribozyme: current status and future prospects.

  1996cited by this paper
• RNA structure at high resolution

  1995cited by this paper
• The sarcin/ricin loop, a modular RNA.

  1995influential reference
• Genetic and comparative analyses reveal an alternative secondary structure in the region of nt 912 of Escherichia coli 16S rRNA.

  1995cited by this paper
• Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA.

  1995influential reference
• The decoding region of 16S RNA; a cross‐linking study of the ribosomal A, P and E sites using tRNA derivatized at position 32 in the anticodon loop.

  1994cited by this paper
• Three-dimensional structure of a hammerhead ribozyme

  1994cited by this paper
• Database on the structure of large ribosomal subunit RNA.

  1994cited by this paper
• Involvement of a GNRA tetraloop in long-range RNA tertiary interactions.

  1994cited by this paper
• A common RNA loop motif as a docking module and its function in the hammerhead ribozyme

  1994cited by this paper
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  1994cited by this paper
• A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme.

  1994cited by this paper
• The Ribosomal Database Project.

  1994cited by this paper
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  1994cited by this paper
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  1994cited by this paper
• 4 Probing RNA Structure, Function, and History by Comparative Analysis

  1993cited by this paper
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  1993cited by this paper
• Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994.

  1993cited by this paper
• The conformation of loop E of eukaryotic 5S ribosomal RNA.

  1993influential reference
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  1993cited by this paper
• Higher order interactions in 23s rRNA.

  1992cited by this paper
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  1992cited by this paper
• A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993.

  1992cited by this paper
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  1991cited by this paper
• RNA-protein interactions in the Escherichia coli ribosome.

  1991cited by this paper
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  1991cited by this paper
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  1990cited by this paper
• Compilation of 5S rRNA and 5S rRNA gene sequences.

  1990cited by this paper
• Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs.

  1990cited by this paper
• Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.

  1990cited by this paper
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  1990cited by this paper
• Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

  1990cited by this paper
• Evidence for several higher order structural elements in ribosomal RNA.

  1989cited by this paper
• The role of highly conserved single-stranded nucleotides of Xenopus 5S RNA in the binding of transcription factor IIIA.

  1989cited by this paper
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  1989cited by this paper
• Comparative and functional anatomy of group II catalytic introns--a review.

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  1989cited by this paper
• Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs.

  1989cited by this paper
• Probing the assembly of the 3' major domain of 16 S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19.

  1988influential reference
• A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs of Xenopus laevis.

  1988cited by this paper
• Model for the three-dimensional folding of 16 S ribosomal RNA.

  1988cited by this paper
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  1988cited by this paper
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  1987cited by this paper
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  1986influential reference
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  1986influential reference
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  1985cited by this paper
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  1985cited by this paper
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  1983cited by this paper
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  1982cited by this paper
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  1978cited by this paper
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  1977cited by this paper
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  1960cited by this paper

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