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Related Experiment Videos

Local RNA structural changes induced by crystallization are revealed by SHAPE.

Quentin Vicens1, Anne R Gooding, Alain Laederach

  • 1Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, Univeristy of Colorado, Boulder, CO 80309-0215, USA. quentin.vicens@colorado.edu

RNA (New York, N.Y.)
|February 15, 2007
PubMed
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This study uses selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to map RNA conformational changes during crystallization. SHAPE identified nucleotides involved in crystal packing and revealed pre-crystallization structural changes, aiding RNA crystallization design.

Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • Crystallization is crucial for determining RNA structures.
  • Understanding conformational changes during crystallization is key for successful structure determination.
  • Selective 2 extquotesingle-hydroxyl acylation analyzed by primer extension (SHAPE) is a method to probe RNA conformation and flexibility.

Purpose of the Study:

  • To develop a method for locating RNA sites that change conformation during crystallization.
  • To investigate conformational changes of the P4-P6DeltaC209 domain from Tetrahymena thermophila group I intron during crystallization.
  • To correlate SHAPE reactivity with RNA structure and crystallization propensity.

Main Methods:

  • Comparative structural mapping of RNA in native solution, crystallization buffer, and crystal forms.

Related Experiment Videos

  • Utilizing selective 2 extquotesingle-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry.
  • Analyzing SHAPE reactivity data to identify nucleotide flexibility and conformational states.

    • Main Results:

    • SHAPE successfully identified structural changes occurring during RNA crystallization.
    • 64% of nucleotides involved in packing contacts were identified through SHAPE.
    • Reactivity differences observed in the crystallization solution suggest pre-stabilization of a crystal-favorable structure.
    • SHAPE data suggest a correlation between reactivity and C2 extquotesingle-endo sugar pucker.

    Conclusions:

    • SHAPE is effective in mapping conformational changes during RNA crystallization.
    • Early structural changes in crystallization solutions can be detected.
    • Understanding these changes can guide the rational design of RNA molecules for improved crystallization outcomes.