Assaying RNA Structure Inside Living Cells with SHAPE

  • Chao Feng
  • Dalen Chan
  • Robert C. SpitaleEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1648)


RNA molecules have emerged as key players in nearly every facet of gene regulation. Such functions are governed by RNA’s unique ability to fold into intricate secondary and tertiary structures. In order to understand, on the molecular level, how such structures from several chemical and enzymatic methods have been developed. One such method is RNA Selective Hydroxyl Acylation analyzed by Primer Extension, or SHAPE. SHAPE has emerged as a premier method of measuring RNA structure, with recent developments extending SHAPE into living cells. Here, we describe the use of SHAPE for measuring RNA structure inside living cells.

Key words

RNA structure SHAPE Chemical Probing 



RNA research in the Spitale lab is supported by startup funds from the University of California, Irvine, the NIH Director’s New Innovator Award (1DP2GM119164 RCS) and 1RO1MH109588 (RCS). Chao Feng and Dalen Chan contributed equally to this manuscript.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Pharmaceutical SciencesUniversity of California, IrvineIrvineUSA
  2. 2.Department of ChemistryUniversity of California, IrvineIrvineUSA

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