RNA Folding pp 177-191 | Cite as

A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding

  • Olga Fedorova
Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1086)

Abstract

Large RNA molecules play important roles in all aspects of cellular metabolism ranging from mRNA splicing and protein biosynthesis to regulation of gene expression. In order to correctly perform its function in the cell, an RNA molecule must fold into a complex tertiary structure. Folding of many large RNAs is slow either due to formation of stable misfolded intermediates or due to high contact order or instability of obligate folding intermediates. Therefore many RNAs use protein cofactors to facilitate their folding in vivo. Folding of the yeast mitochondrial group II intron ai5γ to the native state under physiological conditions is facilitated by the protein cofactor Mss116. This chapter describes the use of Nucleotide Analog Interference Mapping (NAIM) to identify specific substructures within the intron molecule that are directly affected by the protein.

Key words

NAIM DEAD-box protein Ribozyme Group II intron RNA folding 
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Notes

Acknowledgements

I would like to thank Prof. A.M. Pyle for guidance and support and members of the Pyle lab for helpful discussions. I would like to apologize to all our colleagues whose work could not be extensively cited in this chapter. O.F. is a Research Specialist at Howard Hughes Medical Institute.

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Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Olga Fedorova
    • 1
    • 2
  1. 1.Howard Hughes Medical InstituteYale UniversityNew HavenUSA
  2. 2.Department of Molecular, Cellular, and Developmental BiologyYale UniversityNew HavenUSA

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