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Using Molecular Replacement Phasing to Study the Structure and Function of RNA

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Nucleic Acid Crystallography

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1320))

Abstract

In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.

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Acknowledgments

I thank Prof. Anna Pyle and all members of the Pyle lab for constructive discussion and critical reading of the manuscript. All group II intron diffraction data were collected at beamlines 24-ID-C and E, NE-CAT, APS, Argonne (IL), USA, which are supported by a grant from the National Institute of General Medical Sciences (P41 GM103403) from the National Institutes of Health. Use of the Advanced Photon Source, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the US DOE under Contract No. DE-AC02-06CH11357. Specifically, at NE-CAT I thank Dr. Kanagalaghatta Rajashankar for precious discussion and for his help with phased molecular replacement experiments. This project was supported by the National Institute of Health (RO1GM50313).

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  1. European Molecular Biology Laboratory, Grenoble Outstation, 6, rue Jules Horowitz, Grenoble Cedex 09, 38041, France

    Marco Marcia

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  1. Marco Marcia
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Correspondence to Marco Marcia .

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  1. CNRS Inst de Biol Moléculaire et Cellulaire, Strasbourg, France

    Eric Ennifar

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Marcia, M. (2016). Using Molecular Replacement Phasing to Study the Structure and Function of RNA. In: Ennifar, E. (eds) Nucleic Acid Crystallography. Methods in Molecular Biology, vol 1320. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2763-0_15

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  • DOI: https://doi.org/10.1007/978-1-4939-2763-0_15

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