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Nucleic Acid Crystallography

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Eric Ennifar

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

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xi
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Perspectives and Pitfalls in Nucleic Acids Crystallography

      • Eric Westhof
      Pages 3-8

  3. RNA Preparation and Crystallogenesis

    1. Front Matter

      Pages 9-9
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    2. Preparation of Short 5′-Triphosphorylated Oligoribonucleotides for Crystallographic and Biochemical Studies

      • Nikita Vasilyev, Alexander Serganov
      Pages 11-20

    3. Preparation and Crystallization of Riboswitches

      • Alla Peselis, Ang Gao, Alexander Serganov
      Pages 21-36

    4. In Vitro/In Vivo Production of tRNA for X-Ray Studies

      • Clément Dégut, Alexandre Monod, Franck Brachet, Thibaut Crépin, Carine Tisné
      Pages 37-57

    5. Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA

      • Mélanie Meyer, Benoît Masquida
      Pages 59-65

    6. Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs

      • Adrian R. Ferré-D’Amaré
      Pages 67-76

    7. Fab Chaperone-Assisted RNA Crystallography (Fab CARC)

      • Eileen Sherman, Jennifer Archer, Jing-Dong Ye
      Pages 77-109

    8. Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes

      • Martin Egli, Pradeep S. Pallan
      Pages 111-126

    9. Isothermal Titration Calorimetry: Assisted Crystallization of RNA–Ligand Complexes

      • Cyrielle Da Veiga, Joelle Mezher, Philippe Dumas, Eric Ennifar
      Pages 127-143

  4. Data Collection, Phasing and Refinement

    1. Front Matter

      Pages 145-145
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    2. Crystallographic Data and Model Quality

      • Kay Diederichs
      Pages 147-173

    3. Advanced Crystallographic Data Collection Protocols for Experimental Phasing

      • Aaron D. Finke, Ezequiel Panepucci, Clemens Vonrhein, Meitian Wang, Gérard Bricogne, Vincent Oliéric
      Pages 175-191

    4. Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases

      • Huiyan Sun, Sibo Jiang, Zhen Huang
      Pages 193-204

    5. Practical Radiation Damage-Induced Phasing

      • Chloe Zubieta, Max H. Nanao
      Pages 205-218

    6. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data

      • Robert T. Batey, Jeffrey S. Kieft
      Pages 219-232

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

      • Marco Marcia
      Pages 233-257

    8. Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?

      • Alexandre Urzhumtsev, Ludmila Urzhumtseva, Ulrich Baumann
      Pages 259-267
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Keywords

About this book

This volume includes comprehensive and up-to-date coverage of all nucleic-acid-specific steps used in X-ray crystallography, from macromolecule production to structure determination. Chapters dedicated to RNA preparation and crystallogenesis will be of interest to beginners, while chapters focused on data collection, phasing and refinement will be particularly useful to researchers with a higher level of expertise. Several functional case studies are also presented in the last part of the book. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and thorough, Nucleic Acid Crystallography: Methods and Protocols presents protocols that are aimed at both researchers and students who are interested in the structural biology of DNA or RNA, alone or in complex with proteins or ligands.

Editors and Affiliations

  • CNRS Inst de Biol Moléculaire et Cellulaire, Strasbourg, France

    Eric Ennifar

About the editor

Eric Ennifar Institut de Biologie Moléculaire et Cellulaire du CNRS 15 Rue René Descartes F-67084 Strasbourg, France +33 (0)3 88 41 70 02 email: e.ennifar@ibmc-cnrs.unistra.fr.

Bibliographic Information

  • Book Title: Nucleic Acid Crystallography

  • Book Subtitle: Methods and Protocols

  • Editors: Eric Ennifar

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-2762-3Published: 31 July 2015

  • Softcover ISBN: 978-1-4939-4641-9Published: 19 October 2016

  • eBook ISBN: 978-1-4939-2763-0Published: 30 July 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 356

  • Number of Illustrations: 18 b/w illustrations, 98 illustrations in colour

  • Topics: Nucleic Acid Chemistry

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