Nucleic Acid Crystallography: Methods and Protocols

ISBN-13: 9781493946419 / Angielski / Miękka / 2016 / 356 str.

Eric Ennifar

Opis

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.

Spis treści

Part I Introduction

1. Perspectives and Pitfalls in Nucleic Acids Crystallography
Eric Westof

Part II RNA Preparation and crystallogenesis

2. Preparation of Short 5’-Triphosphorylated Oligoribonucleotides for Crystallographic and Biochemical Studies
Nikita Vasilyev and Alexander Serganov

 3. Preparation and Crystallization of Riboswitches
Alla Peselis, Ang Gao, and Alexander Serganov

4. In Vitro/In Vivo Production of tRNA for X-Ray Studies
Clément Dégut, Alexandre Monod, Franck Brachet, Thibaut Crépin, and Carine Tisné

5. Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA
Mélanie Meyer and Benoît Masquida

6. Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs
Adrian R. Ferré-D’Amaré

7. Fab Chaperone-Assisted RNA Crystallography (Fab CARC)
Eileen Sherman, Jennifer Archer, and Jing-Dong Ye

8. Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H: DNA Complexes
Martin Egli and Pradeep S. Pallan

 9. Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes
Cyrielle da Veiga, Joelle Mezher, Philippe Dumas, and Eric Ennifar

 Part III Data Collection, Phasing and Refinement

10. Crystallographic Data and Model Quality
Kay Diederichs

11. Advanced Crystallographic Data Collection Protocols for Experimental Phasing
Aaron D. Finke, Ezequiel Panepucci, Clemens Vonrhein, Meitian Wang, Gérard Bricogne, and Vincent Oliéric

12. Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases
Huiyan Sun, Sibo Jiang, and Zhen Huang

13. Practical Radiation Damage Induced Phasing
Chloe Zubieta and Max H. Nanao

14. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data
Robert T. Batey and Jeffrey S. Kieft

15. Using Molecular Replacement Phasing to Study the Structure and Function of RNA
Marco Marcia

16. Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?
Alexandre Urzhumtsev, Ludmila Urzhumtseva, and Ulrich Baumann

17. RNA Structure Refinement Using the ERRASER-Phenix Pipeline
Fang-Chieh Chou, Nathaniel Echols, Thomas C. Terwilliger, and Rhiju Das

18. Neutron Nucleic Acid Crystallography
Toshiyuki Chatake

Part IV Functional Examples

19. Reconstitution of Functionally Active Thermus thermophilus 30S Ribosomal Subunit from Ribosomal 16S RNA and Ribosomal Proteins
Sultan Agalarov, Marat Yusupov, and Gulnara Yusupova

20. Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers
Jiro Kondo

21. Structure of the HCV Internal Ribosome Entry Site Subdomain IIa RNA in Complex with a Viral Translation Inhibitor
Sergey M. Dibrov and Thomas Hermann

22. Anions in Nucleic Acid Crystallography
Luigi D’Ascenzo and Pascal Auffinger

O autorze

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.