Book Volume 1320 2016

Nucleic Acid Crystallography

Methods and Protocols

Editors:

ISBN: 978-1-4939-2762-3 (Print) 978-1-4939-2763-0 (Online)

Table of contents (22 protocols)

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  1. Front Matter

    Pages i-xi

  2. Introduction

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 3-8

      Perspectives and Pitfalls in Nucleic Acids Crystallography

  3. RNA Preparation and Crystallogenesis

    1. Front Matter

      Pages 9-9

    2. No Access

      Protocol

      Pages 11-20

      Preparation of Short 5′-Triphosphorylated Oligoribonucleotides for Crystallographic and Biochemical Studies

    3. No Access

      Protocol

      Pages 21-36

      Preparation and Crystallization of Riboswitches

    4. No Access

      Protocol

      Pages 37-57

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

    5. No Access

      Protocol

      Pages 59-65

      Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA

    6. No Access

      Protocol

      Pages 67-76

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

    7. No Access

      Protocol

      Pages 77-109

      Fab Chaperone-Assisted RNA Crystallography (Fab CARC)

    8. No Access

      Protocol

      Pages 111-126

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

    9. No Access

      Protocol

      Pages 127-143

      Isothermal Titration Calorimetry: Assisted Crystallization of RNA–Ligand Complexes

  4. Data Collection, Phasing and Refinement

    1. Front Matter

      Pages 145-145

    2. No Access

      Protocol

      Pages 147-173

      Crystallographic Data and Model Quality

    3. No Access

      Protocol

      Pages 175-191

      Advanced Crystallographic Data Collection Protocols for Experimental Phasing

    4. No Access

      Protocol

      Pages 193-204

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

    5. No Access

      Protocol

      Pages 205-218

      Practical Radiation Damage-Induced Phasing

    6. No Access

      Protocol

      Pages 219-232

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

    7. No Access

      Protocol

      Pages 233-257

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

    8. No Access

      Protocol

      Pages 259-267

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

    9. No Access

      Protocol

      Pages 269-282

      RNA Structure Refinement Using the ERRASER-Phenix Pipeline

    10. No Access

      Protocol

      Pages 283-300

      Neutron Nucleic Acid Crystallography

  5. Functional Examples

    1. Front Matter

      Pages 301-301

    2. No Access

      Protocol

      Pages 303-314

      Reconstitution of Functionally Active Thermus thermophilus 30S Ribosomal Subunit from Ribosomal 16S RNA and Ribosomal Proteins

    3. No Access

      Protocol

      Pages 315-327

      Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers

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