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MORE ABOUT THIS BOOK
Main description:
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.
Contents:
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
Clement Degut, Alexandre Monod, Franck Brachet, Thibaut Crepin, and Carine Tisne
5. Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA
Melanie Meyer and Benoit Masquida
6. Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs
Adrian R. Ferre-D'Amare
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, Gerard Bricogne, and Vincent Olieric
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
PRODUCT DETAILS
Publisher: Springer (Humana Press Inc.)
Publication date: July, 2015
Pages: 382
Weight: 9171g
Availability: Available
Subcategories: Biochemistry
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