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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.
List of contents
Perspectives and Pitfalls in Nucleic Acids Crystallography.- Preparation of Short 5'-Triphosphorylated Oligoribonucleotides for Crystallographic and Biochemical Studies.- Preparation and Crystallization of Riboswitches.- In Vitro/In Vivo Production of tRNA for X-Ray Studies.- Polyacrylamide Gel Electrophoresis for Purification of Large Amounts of RNA.- Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs.- Fab Chaperone-Assisted RNA Crystallography (Fab CARC).- Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H: DNA Complexes.- Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes.- Crystallographic Data and Model Quality.- Advanced Crystallographic Data Collection Protocols for Experimental Phasing.- Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases.- Practical Radiation Damage Induced Phasing.- Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data.- Using Molecular Replacement Phasing to Study the Structure and Function of RNA.- Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?.- RNA Structure Refinement Using the ERRASER-Phenix Pipeline.- Neutron Nucleic Acid Crystallography.- Reconstitution of Functionally Active Thermus thermophilus 30S Ribosomal Subunit from Ribosomal 16S RNA and Ribosomal Proteins.- Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers.- Structure of the HCV Internal Ribosome Entry Site Subdomain IIa RNA in Complex with a Viral Translation Inhibitor.- Anions in Nucleic Acid Crystallography.
About the author
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.
Summary
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.
