RNA purification and analysis: sample preparation, extraction, chromatography
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| Main Authors: | , , |
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| Format: | Book |
| Language: | English |
| Published: |
Weinheim
Wiley-VCH
2009
|
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XI, 195 S. Ill., graph. Darst. |
| ISBN: | 9783527321162 |
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Titel: RNA purification and analysis
Autor: Gjerde, Douglas T.
Jahr: 2009
r
Contents
Preface IX
Acknowledgments XI
1 RNA Extraction, Separation, and Analysis 1
1.1 The Need to Be Able to Extract, Mampulate, and Analyze RNA 1
1.2 Using Chemical Tools to Solve the Problem of Analysis of
Biological Processes 3
1.3 The Prmciple of Chromatography and Solid-Phase Extraction 4
1.3.1 Principle of Chromatography 4
1.3.2 Mobile Phase Gradient Controls Elution 5
1.3.3 Different Types of Column and Eluent Chemistries 6
1.3.4 The Principle of Solid-Phase Extraction 8
1.4 RNA Chromatography 10
1.5 Enzymatic Treatment of RNA and Analysis 13
1.5.1 Polyacrylamide Gel Electrophoresis 24
1.5.2 RNA Structure Probing with Ribonuclease Enzymes 14
1.6 Content and Organization of This Book 15
References 16
2 Biological and Chemical RNA 17
2.1 Why Classify RNA with Biology and Chemistry? 17
2.1.1 Chemical Classification of RNA 18
2.1.2 Biological Classification of RNA 19
2.2 Prokaryotic Cellular RNA 20
2.3 Prokaryote Sample Type 23
2.3.1 Escherichia coli 23
2.3.2 Other Bactena 24
2.4 Eukaryotic. Cellular RNA 24
2.5 Eukaryote Sample Type 27
2.5.1 Yeast 29
2.5.2 Other Fungi 30
2.5.3 Simple Multicellular Organism 30
RNA Purification and Analysis: Sample Preparation, Extraction, Chromatography
Douglas T. Gjerde, Lee Hoang, and David Hornby
Copyright © 2009 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978-3-527-32116-2
VI | Contents
2.5.4 Soft Animal 30
2.5.5 Hard Animal 31
2.5.6 Plant 31
2.5.7 Cell Culture 31
2.6 Other Samples 32
2.6.1 Virus 32
2.6.2 Soil and Rock 32
2.7 Synthetic RNA 32
2.7.1 Aptamers 33
2.7.2 SELEX 34
2.7.3 Short Hairpin RNAs 34
References 34
3 RNA Separation: Substrates, Functional Croups, Mechanisms, and
Control 37
3.1 Solid-Phase Interaction 37
3.1.1 Adsorption of Sample Compounds and Sample Matrix
Compounds 37
3.1.2 Roles of Solid-Phase Substrate and Functional Group 39
3.1.3 Correlation of Interaction Type, Functional Group, and
Substrate 40
3.1.4 RNA Structure and Solid Surface Interaction 41
3.2 The Solid-Phase Substrate and Attachment of Functional Groups 43
3.2.1 Polymeric Resm Substrates 44
3.2.2 Porous and Nonporous Polymeric Resins 45
3.2.3 Monolith Polymeric Columns 47
3.2.4 Functionalization of the Polymer 48
3.2.5 Silica-Glass-Based Substrates 50
3.2.6 Functionalization of Silica 51
3.2.7 Agarose and Cellulose Affinity Substrates 53
3.2.8 Dextran and Polyacrylamide Gel Filtration Substrates 53
3.3 Reverse-Phase Ion-Pairmg Separation Mechanism 54
3.4 Ion-Exchange Separation Mechanism 57
3.5 Chaotropic Denaturing Interaction Mechanism 61
3.6 Hybridization 62
3.6.1 SELEX 62
3.7 Gel Filtration 63
References 64
4 RNA Extraction and Analysis 67
4.1 Transcription 67
4.1.1 RNACatalysis 69
4.1.2 RNA-Protein Complex Interactions 69
4.1.3 Pre-mRNA Splicing 71
4.2 Translation 72
Contents VII
4.2.1 Post-Transcriptional Control of Eukaryotic Gene Expression 76
4.3 Gene Regulation 76
4.3.1 RNA Interference Pathway 76
4.3.2 Micro RNAs and Their Role in Gene Regulation 78
4.4 Use of siRNA to Investigate Gene Function 79
References 79
5 RNA Chromatography 81
5.1 Development of RNA Chromatography 81
5.2 RNA Chromatography Instrumentation 85
5.2.1 The Column Oven 85
5.2.2 Ultraviolet (UV) and Fluorescence Detection 86
5.2.3 Fragment Collection 86
5.3 RNA Chromatography Conditions 87
5.4 Temperature Modes of RNA Chromatography 88
5.4.1 Nondenaturing Mode 89
5.4.2 Partially Denaturing Mode 89
5.4.3 Fully Denaturing Mode 90
5.5 Comparison of Gel Electrophoresis and Liquid Chromatography 90
5.5.1 Gel Electrophoresis 90
5.5.2 Liquid Chromatography 93
5.6 Analysis of Human Telomerase RNA Under Nondenaturing
Conditions 95
References 98
6 RNA Chromatography Separation and Analysis 101
6.1 Features of RNA Chromatography 101
6.2 Separation of Double-Stranded and Single-Stranded RNA 102
6.3 Separation ofCellular RNA Species 107
6.4 Separation of Messenger RNA from Total and Ribosomal RNA 108
6.5 Analysis of Transfer RNA 109
6.6 Chromatography and Analysis of Synthetic Oligoribonucleotides 111
6.7 Application of RNA and DNA Chromatography in cDNA Library
Synthesis 114
6.8 DNA Chromatography Analyses of RT-PCR and Competitive
RT-PCR Products 117
6.9 Alternative Splicing 120
6.10 Differential Messenger RNA Display via DNA Chromatography 121
References 124
7 RNA Structure-Function Probing 127
7.1 Definition ofthe Structure-Function Paradigm 127
7.1.1 Francis Cnck, and Predictmg the Existence of tRNA 130
7.1.2 The Discovery of Ribozymes 133
7.2 Structure Determination of RNA 135
VIII Contents
7.2.1 Primary Structure 136
7.2.2 Secondary Structure 136
7.2.3 Tertiary Structure 137
7.2.4 Quaternary Structure 138
7.3 Footprinting, Model Building, and Functional Investigations 139
7.3.1 Chemical Probing and Cleavage 140
7.3.2 Modification Interference 143
7.3.3 FRET 144
References 144
Appendix T
Chromatographie Separation Equations and
Principles for RNA Separation 147
Appendix 2
HPLC Instrumentation and Operation 159
Appendix 3
RNA Chromatographie System Cleaning and
Passivation Treatment 185
Index 191 |
| any_adam_object | 1 |
| author | Gjerde, Douglas T. Hoang, Lee Hornby, David |
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| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
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| spellingShingle | Gjerde, Douglas T. Hoang, Lee Hornby, David RNA purification and analysis sample preparation, extraction, chromatography RNS - Aufreinigung RNS - Chemische Analyse Chromatography methods RNA Analysis Laboratory manuals RNA analysis Sequence Analysis, RNA Solid Phase Extraction methods Chemische Analyse (DE-588)4009840-0 gnd RNS (DE-588)4076759-0 gnd Aufreinigung (DE-588)4781219-9 gnd |
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| title | RNA purification and analysis sample preparation, extraction, chromatography |
| title_auth | RNA purification and analysis sample preparation, extraction, chromatography |
| title_exact_search | RNA purification and analysis sample preparation, extraction, chromatography |
| title_full | RNA purification and analysis sample preparation, extraction, chromatography Douglas T. Gjerde, Lee Hoang, and David Hornby |
| title_fullStr | RNA purification and analysis sample preparation, extraction, chromatography Douglas T. Gjerde, Lee Hoang, and David Hornby |
| title_full_unstemmed | RNA purification and analysis sample preparation, extraction, chromatography Douglas T. Gjerde, Lee Hoang, and David Hornby |
| title_short | RNA purification and analysis |
| title_sort | rna purification and analysis sample preparation extraction chromatography |
| title_sub | sample preparation, extraction, chromatography |
| topic | RNS - Aufreinigung RNS - Chemische Analyse Chromatography methods RNA Analysis Laboratory manuals RNA analysis Sequence Analysis, RNA Solid Phase Extraction methods Chemische Analyse (DE-588)4009840-0 gnd RNS (DE-588)4076759-0 gnd Aufreinigung (DE-588)4781219-9 gnd |
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