Bioanalytics: analytical methods and concepts in biochemistry and molecular biology
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| Format: | Book |
| Language: | English |
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Weinheim
Wiley-VCH Verlag GmbH & Co. KGaA
[2018]
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| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XXIV, 1110 Seiten Illustrationen, Diagramme 27.6 cm x 21 cm |
| ISBN: | 9783527339198 3527339191 |
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MARC
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| 130 | 0 | |a Bioanalytik | |
| 245 | 1 | 0 | |a Bioanalytics |b analytical methods and concepts in biochemistry and molecular biology |c Edited by Friedrich Lottspeich and Joachim Engels |
| 264 | 1 | |a Weinheim |b Wiley-VCH Verlag GmbH & Co. KGaA |c [2018] | |
| 264 | 4 | |c © 2018 | |
| 300 | |a XXIV, 1110 Seiten |b Illustrationen, Diagramme |c 27.6 cm x 21 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 0 | 7 | |a Molekularbiologie |0 (DE-588)4039983-7 |2 gnd |9 rswk-swf |
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| 650 | 0 | 7 | |a Methode |0 (DE-588)4038971-6 |2 gnd |9 rswk-swf |
| 653 | |a Biowissenschaften, Biologie | ||
| 653 | |a Bioanalytical Chemistry | ||
| 653 | |a Bioanalytische Chemie | ||
| 653 | |a Biochemie | ||
| 653 | |a Biochemie u. Chemische Biologie | ||
| 653 | |a Biowissenschaften | ||
| 653 | |a Cell & Molecular Biology | ||
| 653 | |a Chemie | ||
| 653 | |a Chemistry | ||
| 653 | |a Life Sciences | ||
| 653 | |a Molekularbiologie | ||
| 653 | |a Zell- u. Molekularbiologie | ||
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| 700 | 1 | |a Lottspeich, Friedrich |d 1947- |0 (DE-588)120183749 |4 edt | |
| 700 | 1 | |a Engels, Joachim W. |d 1944-2018 |0 (DE-588)120266962 |4 edt | |
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| _version_ | 1804178418229575680 |
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| adam_text | Table of Contents
Preface XV 3 3 Catalysts 37
3 4 Enzymes as Catalysts 37
Introduction XIX 3 5 Rate of Enzyme-Controlled Reactions 38
3 6 Michaelis-Menten Theory 38
3 7 Determination of Km and Vmax 39
Part 1 Protein Analytics 138 Inhibitors 40
381 Competitive Inhibitors 40
1 Protein Purification 3382 Non-competitive Inhibitors 41
1 1 Properties of Proteins 339 Test System Set-up 41
1 2 Protein Localization and Purification Strategy 6391 Analysis of the Physiological Function 42
1 3 Homogenization and Cell Disruption 7392 Selecting the Substrates 42
1 4 Precipitation 9393 Detection System 42
1 5 Centrifugation 11 394 Time Dependence 43
151 Basic Principles 12 395 pH Value 43
152 Centrifugation Techniques 12 396 Selecting the Buffer Substance and the Ionic
1 6 Removal of Salts and Hydrophilic Contaminants 15 Strength 43
1 7 Concentration 17 397 Temperature 44
1 8 Detergents and their Removal 18 398 Substrate Concentration 44
181 Properties of Detergents 18 399 Controls 45
182 Removal of Detergents 20 Further Reading 45
1 9 Sample Preparation for Proteome Analysis 22
Further Reading 22 4 Microcalorimetry 47
4 1 Differential Scanning Calorimetry (DSC) 48
2 Protein determination 23 4 2 Isothermal Titration Calorimetry (ITC) 54
2 1 Quantitative Determination by Staining Tests 25 421 Ligand Binding to Proteins 54
211 Biuret Assay 26 422 Binding of Molecules to Membranes: Insertion
212 Lowry Assay 26 and Peripheral Binding 58
213 Bicinchoninic Acid Assay (BCA Assay) 27 4 3 Pressure Perturbation Calorimetry (PPC) 61
214 Bradford Assay 28 Further Reading 62
2 2 Spectroscopic Methods 28
221 Measurements in the UV Range 29 5 Immunological Techniques 63
222 Fluorescence Method 31 5 1 Antibodies 63
2 3 Radioactive Labeling of Peptides and Proteins 31 511 Antibodies and Immune Defense 63
231 Iodinations 33 512 Antibodies as Reagents 64
Further Reading 33 513 Properties of Antibodies 64
514 Functional Structure of IgG 66
3 Enzyme Activity Testing 35 515 Antigen Interaction at the Combining Site 67
3 1 The Driving Force behind Chemical Reactions 35 516 Handling of Antibodies 68
3 2 Rate of Chemical Reactions 36 5 2 Antigens 69
VI Table of Contents
5 3 Antigen-Antibody Reaction 71 742 Molecular Vibrations 164
531 Immunoagglutination 72 743 Technical aspects of Infrared Spectroscopy 165
532 Immunoprecipitation 73 744 Infrared Spectra of Proteins 168
533 Immune Binding 84 7 5 Raman Spectroscopy 171
5 4 Complement Fixation 94 751 Basic Principles of Raman Spectroscopy 171
5 5 Methods in Cellular Immunology 95 752 Raman Experiments 172
5 6 Alteration of Biological Functions 97 753 Resonance Raman Spectroscopy 173
5 7 Production of Antibodies 98 7 6 Single Molecule Spectroscopy 174
571 Types of Antibodies 98 7 7 Methods using Polarized Light 175
572 New Antibody Techniques (Antibody Engineering) 99 771 Linear Dichroism 175
573 Optimized Monoclonal Antibody Constructs with 772 Optical Rotation Dispersion and Circular
Effector Functions for Therapeutic Application 102 Dichroism 178
5 8 Outlook: Future Expansion of the Binding Further Reading 180
Concepts 106
Dedication 106 8 Light Microscopy Techniques - Imaging 181
Further Reading 106 8 1 Steps on the Road to Microscopy - from Simple
Lenses to High Resolution Microscopes 181
6 Chemical Modification of Proteins and 8 2 Modem Applications 182
Protein Complexes 107 8 3 Basic Physical Principles 183
6 1 Chemical Modification of Protein Functional Groups 108 8 4 Detection Methods 189
6 2 Modification as a Means to Introduce Reporter 8 5 Sample Preparation 195
Groups 116 8 6 Special Fluorescence Microscopic Analysis 197
621 Investigation with Naturally Occurring Proteins 116 Further Reading 205
622 Investigation of Recombinant and Mutated 9 Cleavage of Proteins 207
Proteins 120 9 1 Proteolytic Enzymes 207
6 3 Protein Crosslinking for the Analysis of Protein 9 2 Strategy 208
Interaction 121 9 3 Denaturation of Proteins 209
631 Bifunctional Reagents 121 9 4 Cleavage of Disulfide Bonds and Alkylation 209
632 Photoaffinity Labeling 121 9 5 Enzymatic Fragmentation 210
Further Reading 129 951 Proteases 210
952 Conditions for Proteolysis 215
7 Spectroscopy 131 9 6 Chemical Fragmentation 216
7 1 Physical Principles and Measuring Techniques 132 9 7 Summary 217
711 Physical Principles of Optical Spectroscopic Further Reading 218
Techniques 132
712 Interaction of Light with Matter 133 10 Chromatographic Separation Methods 219
713 Absorption Measurement and the Lambert-Beer 10 1 Instrumentation 219
Law 140 10 2 Fundamental Terms and Concepts in
714 Photometer 143 Chromatography 220
715 Time-Resolved Spectroscopy 144 10 3 Biophysical Properties of Peptides and Proteins 224
7 2 UV/VIS/NIR Spectroscopy 146 10 4 Chromatographic Separation Modes for Peptides
721 Basic Principles 146 and Proteins 225
722 Chromoproteins 147 10 4 1 High-Performance Size Exclusion
7 3 Fluorescence Spectroscopy 154 Chromatography 227
731 Basic Principles of Fluorescence Spectroscopy 154 10 4 2 High-Performance Reversed-Phase
732 Fluorescence: Emission and Action Spectra 156 Chromatography (HP-RPC) 227
733 Fluorescence Studies using Intrinsic and Extrinsic 10 4 3 High-Performance Normal-Phase
Probes 157 Chromatography (HP-NPC) 228
734 Green Fluorescent Protein (GFP) as a Unique 10 4 4 High-Performance Hydrophilic Interaction
Fluorescent Probe 158 Chromatography (HP-HILIC) 229
735 Quantum Dots as Fluorescence Labels 159 10 4 5 High-Performance Aqueous Normal Phase
736 Special Fluorescence Techniques: FRAP, Chromatography (HP-ANPC) 230
FLIM, FCS, TIRF 160 10 4 6 High-Performance Hydrophobic Interaction
737 Förster Resonance Energy Transfer (FRET) 160 Chromatography (HP-HIC) 230
738 Frequent Mistakes in Fluorescence Spectroscopy: 10 4 7 High-Performance Ion Exchange Chromatography
“The Seven Sins of Fluorescence Measurements” 161 (HP-EEX) 232
7 4 Infrared Spectroscopy 163 10 4 8 High-Performance Affinity Chromatography
741 Basic Principles of IR Spectroscopy 163 (HP-AC) 233
Table of Contents
VII
10 5 Method Development from Analytical to 12 3 3 Joule Heating 279
Preparative Scale Illustrated for HP-RPC 234 12 3 4 Detection Methods 279
10 5 1 Development of an Analytical Method 234 12 4 Capillary Electrophoresis Methods 281
10 5 2 Scaling up to Preparative Chromatography 236 12 4 1 Capillary Zone Electrophoresis (CZE) 281
10 5 3 Fractionation 237 12 4 2 Affinity Capillary Electrophoresis (ACE) 285
10 5 4 Analysis of Fractionations 238 12 4 3 Micellar Electrokinetic Chromatography (MEKC) 286
10 6 Multidimensional HPLC 238 12 4 4 Capillary Electrochromatography (CEC) 288
10 6 1 Purification of Peptides and Proteins by 12 4 5 Chiral Separations 289
MD-HPLC Methods 238 12 4 6 Capillary Gel Electrophoresis (CGE) 290
10 6 2 Fractionation of Complex Peptide and Protein 12 4 7 Capillary Isoelectric Focusing (CIEF) 291
Mixtures by MD-HPLC 239 12 4 8 Isotachophoresis (ITP) 293
10 6 3 Strategies for MD-HPLC Methods 239 12 5 Special Techniques 295
10 6 4 Design of an Effective MD-HPLC Scheme 240 12 5 1 Sample Concentration 295
10 7 Final Remarks 242 12 5 2 Online Sample Concentration 295
Further Reading 242 12 5 3 Fractionation 296
12 5 4 Microchip Electrophoresis 297
11 Electrophoretic Techniques 243 12 6 Outlook 297
11 1 Historical Review 244 Further Reading 299
11 2 Theoretical Fundamentals 245
11 3 Equipment and Procedures of Gel Electrophoreses 248 13 Amino Acid Analysis 301
11 3 1 Sample Preparation 249 13 1 Sample Preparation 302
11 3 2 Gel Media for Electrophoresis 250 13 1 1 Acidic Hydrolysis 302
11 3 3 Detection and Quantification of the Separated 13 1 2 Alkaline Hydrolysis 303
Proteins 251 13 1 3 Enzymatic Hydrolysis 303
11 3 4 Zone Electrophoresis 253 13 2 Free Amino Acids 303
11 3 5 Porosity Gradient Gels 254 13 3 Liquid Chromatography with Optical Detection
11 3 6 Buffer Systems 255 Systems 303
11 3 7 Disc Electrophoresis 255 13 3 1 Post-Column Derivatization 303
11 3 8 Acidic Native Electrophoresis 257 13 3 2 Pre-column Derivatization 305
11 3 9 SDS Polyacrylamide Gel Electrophoresis 257 13 4 Amino Acid Analysis using Mass Spectrometry 309
11 3 10 Cationic Detergent Electrophoresis 258 13 5 Summary 310
11 3 11 Blue Native Polyacrylamide Gel Electrophoresis 259 Further Reading 311
11 3 12 Isoelectric Focusing 259
11 4 Preparative Techniques 263 14 Protein Sequence Analysis 313
11 4 1 Electroelution from Gels 263 14 1 N-Terminal Sequence Analysis: The Edman
11 4 2 Preparative Zone Electrophoresis 264 Degradation 315
11 4 3 Preparative Isoelectric Focusing 265 14 1 1 Reactions of the Edman Degradation 315
11 5 Free Flow Electrophoresis 266 14 1 2 Identification of the Amino Acids 316
11 6 High-Resolution Two-Dimensional Electrophoresis 267 14 1 3 Quality of Edman Degradation: the Repetitive
11 6 1 Sample Preparation 268 Yield 317
11 6 2 Prefractionation 268 14 1 4 Instrumentation 319
11 6 3 First Dimension: IEF in IPG Strips 269 14 1 5 Problems of Amino Acid Sequence Analysis 322
11 6 4 Second Dimension: SDS Polyacrylamide Gel 14 1 6 State of the Art 325
Electrophoresis 270 14 2 C-Terminal Sequence Analysis 325
11 6 5 Detection and Identification of Proteins 270 14 2 1 Chemical Degradation Methods 325
11 6 6 Difference Gel Electrophoresis (DIGE) 270 14 2 2 Peptide Quantities and Quality of the Chemical
11 7 Electroblotting 272 Degradation 327
11 7 1 Blot Systems 272 14 2 3 Degradation of Polypeptides with
11 7 2 Transfer Buffers 273 Carboxypeptidases 327
11 7 3 Blot Membranes 273 Further Reading 328
Further Reading 273
15 Mass Spectrometry 329
12 Capillary Electrophoresis 275 15 1 Ionization Methods 330
12 1 Historical Overview 275 15 1 1 Matrix Assisted Laser Desorption Ionization Mass
12 2 Capillary Electrophoresis Setup 276 Spectrometry (MALDI-MS) 330
12 3 Basic Principles of Capillary Electrophoresis 277 15 1 2 Electrospray Ionization (ESI) 335
12 3 1 Sample Injection 277 15 2 Mass Analyzer 341
12 3 2 The Engine: Electroosmotic Flow (EOF) 278 15 2 1 Time-of-Flight Analyzers (TOF) 343
VIII Table of Contents
15 2 2 Quadrupole Analyzer 345 16 8 1 Principles of Instrumentation 410
15 2 3 Electric Ion Traps 348 16 8 2 Basics of Centrifugation 411
15 2 4 Magnetic Ion Trap 349 16 8 3 Sedimentation Velocity Experiments 412
15 2 5 Orbital Ion Trap 350 16 8 4 Sedimentation-Diffusion Equilibrium Experiments 415
15 2 6 Hybrid Instruments 351 Further Reading 416
15 3 Ion Detectors 355
15 3 1 Secondary Electron Multiplier (SEV) 356 17 Biosensors 419
15 3 2 Faraday Cup 357 17 1 Dry Chemistry: Test Strips for Detecting and
15 4 Fragmentation Techniques 357 Monitoring Diabetes 420
15 4 1 Collision Induced Dissociation (CID) 357 17 2 Biosensors 420
15 4 2 Prompt and Metastable Decay (ISD, PSD) 358 17 2 1 Concept of Biosensors 420
15 4 3 Photon-Induced Dissociation (PID, IRMPD) 360 17 2 2 Construction and Function of Biosensors 421
15 4 4 Generation of Free Radicals (ECD, HECD, ETD) 360 17 2 3 Cell Sensors 425
15 5 Mass Determination 362 17 2 4 Immunosensors 426
15 5 1 Calculation of Mass 362 17 3 Biomimetic Sensors 427
15 5 2 Influence of Isotopy 362 17 4 From Glucose Enzyme Electrodes to
15 5 3 Calibration 365 Electronic DNA Biochips 428
15 5 4 Determination of the Number of Charges 365 17 5 Resume: Biosensor or not Biosensor is no
15 5 5 Signal Processing and Analysis 366 Longer the Question 429
15 5 6 Derivation of the Mass 366 Further Reading 429
15 5 7 Problems 366
15 6 Identification, Detection, and Structure Elucidation 368
15 6 1 Identification 368 Part II 3D Structure
15 6 2 15 6 3 Verification Structure Elucidation 369 369 Determination 431
15 7 LC-MS and LC-MS/MS 375
15 7 1 LC-MS 375 18 Magnetic Resonance Spectroscopy
15 7 2 LC-MS/MS 376 of Biomolecules 433
15 7 3 Ion Mobility Spectrometry (IMS) 378 18 1 NMR Spectroscopy of Biomolecules 433
15 8 Quantification 378 18 1 1 Theory of NMR Spectroscopy 434
Further Reading 379 18 1 2 One-Dimensional NMR Spectroscopy 438
18 1 3 Two-Dimensional NMR Spectroscopy 443
16 Protein-Protein Interactions 381 18 1 4 Three-Dimensional NMR Spectroscopy 449
16 1 The Two-Hybrid System 381 18 1 5 Resonance Assignment 452
16 1 1 Principle of Two-Hybrid Systems 381 18 1 6 Protein Structure Determination 457
16 1 2 Elements of the Two-Hybrid System 382 18 1 7 Protein Structures and more — an Overview 462
16 1 3 Construction of Bait and Prey Proteins 382 18 2 EPR Spectroscopy of Biological Systems 466
16 1 4 Which Bait Proteins can be used in a Y2H Screen? 385 18 2 1 Basics of EPR Spectroscopy 467
16 1 5 AD Fusion Proteins and cDNA Libraries 385 18 2 2 cw- EPR Spectroscopy 468
16 1 6 Carrying out a Y2H Screen 386 18 2 3 g-Value 469
16 1 7 Other Modifications and Extensions of the 18 2 4 Electron Spin Nuclear Spin Coupling (Hyperfine
Two-Hybrid-Technology 391 Coupling) 469
16 1 8 Biochemical and Functional Analysis of 18 25g and Hyperfine Anisotropy 470
Interactions 393 18 2 6 Electron Spin-Electron Spin Coupling 472
16 2 TAP-Tagging and Purification of Protein 18 2 7 Pulsed EPR Experiments 473
Complexes 394 18 2 8 Further Examples of EPR Applications 479
16 3 Analyzing Interactions In Vitro: GST- Pulldown 397 18 2 9 General Remarks on the Significance of EPR
16 4 Co-immunoprecipitation 398 Spectra 481
16 5 Far-Western 399 18 2 10 Comparison EPR/NMR 481
16 6 Surface Plasmon Resonance Spectroscopy 400 Acknowledgements 482
16 7 Fluorescence Resonance Energy Transfer (FRET) 402 Further Reading 482
16 7 1 Introduction 402
16 7 2 Key Physical Principles of FRET 403 19 Electron Microscopy 485
16 7 3 Methods of FRET Measurements 403 19 1 Transmission Electron Microscopy -
16 7 4 Fluorescent Probes for FRET 406 Instrumentation 487
16 7 5 Alternative Tools for Probing Protein-Protein 19 2 Approaches to Preparation 488
Interactions: LINC and STET 408 19 2 1 Native Samples in Ice 488
16 8 Analytical Ultracentrifugation 409 19 2 2 Negative Staining 490
Table of Contents
IX
19 2 3 Metal Coating by Evaporation 491
19 2 4 Labeling of Proteins 492
19 3 Imaging Process in the Electron Microscope 492
19 3 1 Resolution of a Transmission Electron Microscope 492
19 3 2 Interactions of the Electron Beam with the Object 493
19 3 3 Phase Contrast in Transmission Electron
Microscopy 495
19 3 4 Electron Microscopy with a Phase Plate 495
19 3 5 Imaging Procedure for Frozen-Hydrated
Specimens 496
19 3 6 Recording Images - Cameras and the Impact of
Electrons 497
19 4 Image Analysis and Processing of Electron
Micrographs 498
19 4 1 Pixel Size 498
19 4 2 Fourier Transformation 499
19 4 3 Analysis of the Contrast Transfer Function and
Object Features 501
19 4 4 Improving the Signal-to-Noise Ratio 504
19 4 5 Principal Component Analysis and
Classification 506
19 5 Three-Dimensional Electron Microscopy 508
19 5 1 Three-Dimensional Reconstruction of Single
Particles 509
19 5 2 Three-Dimensional Reconstruction of Regularly
Arrayed Macromolecular Complexes 511
19 5 3 Electron Tomography of Individual Objects 512
19 6 Analysis of Complex 3D Data Sets 514
19 6 1 Hybrid Approach: Combination of EM and X-Ray
Data 514
19 6 2 Segmenting Tomograms and Visualization 515
19 6 3 Identifying Protein Complexes in Cellular
Tomograms 515
19 7 Perspectives of Electron Microscopy 516
Further Reading 517
20 Atomic Force Microscopy 519
20 1 Introduction 519
20 2 Principle of the Atomic Force Microscope 520
20 3 Interaction between Tip and Sample 521
20 4 Preparation Procedures 522
20 5 Mapping Biological Macromolecules 522
20 6 Force Spectroscopy of Single Molecules 524
20 7 Detection of Functional States and Interactions of
Individual Proteins 526
Further Reading 527
21 X-Ray Structure Analysis 529
21 1 X-Ray Crystallography 530
21 1 1 Crystallization 531
21 1 2 Crystals and X-Ray Diffraction 533
21 1 3 The Phase Problem 538
21 1 4 Model Building and Structure Refinement 542
21 2 Small Angle X-Ray Scattering (SAXS) 543
21 2 1 Machine Setup 544
21 2 2 Theory 545
21 2 3 Data Analysis 547
21 3 X-Ray Free Electron LASER (XFEL) 549
21 3 1 Machine Setup and Theory 549
Acknowledgement 550
Further Reading 551
Part III Peptides,
Carbohydrates, and Lipids 553
22 Analytics of Synthetic Peptides 555
22 1 Concept of Peptide Synthesis 555
22 2 Purity of Synthetic Peptides 560
22 3 Characterization and Identity of Synthetic
Peptides 562
22 4 Characterization of the Structure of Synthetic
Peptides 564
22 5 Analytics of Peptide Libraries 567
Further Reading 569
23 Carbohydrate Analysis 571
23 1 General Stereochemical Basics 572
23 1 1 The Series of D-Sugars 572
23 1 2 Stereochemistry of D-Glucose 573
23 1 3 Important Monosaccharide Building Blocks 574
23 1 4 The Series of L-Sugars 574
23 1 5 The Glycosidic Bond 574
23 2 Protein Glycosylation 579
23 2 1 Structure of the iV-Glycans 580
23 2 2 Structure of the O-Glycans 580
23 3 Analysis of Protein Glycosylation 581
23 3 1 Analysis on the Basis of the Intact
Glycoprotein 582
23 3 2 Mass Spectrometric Analysis on the Basis
of Glycopeptides 588
23 3 3 Release and Isolation of the A-Glycan Pool 590
23 3 4 Analysis of Individual V-Glycans 599
23 4 Genome, Proteome, Glycome 610
23 5 Final Considerations 611
Further Reading 612
24 Lipid Analysis 613
24 1 Structure and Classification of Lipids 613
24 2 Extraction of Lipids from Biological
Sources 615
24 2 1 Liquid Phase Extraction 616
24 2 2 Solid Phase Extraction 616
24 3 Methods for Lipid Analysis 618
24 3 1 Chromatographic Methods 618
24 3 2 Mass Spectrometry 622
24 3 3 Immunoassays 622
24 3 4 Further Methods in Lipid Analysis 623
24 3 5 Combining Different Analytical Systems 623
24 4 Analysis of Selected Lipid Classes 626
24 4 1 Whole Lipid Extracts 626
24 4 2 Fatty Acids 627
24 4 3 Nonpolar Neutral Lipids 628
24 4 4 Polar Ester Lipids 630
X
Table of Contents
24 4 5 Lipid Hormones and Intracellular Signaling 26 6 Isolation of RNA 676
Molecules 633 26 6 1 Isolation of Cytoplasmic RNA 677
24 5 Lipid Vitamins 638 26 6 2 Isolation of Poly(A) RNA 678
24 6 Lipidome Analysis 640 26 6 3 Isolation of Small RNA 679
24 7 Perspectives 642 26 7 Isolation of Nucleic Acids using Magnetic Particles 679
Further Reading 644 26 8 Lab-on-a-chip 680
Further Reading 680
25 Analysis of Post-translational Modifications:
Phosphorylation and Acetylation of Proteins 645 27 Analysis of Nucleic Acids 681
25 1 Functional Relevance of Phosphorylation and 27 1 Restriction Analysis 681
Acetylation 645 27 1 1 Principle of Restriction Analyses 681
25 1 1 Phosphorylation 645 27 1 2 Historical Overview 682
25 1 2 Acetylation 646 27 1 3 Restriction Enzymes 682
25 2 Strategies for the Analysis of Phosphorylated and 27 1 4 In Vitro Restriction and Applications 685
Acetylated Proteins and Peptides 647 27 2 Electrophoresis 690
25 3 Separation and Enrichment of Phosphorylated 27 2 1 Gel Electrophoresis of DNA 691
and Acetylated Proteins and Peptides 649 27 2 2 Gel Electrophoresis of RNA 697
25 4 Detection of Phosphorylated and Acetylated 27 2 3 Pulsed-Field Gel Electrophoresis (PFGE) 698
Proteins and Peptides 651 27 2 4 Two-Dimensional Gel Electrophoresis 700
25 4 1 Detection by Enzymatic, Radioactive, 27 2 5 Capillary Gel Electrophoresis 701
Immunochemical, and Fluorescence Based 27 3 Staining Methods 702
Methods 651 27 3 1 Fluorescent Dyes 702
25 4 2 Detection of Phosphorylated and Acetylated 27 3 2 Silver Staining 704
Proteins by Mass Spectrometry 653 27 4 Nucleic Acid Blotting 704
25 5 Localization and Identification of 27 4 1 Nucleic Acid Blotting Methods 704
Post-translationally Modified Amino Acids 653 27 4 2 Choice of Membrane 704
25 5 1 Localization of Phosphorylated and Acetylated 27 4 3 Southern Blotting 705
Amino Acids by Edman Degradation 654 27 4 4 Northern Blotting 706
25 5 2 Localization of Phosphorylated and Acetylated 27 4 5 Dot- and Slot-Blotting 707
Amino Acids by Tandem Mass Spectrometry 654 27 4 6 Colony and Plaque Hybridization 707
25 6 Quantitative Analysis of Post-translational 27 5 Isolation of Nucleic Acid Fragments 708
Modifications 659 27 5 1 Purification using Glass Beads 708
25 7 Future of Post-translational Modification Analysis 661 27 5 2 Purification using Gel Filtration or Reversed Phase 708
Further Reading 661 27 5 3 Purification using Electroelution 708
27 5 4 Other Methods 709
27 6 LC-MS of Oligonucleotides 709
Part IV Nucleic Acid 27 6 1 Principles of the Synthesis of Oligonucleotides 709
27 6 2 Investigation of the Purity and Characterization of
Analytics 6 63 Oligonucleotides 711
27 6 3 Mass Spectrometric Investigation of
26 Isolation and Purification of Nucleic Acids 665 Oligonucleotides 712
26 1 Purification and Determination of Nucleic Acid 27 6 4 IP-RP-HPLC-MS Investigation of a
Concentration 665 Phosphorothioate Oligonucleotide 714
26 1 1 Phenolic Purification of Nucleic Acids 665 Further Reading 717
26 1 2 Gel Filtration 666
26 1 3 Precipitation of Nucleic Acids with Ethanol 667 28 Techniques for the Hybridization and Detection
26 1 4 Determination of the Nucleic Acid Concentration 668 of Nucleic Acids 719
26 2 Isolation of Genomic DNA 669 28 1 Basic Principles of Hybridization 720
26 3 Isolation of Low Molecular Weight DNA 670 28 1 1 Principle and Practice of Hybridization 721
26 3 1 Isolation of Plasmid DNA from Bacteria 670 28 1 2 Specificity of the Hybridization and Stringency 722
26 3 2 Isolation of Eukaryotic Low Molecular Weight 28 1 3 Hybridization Methods 723
DNA 674 28 2 Probes for Nucleic Acid Analysis 729
26 4 Isolation of Viral DNA 674 28 2 1 DNA Probes 730
26 4 1 Isolation of Phage DNA 674 28 2 2 RNA Probes 731
26 4 2 Isolation of Eukaryotic Viral DNA 675 28 2 3 PNA Probes 732
26 5 Isolation of Single-Stranded DNA 676 28 2 4 LNA Probes 732
26 5 1 Isolation of M13 Phage DNA 676 28 3 Methods of Labeling 733
26 5 2 Separation of Single- and Double-Stranded DNA 676 28 3 1 Labeling Positions 733
Table of Contents
XI
28 3 2 Enzymatic Labeling
28 3 3 Photochemical Labeling Reactions
28 3 4 Chemical Labeling
28 4 Detection Systems
28 4 1 Staining Methods
28 4 2 Radioactive Systems
28 4 3 Non-radioactive Systems
28 5 Amplification Systems
28 5 1 Target Amplification
28 5 2 Target-Specific Signal Amplification
28 5 3 Signal Amplification
Further Reading
29 Polymerase Chain Reaction
29 1 Possibilities of PCR
29 2 Basics
29 2 1 Instruments
29 2 2 Amplification of DNA
29 2 3 Amplification of RNA (RT-PCR)
29 2 4 Optimizing the Reaction
29 2 5 Quantitative PCR
29 3 Special PCR Techniques
29 3 1 Nested PCR
29 3 2 Asymmetric PCR
29 3 3 Use of Degenerate Primers
29 3 4 Multiplex PCR
29 3 5 Cycle sequencing
29 3 6 In Vitro Mutagenesis
29 3 7 Homogeneous PCR Detection Procedures
29 3 8 Quantitative Amplification Procedures
29 3 9 In Situ PCR
29 3 10 Other Approaches
29 4 Contamination Problems
29 4 1 Avoiding Contamination
29 4 2 Decontamination
29 5 Applications
29 5 1 Detection of Infectious Diseases
29 5 2 Detection of Genetic Defects
29 5 3 The Human Genome Project
29 6 Alternative Amplification Procedures
29 6 1 Nucleic Acid Sequence-Based Amplification
(NASBA)
29 6 2 Strand Displacement Amplification (SDA)
29 6 3 Helicase-Dependent Amplification (HDA)
29 6 4 Ligase Chain Reaction (LCR)
29 6 5 Qß Amplification
29 6 6 Branched DNA Amplification (bDNA)
29 7 Prospects
Further Reading
30 DNA Sequencing
30 1 Gel-Supported DNA Sequencing Methods
30 1 1 Sequencing according to Sanger: The Dideoxy
Method
30 1 2 Labeling Techniques and Methods of Verification
30 1 3 Chemical Cleavage according to Maxam and
Gilbert
30 2 Gel-Free DNA Sequencing Methods - The Next
Generation 806
30 2 1 Sequencing by Synthesis 807
30 2 2 Single Molecule Sequencing 813
Further Reading 815
31 Analysis of Epigenetic Modifications 817
31 1 Overview of the Methods to Detect
DNA-Modifications 818
31 2 Methylation Analysis with the Bisulfite Method 819
31 2 1 Amplification and Sequencing of
Bisulfite-Treated DNA 819
31 2 2 Restriction Analysis after Bisulfite PCR 820
31 2 3 Methylation Specific PCR 822
31 3 DNA Analysis with Methylation Specific
Restriction Enzymes 823
31 4 Methylation Analysis by Methylcytosine-Binding
Proteins 825
31 5 Methylation Analysis by Methylcytosine-Specific
Antibodies 826
31 6 Methylation Analysis by DNA Hydrolysis and
Nearest Neighbor-Assays 827
31 7 Analysis of Epigenetic Modifications of Chromatin 828
31 8 Chromosome Interaction Analyses 828
31 9 Outlook 829
Further Reading 829
32 Protein-Nucleic Acid Interactions 831
32 1 DNA-Protein Interactions 831
32 1 1 Basic Features for DNA-Protein Recognition:
Double-Helical Structures 831
32 1 2 DNA Curvature 832
32 1 3 DNA Topology 833
32 2 DNA-Binding Motifs 835
32 3 Special Analytical Methods 836
32 3 1 Filter Binding 836
32 3 2 Gel Electrophoresis 836
32 3 3 Determination of Dissociation Constants 839
32 3 4 Analysis of DNA-Protein Complex Dynamics 840
32 4 DNA Footprint Analysis 841
32 4 1 DNA Labeling 843
32 4 2 Primer Extension Reaction for DNA Analysis 843
32 4 3 Hydrolysis Methods 844
32 4 4 Chemical Reagents for the Modification of
DNA-Protein Complexes 846
32 4 5 Interference Conditions 848
32 4 6 Chemical Nucleases * 849
32 4 7 Genome-Wide DNA-Protein Interactions 850
32 5 Physical Analysis Methods 851
32 5 1 Fluorescence Methods 851
32 5 2 Fluorophores and Labeling Procedures 851
32 5 3 Fluorescence Resonance Energy Transfer (FRET) 852
32 5 4 Molecular Beacons 853
32 5 5 Surface Plasmon Resonance (SPR) 853
32 5 6 Scanning Force Microscopy (SFM) 854
32 5 7 Optical Tweezers 855
32 5 8 Fluorescence Correlation Spectroscopy (FCS) 856
32 6 RNA-Protein Interactions 856
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XII Table of Contents
32 6 1 Functional Diversity of RNA 856 34 1 1 Overview 895
32 6 2 RNA Secondary Structure Parameters and unusual 34 1 2 Nuclease SI Analysis of RNA 896
Base Pairs 857 34 1 3 Ribonuclease-Protection Assay (RPA) 898
32 6 3 Dynamics of RNA-Protein Interactions 857 34 1 4 Primer Extension Assay 901
32 7 Characteristic RNA-Binding Motifs 859 34 1 5 Northern Blot and Dot- and Slot-Blot 902
32 8 Special Methods for the Analysis of RNA-Protein 34 1 6 Reverse Transcription Polymerase Chain Reaction
Complexes 860 (RT-PCR and RT-qPCR) 904
32 8 1 Limited Enzymatic Hydrolyses 861 34 2 Analysis of RNA Synthesis In Vivo 905
32 8 2 Labeling Methods 861 34 2 1 Nuclear-run-on Assay 905
32 8 3 Primer Extension Analysis of RNA 862 34 2 2 Labeling of Nascent RNA with 5-Fluoro-uridine
32 8 4 Customary RNases 862 (FUrd) 906
32 8 5 Chemcal Modification of RNA-Protein 34 3 In Vitro Transcription in Cell-Free Extracts 907
Complexes 863 34 3 1 Components of an In Vitro Transcription
32 8 6 Chemical Crosslinking 866 Assay 907
32 8 7 Incorporation of Photoreactive Nucleotides 867 34 3 2 Generation of Transcription-Competent Cell
32 8 8 Genome-Wide Identification of Transcription Start Extracts and Protein Fractions 908
Sites (TSS) 867 34 3 3 Template DNA and Detection of In Vitro
32 9 Genetic Methods 868 Transcripts 908
32 9 1 Tri-hybrid Method 868 34 4 In Vivo Analysis of Promoter Activity in
32 9 2 Aptamers and the Selex Procedure 869 Mammalian Cells 911
32 9 3 Directed Mutations within Binding Domains 870 34 4 1 Vectors for Analysis of Gene-Regulatory
Further Reading 870 cis-Elements 911
34 4 2 Transfer of DNA into Mammalian Cells 912
34 4 3 Analysis of Reporter Gene Expression 914
Part V Functional and Further Reading 916
Systems Analytics 873 35 Fluorescent In Situ Hybridization in Molecular
33 Sequence Data Analysis 875 Cytogenetics 917
33 1 Sequence Analysis and Bioinformatics 875 35 1 Methods of Fluorescent DNA Hybridization 917
33 2 Sequence: An Abstraction for Biomolecules 876 35 1 1 Labeling Strategy 917
33 3 Internet Databases and Services 877 35 1 2 DNA Probes 918
33 3 1 Sequence Retrieval from Public Databases 878 35 1 3 Labeling of DNA Probes 918
33 3 2 Data Contents and File Format 879 35 1 4 In Situ Hybridization 919
33 3 3 Nucleotide Sequence Management in the 35 1 5 Evaluation of Fluorescent Hybridization Signals 920
Laboratory 881 35 2 Application: FISH and CGH 920
33 4 Sequence Analysis on the Web 881 35 2 1 FISH Analysis of Genomic DNA 920
33 4 1 EMBOSS 881 35 2 2 Comparative Genomic Hybridization (CGH) 921
33 5 Sequence Composition 882 Further Reading 924
33 6 Sequence Patterns 882
33 6 1 Transcription Factor Binding Sites 884 36 Physical and Genetic Mapping of Genomes 925
33 6 2 Identification of Coding Regions 885 36 1 Genetic Mapping: Localization of Genetic
33 6 3 Protein Localization 886 Markers within the Genome 925
33 7 Homology 887 36 1 1 Recombination 925
33 7 1 Identity, Similarity, Homology 887 36 1 2 Genetic Markers 927
33 7 2 Optimal Sequence Alignment 888 36 1 3 Linkage Analysis - the Generation of Genetic
33 7 3 Alignment for Fast Database Searches: BLAST 890 Maps 929
33 7 4 Profile-Based Sensitive Database Search: 36 1 4 Genetic Map of the Human Genome 931
PSI-BLAST 890 36 1 5 Genetic Mapping of Disease Genes 932
33 7 5 Homology Threshold 891 36 2 Physical Mapping 932
33 8 Multiple Alignment and Consensus 36 2 1 Restriction Mapping of Whole Genomes 932
Sequences 891 36 2 2 Mapping of Recombinant Clones 934
33 9 Structure Prediction 892 36 2 3 Generation of a Physical Map 935
33 10 Outlook 893 36 2 4 Identification and Isolation of Genes 937
36 2 5 Transcription Maps of the Human Genome 939
34 Analysis of Promoter Strength and Nascent 36 2 6 Genes and Hereditary Disease - Search for
RNA Synthesis 895 Mutations 940
34 1 Methods for the Analysis of RNA Transcripts 895 36 3 Integration of Genome Maps 940
Table of Contents
XIII
36 4 The Human Genome 942 39 4 1 Two-Dimensional-Gel-Based Proteomics 982
Further Reading 942 39 4 2 Two-Dimensional Differential Gel Electrophoresis
(2D DIGE) 986
37 DNA-Microarray Technology 945 39 4 3 Top-Down Proteomics using Isotope Labels 986
37 1 RNA Analyses 946 39 4 4 Top-Down Proteomics using Intact Protein Mass
37 1 1 Transcriptome Analysis 946 Spectrometry 987
37 1 2 RNA Splicing 947 39 4 5 Concepts in Intact Protein Mass Spectrometry 987
37 1 3 RNA Structure and Functionality 947 39 5 Peptide Based Quantitative Proteome Analysis
37 2 DNA Analyses 948 (Bottom-Up Proteomics) 998
37 2 1 Genotyping 948 39 5 1 Introduction 998
37 2 2 Methylation Studies 948 39 5 2 Bottom-Up Proteomics 998
37 2 3 DNA Sequencing 949 39 5 3 Complexity of the Proteome 1000
37 2 4 Comparative Genomic Hybridization (CGH) 951 39 5 4 Bottom-Up Proteomic Strategies 1000
37 2 5 Protein-DNA Interactions 951 39 5 5 Peptide Quantification 1001
37 3 Molecule Synthesis 952 39 5 6 Data Dependent Analysis (DDA) 1002
37 3 1 DNA Synthesis 952 39 5 7 Selected Reaction Monitoring 1003
37 3 2 RNA Production 953 39 5 8 SWATH-MS 1010
37 3 3 On-Chip Protein Expression 953 39 5 9 Summary 1012
37 4 Other Approaches 954 39 5 10 Extensions 1012
37 4 1 Barcode Identification 954 39 6 Stable Isotope Labeling in Quantitative
37 42A Universal Microarray Platform 955 Proteomics 1013
37 5 New Avenues 956 39 6 1 Stable Isotope Label in Top-Down Proteomics 1013
37 5 1 Structural Analyses 956 39 6 2 Stable Isotope Labeling in Bottom-Up Proteomics 1019
37 5 2 Beyond Nucleic Acids 956 Further Reading 1021
Further Reading 957
38 The Use of Oligonucleotides as Tools in 40 Metabolomics and Peptidomics 1023
Cell Biology 959 40 1 Systems Biology and Metabolomics 1025
38 1 Antisense Oligonucleotides 960 40 2 Technological Platforms for Metabolomics 1026
38 1 1 Mechanisms of Antisense Oligonucleotides 960 40 3 Metabolomic Profiling 1027
38 1 2 Triplex-Forming Oligonucleotides 961 40 4 Peptidomics 1028
38 1 3 Modifications of Oligonucleotides to Decrease 40 5 Metabolomics - Knowledge Mining 1029
their Susceptibility to Nucleases 962 40 6 Data Mining 1030
38 1 4 Use of Antisense Oligonucleotides in 40 7 Fields of Application 1032
Cell Culture and in Animal Models 964 40 8 Outlook 1032
38 1 5 Antisense Oligonucleotides as Therapeutics 964 Further Reading 1032
38 2 Ribozymes 965
38 2 1 Discovery and Classification of Ribozymes 965 41 Interactomics - Systematic Protein-Protein
|
| any_adam_object | 1 |
| author2 | Lottspeich, Friedrich 1947- Engels, Joachim W. 1944-2018 |
| author2_role | edt edt |
| author2_variant | f l fl j w e jw jwe |
| author_GND | (DE-588)120183749 (DE-588)120266962 |
| author_facet | Lottspeich, Friedrich 1947- Engels, Joachim W. 1944-2018 |
| building | Verbundindex |
| bvnumber | BV044880442 |
| classification_rvk | WC 4150 |
| classification_tum | UMW 045f |
| ctrlnum | (OCoLC)1032677682 (DE-599)DNB1070857211 |
| discipline | Biologie Umwelt |
| format | Book |
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| illustrated | Illustrated |
| indexdate | 2024-07-10T08:03:39Z |
| institution | BVB |
| institution_GND | (DE-588)16179388-5 |
| isbn | 9783527339198 3527339191 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030274675 |
| oclc_num | 1032677682 |
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| owner | DE-29T DE-B768 DE-11 DE-703 DE-M49 DE-BY-TUM DE-1028 DE-91 DE-BY-TUM DE-355 DE-BY-UBR DE-12 DE-19 DE-BY-UBM DE-83 DE-634 DE-523 DE-20 |
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| physical | XXIV, 1110 Seiten Illustrationen, Diagramme 27.6 cm x 21 cm |
| publishDate | 2018 |
| publishDateSearch | 2018 |
| publishDateSort | 2018 |
| publisher | Wiley-VCH Verlag GmbH & Co. KGaA |
| record_format | marc |
| spelling | Bioanalytik Bioanalytics analytical methods and concepts in biochemistry and molecular biology Edited by Friedrich Lottspeich and Joachim Engels Weinheim Wiley-VCH Verlag GmbH & Co. KGaA [2018] © 2018 XXIV, 1110 Seiten Illustrationen, Diagramme 27.6 cm x 21 cm txt rdacontent n rdamedia nc rdacarrier Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Biochemische Analyse (DE-588)4255721-5 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf Biowissenschaften, Biologie Bioanalytical Chemistry Bioanalytische Chemie Biochemie Biochemie u. Chemische Biologie Biowissenschaften Cell & Molecular Biology Chemie Chemistry Life Sciences Molekularbiologie Zell- u. Molekularbiologie Biochemische Analyse (DE-588)4255721-5 s DE-604 Molekularbiologie (DE-588)4039983-7 s Methode (DE-588)4038971-6 s Lottspeich, Friedrich 1947- (DE-588)120183749 edt Engels, Joachim W. 1944-2018 (DE-588)120266962 edt Wiley-VCH (DE-588)16179388-5 pbl Erscheint auch als Online-Ausgabe, ePDF 978-3-527-694444-0 Erscheint auch als Online-Ausgabe, ePUB 978-3-527-694446-4 Erscheint auch als Online-Ausgabe, MOBI 978-3-527-694447-1 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=5249475&prov=M&dok_var=1&dok_ext=htm Inhaltstext HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030274675&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bioanalytics analytical methods and concepts in biochemistry and molecular biology Molekularbiologie (DE-588)4039983-7 gnd Biochemische Analyse (DE-588)4255721-5 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4255721-5 (DE-588)4038971-6 |
| title | Bioanalytics analytical methods and concepts in biochemistry and molecular biology |
| title_alt | Bioanalytik |
| title_auth | Bioanalytics analytical methods and concepts in biochemistry and molecular biology |
| title_exact_search | Bioanalytics analytical methods and concepts in biochemistry and molecular biology |
| title_full | Bioanalytics analytical methods and concepts in biochemistry and molecular biology Edited by Friedrich Lottspeich and Joachim Engels |
| title_fullStr | Bioanalytics analytical methods and concepts in biochemistry and molecular biology Edited by Friedrich Lottspeich and Joachim Engels |
| title_full_unstemmed | Bioanalytics analytical methods and concepts in biochemistry and molecular biology Edited by Friedrich Lottspeich and Joachim Engels |
| title_short | Bioanalytics |
| title_sort | bioanalytics analytical methods and concepts in biochemistry and molecular biology |
| title_sub | analytical methods and concepts in biochemistry and molecular biology |
| topic | Molekularbiologie (DE-588)4039983-7 gnd Biochemische Analyse (DE-588)4255721-5 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | Molekularbiologie Biochemische Analyse Methode |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=5249475&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030274675&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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