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Copyright, iv
Dedication, v
Preface, vii
Reviewers, ix
Acknowledgments, xi
Section 1. Fundamentals of Nucleic Acid Biochemistry: An Overview, 1
Chapter 1. DNA, 1
DNA, 2
DNA Structure, 2
Nucleotides, 3
Nucleic Acid, 6
DNA Replication, 7
Polymerases, 8
Enzymes that Metabolize DNA, 12
Restriction Enzymes, 12
DNA Ligase, 14
Other DNA Metabolizing Enzymes, 14
Recombination in Sexually Reproducing Organisms, 17
Recombination in Asexual Reproduction, 18
Conjugation, 19
Transduction, 20
Transformation, 21
Plasmids, 22
Chapter 2. RNA, 27
Transcription, 28
Types/Structures, 29
Ribosomal RNA, 30
Messenger RNA, 30
Small Nuclear RNA, 34
Small Interfering RNA, 34
Transfer RNA, 34
Micro RNAs, 35
Other Small RNAs, 36
RNA Polymerases, 36
Other RNA-Metabolizing Enzymes, 37
Ribonucleases, 37
RNA Helicases, 38
Regulation of Transcription, 38
Epigenetics, 42
Chapter 3. Proteins, 48
Amino Acids, 49
Genes and the Genetic Code, 54
The Genetic Code, 55
Translation, 57
Amino Acid Charging, 57
Protein Synthesis, 57
Section 2. Common Techniques in Molecular Biology, 65
Chapter 4. Nucleic Acid Extraction Methods, 65
Isolation of DNA, 66
Preparing the Sample, 66
Organic Isolation Methods, 67
Inorganic Isolation Methods, 68
Solid-Phase Isolation, 69
Crude Lysis, 71
Isolation of Mitochondrial DNA, 71
Isolation of RNA, 72
Total RNA, 72
Extraction of Total RNA, 72
Isolation of polyA (messenger) RNA, 74
Measurement of Nucleic Acid Quality and Quantity, 75
Electrophoresis, 75
Spectrophotometry, 76
Fluorometry, 77
Chapter 5. Resolution and Detection of Nucleic Acids, 80
Electrophoresis, 81
Gel Systems, 81
Agarose Gels, 81
Polyacrylamide Gels, 84
Capillary Electrophoresis, 85
Buffer Systems, 86
Buffer Additives, 88
Electrophoresis Equipment, 88
Gel Loading, 90
Detection Systems, 91
Nucleic Acid–Specific Dyes, 91
Silver Stain, 92
Chapter 6. Analysis and Characterization of Nucleic Acids and Proteins, 94
Restriction Enzyme Mapping, 95
Hybridization Technologies, 96
Southern Blots, 96
Northern Blots, 101
Western Blots, 102
Probes, 103
DNA Probes, 103
RNA Probes, 103
Other Nucleic Acid Probe Types, 104
Protein Probes, 104
Probe Labeling, 105
Nucleic Acid Probe Design, 106
Hybridization Conditions, Stringency, 107
Detection Systems, 109
Interpretation of Results, 111
Array-Based Hybridization, 112
Dot/Slot Blots, 112
Genomic Array Technology, 113
Solution Hybridization, 117
Chapter 7. Nucleic Acid Amplification, 121
Target Amplification, 122
Polymerase Chain Reaction, 122
Transcription-Based Amplification Systems, 142
Probe Amplification, 144
Ligase Chain Reaction, 144
Strand Displacement Amplification, 144
Qβ Replicase, 145
Signal Amplification, 147
Branched DNA Amplification, 147
Hybrid Capture Assays, 148
Cleavage-Based Amplification, 148
Cycling Probe, 149
Chapter 8. Chromosomal Structure and Chromosomal Mutations, 155
Chromosomal Structure and Analysis, 157
Chromosomal Compaction and Histones, 157
Chromosomal Morphology, 159
Visualizing Chromosomes, 159
Detection of Genome and Chromosomal Mutations, 161
Karyotyping, 161
Fluorescence In Situ Hybridization, 166
Chapter 9. Gene Mutations, 173
Types of Gene Mutations, 174
Detection of Gene Mutations, 174
Hybridization-Based Methods, 175
Sequencing (Polymerization)-Based Methods, 185
Cleavage Methods, 189
Other Methods, 193
Gene Mutation Nomenclature, 194
Chapter 10. DNA Sequencing, 203
Direct Sequencing, 204
Manual Sequencing, 204
Automated Fluorescent Sequencing, 210
Pyrosequencing, 214
Bisulfite DNA Sequencing, 216
Bioinformatics, 218
The Human Genome Project, 219
Section 3. Techniques in the Clinical Lab, 225
Chapter 11. DNA Polymorphisms and Human Identification, 225
Types of Polymorphisms, 226
RFLP Typing, 226
Genetic Mapping With RFLPs, 228
RFLP and Parentage Testing, 229
Human Identification Using RFLP, 229
STR Typing by PCR, 231
STR Nomenclature, 232
Gender Identification, 234
Analysis of Test Results, 235
Y-STR, 241
Matching with Y-STRs, 242
Engraftment Testing Using DNA Polymorphisms, 245
Linkage Analysis, 249
Quality Assurance of Tissue Sections Using STR, 251
Single Nucleotide Polymorphisms, 252
The Human Haplotype (Hap Map) Mapping Project, 252
Mitochondrial DNA Polymorphisms, 253
Chapter 12. Detection and Identification of Microorganisms, 263
Specimen Collection, 264
Sample Preparation, 266
Quality Control, 266
Bacterial Targets of Molecular-Based Tests, 268
Selection of Sequence Targets for Detection of Microorganisms, 268
Molecular Detection of Bacteria, 269
Respiratory Tract Pathogens, 270
Urogenital Tract Pathogens, 276
Antimicrobial Agents, 280
Resistance to Antimicrobial Agents, 280
Molecular Detection of Resistance, 282
Molecular Epidemiology, 284
Molecular Strain Typing Methods for Epidemiological Studies, 284
Comparison of Typing Methods, 289
Viruses, 291
Human Immunodeficiency Virus, 292
Hepatitis C Virus, 298
Summary, 299
Fungi, 299
Parasites, 300
Chapter 13. Molecular Detection of Inherited Diseases, 310
The Molecular Basis of Inherited Diseases, 311
Chromosomal Abnormalities, 311
Patterns of Inheritance in Single-Gene Disorders, 312
Molecular Basis of Single-Gene Disorders, 314
Lysosomal Storage Diseases, 315
Molecular Diagnosis of Single-Gene Disorders, 316
Factor V Leiden, 316
Hemochromatosis, 317
Cystic Fibrosis, 318
Cytochrome P-450, 319
Single-Gene Disorders with Nonclassical Patterns of Inheritance, 319
Mutations in Mitochondrial Genes, 319
Trinucleotide Repeat Expansion Disorders, 322
Genomic Imprinting, 325
Multifactorial Inheritance, 326
Limitations to Molecular Testing, 326
Chapter 14. Molecular Oncology, 332
Classification of Neoplasms, 333
Molecular Basis of Cancer, 333
Analytical Targets of Molecular Testing, 334
Gene and Chromosomal Mutations in Solid Tumors, 335
Microsatellite Instability, 343
Loss of Heterozygosity, 346
Gene Rearrangements in Leukemia and Lymphoma, 346
V(D)J Recombination, 347
Detection of Clonality, 350
Translocations in Hematological Malignancies, 356
Chapter 15. DNA-Based Tissue Typing, 376
The MHC Locus, 377
HLA Polymorphisms, 379
HLA Nomenclature, 380
Molecular Analysis of the MHC, 384
Serological Analysis, 384
DNA-Based Typing, 388
Combining Typing Results, 392
HLA Test Discrepancies, 393
Coordination of HLA Test Methods, 393
Additional Recognition Factors, 393
Minor Histocompatibility Antigens, 393
Nonconventional MHC Antigens, 393
Killer Cell Immunoglobulin-like Receptors, 394
MHC Disease Association, 394
Summary of Laboratory Testing, 395
Chapter 16. Quality Assurance and Quality Control in the Molecular Laboratory, 403
Specimen Handling, 404
Collection Tubes for Molecular Testing, 405
Precautions, 406
Holding and Storage Requirements, 407
Test Performance, 409
Controls, 412
Quality Assurance, 412
Instrument Maintenance, 413
Calibrations, 416
Reagents, 417
Chemical Safety, 418
Proficiency Testing, 419
Documentation of Test Results, 420
Gene Sequencing Results, 421
Reporting Results, 421
Appendix, 427
Index, 441

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