Note: Intro -- PCR Protocols: Second Edition -- Preface -- Contents -- Contributors -- PART I. INTRODUCTION TO PCR -- 1 A Short History of the Polymerase Chain Reaction -- 2 PCR Patent Issues -- 3 Equipping and Establishing a PCR Laboratory -- 4 Quality Control in PCR -- PART II. PREPARATION OF NUCLEIC ACID TEMPLATES -- 5 Extraction of Nucleic Acid Templates -- 6 Extraction of DNA from Whole Blood -- 7 DNA Extraction from Tissue -- 8 Extraction of DNA from Microdissected Archival Tissues -- 9 RNA Extraction from Blood -- 10 RNA Extraction from Frozen Tissue -- 11 RNA Extraction from Tissue Sections -- 12 Dual DNA/RNA Extraction -- 13 DNA Extraction from Fungi, Yeast, and Bacteria -- 14 Isolation of RNA Viruses from Biological Materials -- 15 Extraction of Ancient DNA -- 16 DNA Extraction from Plasma and Serum -- 17 Technical Notes for the Detection of Nucleic Acids -- 18 Technical Notes for the Recovery and Purification of PCR Products from Acrylamide Gels -- PART III. BASIC PCR METHODS -- 19 PCR Primer Design -- 20 Optimization of Polymerase Chain Reactions -- 21 Subcycling PCR for Long-Distance Amplifications of Regions with High and Low Guanine-Cystine Content: Amplification of the Intron 22 Inversion of the FVIII Gene -- 22 Rapid Amplification of cDNA Ends -- 23 Randomly Amplified Polymorphic DNA Fingerprinting: The Basics -- 24 Microsphere-Based Single Nucleotide Polymorphism Genotyping -- 25 Ligase Chain Reaction -- 26 Nested RT-PCR in a Single Closed Tube -- 27 Direct PCR from Serum: Application to Viral Genome Detection -- 28 Long PCR Amplification of Large Fragments of Viral Genomes: A Technical Overview -- 29 Long PCR Methodology -- PART IV. ULTRASENSITIVE AND QUANTITATIVE PCR -- 30 Qualitative and Quantitative PCR A Technical Overview -- 31 Ultrasensitive PCR Detection of Tumor Cells in Myeloma. , 32 Ultrasensitive Quantitative PCR to Detect RNA Viruses -- 33 Quantitative PCR for cAMP RI Alpha mRNA Use of Site-Directed Mutation and PCR Mimics -- 34 Quantitation of Multiple RNA Species -- PART V. TRANSCRIPTOME ANALYSIS VTRANSCRIPTOME ANALYSIS VTRANSCRIPTOME ANALYSIS -- 35 Differential Display: A Technical Overview -- 36 AU-Differential Display, Reproducibility of a Differential mRNA Display Targeted to AU Motifs -- 37 PCR Fluorescence Differential Display -- 38 Microarray Analysis Using RNA Arbitrarily Primed PCR -- 39 Oligonucleotide Arrays for Genotyping: Enzymatic Methods for Typing Single Nucleotide Polymorphisms and Short Tandem Repeats -- 40 Serial Analysis of Gene Expression -- PART VI. MUTATIONS AND POLYMORPHISMS -- 41 Mutation and Polymorphism Detection: A Technical Overview -- 42 Combining Multiplex and Touchdown PCR for Microsatellite Analysis -- 43 Detection of Microsatellite Instability and Loss of Heterozygosity Using DNA Extracted from Formalin-Fixed Paraffin-Embedded Tumor Material by Fluorescence-Based Multiplex Microsatellite PCR -- 44 Reduction of Shadow Band Synthesis During PCR Amplification of Repetitive Sequences from Modern and Ancient DNA -- 45 Degenerate Oligonucleotide-Primed PCR -- 46 Mutation Detection Using RT-PCR-RFLP -- 47 Multiplex Amplification Refractory Mutation System for the Detection of Prothrombotic Polymorphisms -- 48 PCR-SSCP Analysis of Polymorphism: A Simple and Sensitive Method for Detecting Differences Between Short Segments of DNA -- PART VII. PCR-BASED SEQUENCING -- 49 Sequencing: A Technical Overview -- 50 Preparation and Direct Automated Cycle Sequencing of PCR Products -- 51 Nonradioactive PCR Sequencing Using Digoxigenin -- 52 Direct Sequencing by Thermal Asymmetric PCR -- 53 Analysis of Nucleotide Sequence Variations by Solid-Phase Minisequencing. , 54 Direct Sequencing with Highly Degenerate and Inosine-Containing Primers -- 55 Determination of Unknown Genomic Sequences Without Cloning -- 56 Cloning PCR Products for Sequencing in M13 Vectors -- 57 DNA Rescue by the Vectorette Method -- 58 Technical Notes for Sequencing Difficult Templates -- PART VIII. IN SITU PCR AND PRINS -- 59 PCR-Based Detection of Nucleic Acids in Chromosomes, Cells, and Tissues: Technical Considerations on PRINS and In Situ PCR and Comparison with In Situ Hybridization -- 60 Cycling Primed In Situ Amplification -- 61 Direct and Indirect In Situ PCR -- 62 Reverse Transcriptase In Situ PCR: New Methods in Cellular Interrogation -- 63 Primed In Situ Nucleic Acid Labeling Combined with Immunocytochemistry to Simultaneously Localize DNA and Proteins in Cells and Chromosomes -- 64 Cloning and Mutagenesis: A Technical Overview -- 65 Using T4 DNA Polymerase to Generate Clonable PCR Products -- 66 A T-Linker Strategy for Modification and Directional Cloning of PCR Products -- 67 Cloning Gene Family Members Using PCR with Degenerate Oligonucleotide Primers -- 68 cDNA Libraries from a Low Amount of Cells -- 69 Creation of Chimeric Junctions, Deletions, and Insertions by PCR -- 70 Recombination and Site-Directed Mutagenesis Using Recombination PCR -- 71 Megaprimer PCR: Application in Mutagenesis and Gene Fusion -- Index.