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The newest and most up-to-date collection, PCR Protocols offers detailed laboratory procedures for the use of polymerase chain reactions in a wide range of applications. Although specific examples and experimental systems are described, the book’s focus is on general applications that can be modified to suit a broad spectrum of research systems, thus making its scope appealing to nearly all researchers. PCR Protocols features clear, easy-to-follow descriptions of procedures and a Notes section in each chapter to provide tips, alternative suggestions, and other enhancements of the protocols. Key Topics and Techniques: basic startup procedures for PCR - PCR in detecting DNA and RNA - PCR in DNA synthesis and mutagenesis - PCR cloning of DNA - selection of primers - radioactive and nonradioactive labeling - quantitation of PCR products by HPLC - chromosome assignment - PCR mapping of HLA genes - sequencing of PCR products - genomic footprinting - quantitation of tumor gene expression - screening of phage libraries - SSP-PCR and genome walking - subcloning of PCR products. Authors: White, Bruce A.

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Table of Contents

1. Polymerase Chain Reaction: Basic Protocols (pp. 1-30)
   Delidow, Beverly C.; Lynch, John P.; Peluso, John J.; White, Bruce A.
2. Selection of Primers for Polymerase Chain Reaction (pp. 31-40)
   Rychlik, Wojciech
3. Direct Radioactive Labeling of Polymerase Chain Reaction Products (pp. 41-44)
   McDaniel, Tim; Meltzer, Stephen J.
4. Use of Arithmetic Polymerase Chain Reaction for Synthesis of Single-Stranded Probes for S1 Nuclease Assays (pp. 45-50)
   Agarwal, Puja; White, Bruce A.
5. Nonradioactive Labeling of Polymerase Chain Reaction Products (pp. 51-62)
   Reischl, Udo; Ruger, Rudiger; Kessler, Christoph
6. Quantitation and Purification of Polymerase Chain Reaction Products by High-Performance Liquid Chromatography (pp. 63-74)
   Katz, Elena D.
7. Use of Polymerase Chain Reaction for Screening Transgenic Mice (pp. 75-80)
   Chen, Shizhong; Evans, Glen A.
8. Polymerase Chain Reaction Analysis of DNA from Paraffin-Embedded Tissue (pp. 81-88)
   Volkenandt, Matthias; Dicker, Adam P.; Fanin, Renato; Banerjee, Debabrata; Albino, Anthony; Bertino, Joseph R.
9. The Use of Polymerase Chain Reaction for Chromosome Assignment (pp. 89-94)
   Jaye, Michael; Dionne, Craig A.
10. Mapping MHC Class II Genes and Disease-Susceptibility: Use of Polymerase Chain Reaction and Dot Hybridization for Human Leukocyte Antigen Allele Typing (pp. 95-112)
    Bain, Stephen C.; Todd, John A.
11. The Use of the Polymerase Chain Reaction and the Detection of Amplified Products (pp. 113-128)
    Allen, Robert C.; Budowle, Bruce
12. Determination of Loss of Heterozygosity Using Polymerase Chain Reaction (pp. 129-136)
    Meltzer, Stephen J.
13. Direct Sequencing of Polymerase Chain Reaction Products (pp. 137-142)
    Meltzer, Stephen J.
14. Manual and Automated Direct Sequencing of Product Generated by the Polymerase Chain Reaction (pp. 143-152)
    Dicker, Adam P.; Volkenandt, Matthias; Bertino, Joseph R.
15. Genomic Footprinting by Ligation Mediated Polymerase Chain Reaction (pp. 153-168)
    Pfeifer, Gerd P.; Riggs, Arthur D.
16. RNA Template-Specific Polymerase Chain Reaction (RS-PCR): A Modification of RNA-PCR that Dramatically Reduces the Frequency of False Positives (pp. 169-176)
    Shuldiner, Alan R.; Perfetti, Riccardo; Roth, Jesse
17. Quantitative Measurement of Relative Gene Expression in Human Tumors (pp. 177-188)
    Horikoshi, Tetsuro; Danenberg, Kathleen; Volkenandt, Matthias; Stadlbauer, Thomas; Danenberg, Peter V.
18. Identification of Alternatively Spliced mRNAs and Localization of 5??? Ends by Polymerase Chain Reaction Amplification (pp. 189-198)
    Chiang, Cheng-Ming; Chow, Louise T.; Broker, Thomas R.
19. Utilization of Polymerase Chain Reaction for Clonal Analysis of Gene Expression (pp. 199-204)
    Witsell, Alice L.; Schook, Lawrence B.
20. Sequencing DNA Amplified Directly from a Bacterial Colony (pp. 205-210)
    Hofmann, Martin A; Brian, David A.
21. Use of Polymerase Chain Reaction to Screen Phage Libraries (pp. 211-216)
    Yu, Lei; Bloem, Laura J.
22. Molecular Cloning of Polymerase Chain Reaction Fragments with Cohesive Ends (pp. 217-228)
    Delidow, Beverly C.
23. Rapid (Ligase-Free) Subcloning of Polymerase Chain Reaction Products (pp. 229-240)
    Shuldiner, Alan R.; Tanner, Keith
24. Use of Polymerase Chain Reaction for Making Recombinant Constructs (pp. 241-250)
    Jones, Douglas H.; Winistorfer, Stanley C.
25. In Vitro Recombination and Mutagenesis of DNA: SOEing Together Tailor-Made Genes (pp. 251-262)
    Horton, Robert M.
26. Use of Polymerase Chain Reaction for the Rapid Construction of Synthetic Genes (pp. 263-268)
    Dillon, Patrick J.; Rosen, Craig A.
27. Recombinant Circle Polymerase Chain Reaction for Site-Directed Mutagenesis (pp. 269-276)
    Jones, Douglas H.
28. Site-Directed Mutagenesis by Double Polymerase Chain Reaction: Megaprimer Method (pp. 277-286)
    Barik, Sailen
29. Generation of a Polymerase Chain Reaction Renewable Source of Subtractive cDNA (pp. 287-304)
    Kuehl, W. Michael; Battey, James
30. PCR-Based Full-Length cDNA Cloning Utilizing the Universal-Adaptor/Specific DOS Primer-Pair Strategy (pp. 305-316)
    Cooper, David L.; Isola, Narayana R.
31. Use of Degenerate Oligonucleotide Primers and the Polymerase Chain Reaction to Clone Gene Family Members (pp. 317-338)
    Preston, Gregory M.
32. Single Specific Primer-Polymerase Chain Reaction (SSP-PCR) and Genome Walking (pp. 339-348)
    Shyamala, Venkatakrishna; Ames, Giovanna Ferro-Luzzi
33. cDNA Cloning by Inverse Polymerase Chain Reaction (pp. 349-356)
    Huang, Sheng-He; Wu, Chun-Hua; Cai, Bing; Holcenberg, John
34. Amplification of Gene Ends from Gene Libraries by Polymerase Chain Reaction with Single-Sided Specificity (pp. 357-364)
    Huang, Sheng-He; Jong, Ambrose Y.; Yang, Wu; Holcenberg, John
35. Anchoring a Defined Sequence to the 5??? Ends of mRNAs: The Bolt to Clone Rare Full Length mRNAs and Generate cDNA Libraries from a Few Cells (pp. 365-386)
    Edwards, Jean Baptiste Dumas Milne; Delort, Jacques; Mallet, Jacques