PCR strategies

Part One KEY CONCEPTS FOR PCR 1. The Use of Cosolvents to Enhance Amplification by the Polymerase Chain Reaction 3 P. A. Landre, D. H. Gelfand, and R. M. Watson 2. DNA Polymerase Fidelity: Misinsertions and Mismatched Extensions 17 Myron F. Goodman 3. Extraction of Nucleic Acids: Sample Preparation from Paraffin-Embedded Tissues 32 Hiroko Shimizu and lane C. Burns 4. Thermostable DNA Polymerases Richard D. Abramson 39 5. Amplification of RNA: High-Temperature Reverse Transcription and DNA Amplification with Thermus thermophilus DNA Polymerase 58 Thomas W. Myers and Christopher L. Sigua 6. Nucleic Acid Hybridization and Unconventional Bases 69 James G. Wetmur and John I. Sninsky vi Contents 7. Practical Considerations for the Design of Quantitative PCR Assays 84 Robert Diaco Part Two ANALYSIS OF PCR PRODUCTS 8. Carrier Detection of Cystic Fibrosis Mutations Using PCR-Amplified DNA and a Mismatch-Binding Protein, MutS 111 Alla Lishanski and Jasper Rine 9. Single-Stranded Conformational Polymorphisms Anne L. Bailey 121 10. Analysis of PCR Products by Covalent Reverse Dot Blot Hybridization 130 Farid F. Chehab, Jeff Wall, and Shi-ping Cai 11. High-Performance Liquid Chromatography Analysis of PCR Products 140 John M. Wages, Xumei Zhao, and Elena D. Katz 12. Heteroduplex Mobility Assays for Phylogenetic Analysis 154 Eric L. Delwart, Eugene G. Shpaer, and James I. Mullins 13. PCR Amplification of VNTRs S. Scharf 161 Part Three RESEARCH APPLICATIONS 14. Site-Specific Mutagenesis Using the Polymerase Chain Reaction 179 Jonathan Silver, Teresa Limjoco, and Stephen Feinstone Contents vii 15. Exact Quantification of DNA-RNA Copy Numbers by PCR-TGGE 189 Jie Kang, Peter Schiifer, Joachim E. Kfihn, Andreas Immelmann, and Karsten Henco 16. The in Situ PCR" Amplication and Detection of DNA in a Cellular Context 199 Ernest Retzel, Katherine A. Staskus, Janet E. Embretson, and Ashley T. Haase 17. Y Chromosome-Specific PCR" Maternal Blood Diana W. Bianchi 213 18. Genomic Subtraction Don Straus 220 19. DNA Amplification-Restricted Transcription Translation (DARTT)" Analysis of in Wtro and in Situ Protein Functions and Intermolecular Assembly 237 Erich R. Mackow 20. DNA and RNA Fingerprinting Using Arbitrarily Primed PCR 249 John Welsh, David Ralph, and Michael McClelland 21. PCR-Based Screening of Yeast Artificial Chromosome Libraries 277 Eric D. Green 22. Oligonucleotide Ligands That Discriminate between Theophylline and Caffeine 289 Rob ]enison, Stanley Gill, Jr., and Barry Polisky 23. Generation of Single-Chain Antibody Fragments by PCR 300 Jeffrey R. Stinson, Vaughan Wittman, and Hing C. Wong 24. Longer PCR Amplifications Suzanne Cheng 313 viii Contents 25. Direct Analysis of Specific Bonds from Arbitrarily Primed PCR Reactions 325 D. A. Carter, A. Burt, and I. W. Taylor Part Four ALTERNATIVE AMPLIFICATION STRATEGIES 26. Detection of Leber's Hereditary Optic Neuropathy by Nonradioactive Ligase Chain Reaction 335 John A. Zebala and Francis Barany 27. Detection of Listeria monocytogenes by PCR-Coupled Ligase Chain Reaction 347 Martin Wiedmann, Francis Barany, and Carl A. Batt Index 363