PCR Protocols

Part I: PCR Husbandry 1. Setup of a PCR Laboratory Zaheer Khan Part II: Cloning and Sequencing 2. Long Range PCR with a DNA Polymerase Fusion Holly H. Hogrefe and Michael C. Borns 3. Isolation of Genomic Insertion Sites of Proviruses Using Splinkerette-PCR-Based Procedures Bin Yin 4. Lariat-Dependent Nested PCR for Flanking Sequence Determination Daniel J. Park 5. CODEHOP PCR and CODEHOP PCR Primer Design Jeannette P. Staheli, Richard Boyce, Dina Kovarik, and Timothy M. Rose 6. Sequencing of Difficult DNA Regions by SAM Sequencing Keith R. Mitchelson Part III: Expression, Epigenetic and Copy Number Analysis 7. A Global Single-Cell cDNA Amplification Method for Quantitative Microarray Analysis Kazuki Kurimoto and Mitinori Saitou 8. Quantitation of MicroRNAs by Real-Time RT-qPCR Caifu Chen, Ruoying Tan, Linda Wong, Richard Fekete, and Jason Halsey 9. High-Throughput SuperSAGE Hideo Matsumura, Kentaro Yoshida, Shujun Luo, Detlev H. Kruger, Gunter Kahl, Gary P. Schroth, and Ryohei Terauchi 10. Deep Cap Analysis of Gene Expression (Deep CAGE) Junpei Kurosawa, Hiromi Nishiyori, and Yoshihide Hayashizaki 11. Linking Emulsion PCR Haplotype Analysis James G. Wetmur and Jia Chen 12. PAP-LMPCR: An Improved, Sequence-Selective Method for the In vivo Analysis of Transcription Factor Occupancy and Chromatin Fine Structure Richard Ingram, Arthur Riggs, and Constanze Bonifer 13. The Many Faces of MLPA Thomas Ohnesorg, Erin Turbitt, and Stefan J. White 14. Assessing Gene-Specific Methylation Using HRM-Based Analysis Ee Ming Wong and Alexander Dobrovic Part IV: Probes and Assays 15. Alu PCR Maurizio Cardelli 16. Asynchronous PCR Caifu Chen, David Ruff, and Jason Halsey 17. Novel Applications of PCR through the Use of DNA Substrates Stuart M. Wilson 18. Enhanced Solid Phase PCR for Increased Loading of Amplicon onto Solid Support Daniel J. Park 19. Application of Blocking Oligonucleotides to Improve Signal to Noise Ratio in a PCR Hege Vestheim, Bruce E. Deagle, and Simon N. Jarman Part V: Engineering and Screening 20. Asymmetric Overlap Extension PCR Method for Site-Directed Mutagenesis Yue-Hua Xiao and Yan Pei 21. Ribosome Display: A Technology for Selecting and Evolving Proteins from Large Libraries Birgit Dreier and Andreas Pluckthun 22. GLOBE: Analysis of DNA-Protein Interaction Analysis Takaaki Kojima and Hideo Nakano 23. PCR DNA-Array Profiling of DNA-Binding Transcription Factor Activities in Adult Mouse Tissues Yimin Sun, Jing Cheng, and Keith R. Mitchelson 24. Nucleotide Exchange and Excision Technology (NExT) DNA Shuffling and Directed Evolution Janina Speck, Sabine C. Stebel, Katja M. Arndt, and Kristian M. Muller