PCR cloning protocols

Preface .............................................................................................................v Contributors .....................................................................................................xi PART I. PERFORMING AND OPTIMIZING PCR 1 Polymerase Chain Reaction: Basic Principles and Routine Practice Lori A. Kolmodin and David E. Birch .................................................. 3 2 Computer Programs for PCR Primer Design and Analysis Bing-Yuan Chen, Harry W. Janes, and Steve Chen ........................ 19 3 Single-Step PCR Optimization Using Touchdown and Stepdown PCR Programming Kenneth H. Roux .................................................................................. 31 4 XL PCR Amplification of Long Targets from Genomic DNA Lori A. Kolmodin .................................................................................. 37 5 Coupled One-Step Reverse Transcription and Polymerase Chain Reaction Procedure for Cloning Large cDNA Fragments Jyrki T. Aatsinki ................................................................................... 53 6 Long Distance Reverse-Transcription PCR Volker Thiel, Jens Herold, and Stuart G. Siddell ............................. 59 7 Increasing PCR Sensitivity for Amplification from Paraffin-Embedded Tissues Abebe Akalu and Juergen K. V. Reichardt ....................................... 67 8 GC-Rich Template Amplification by Inverse PCR: DNA Polymerase and Solvent Effects Alain Moreau, Da Shen Wang, Steve Forget, Colette Duez, and Jean Dusart............................................................................... 75 9 PCR Procedure for the Isolation of Trinucleotide Repeats Teruaki Tozaki ...................................................................................... 81 10 Methylation-Specific PCR Haruhiko Ohashi .................................................................................. 91 viii Contents 11 Direct Cloning of Full-Length Cell Differentially Expressed Genes by Multiple Rounds of Subtractive Hybridization Based on Long-Distance PCR and Magnetic Beads Xin Huang, Zhenglong Yuan, and Xuetao Cao ................................ 99 PART II. CLONING PCR PRODUCTS 12 Cloning PCR Products: An Overview Baotai Guo and Yuping Bi ................................................................ 111 13 Using T4 DNA Polymerase to Generate Clonable PCR Products Kai Wang ............................................................................................. 121 14 Enzyme-Free Cloning of PCR Products and Fusion Protein Expression Brett A. Neilan and Daniel Tillett ..................................................... 125 15 Directional Restriction Site-Free Insertion of PCR Products into Vectors Guo Jun Chen .................................................................................... 133 16 Autosticky PCR: Directional Cloning of PCR Products with Preformed 5' Overhangs József Gál and Miklós Kálmán......................................................... 141 17 A Rapid and Simple Procedure for Direct Cloning of PCR Products into Baculoviruses Tamara S. Gritsun, Michael V. Mikhailov, and Ernest A. Gould ...................................................................... 153 PART III. MUTAGENESIS AND RECOMBINATION 18 PCR Approaches to DNA Mutagenesis and Recombination: An Overview Binzhang Shen ................................................................................... 167 19 In-Frame Cloning of Synthetic Genes Using PCR Inserts James C. Pierce ................................................................................. 175 20 Megaprimer PCR Sailen Barik ........................................................................................ 189 21 PCR-Mediated Recombination: A General Method Applied to Construct Chimeric Infectious Molecular Clones Guowei Fang, Barbara Weiser, Aloise Visosky, Timothy Moran, and Harold Burger ......................................................................... 197 22 PCR Method for Generating Multiple Mutations at Adjacent Sites Jiri Adamec ......................................................................................... 207 Contents ix 23 A Fast Polymerase Chain Reaction-Mediated Strategy for Introducing Repeat Expansions into CAG-Repeat Containing Genes Franco Laccone ................................................................................. 217 24 PCR Screening in Signature-Tagged Mutagenesis of Essential Genes Dario E. Lehoux and Roger C. Levesque ....................................... 225 25 Staggered Extension Process (StEP) In Vitro Recombination Anna Marie Aguinaldo and Frances Arnold ................................... 235 26 Random Mutagenesis by Whole-Plasmid PCR Amplification Donghak Kim and F. Peter Guengerich .......................................... 241 PART IV. CLONING UNKNOWN NEIGHBORING DNA 27 PCR-Based Strategies to Clone Unknown DNA Regions from Known Foreign Integrants: An Overview Eric Ka-Wai Hui, Po-Ching Wang, and Szecheng J. Lo ................ 249 28 Long Distance Vectorette PCR (LDV PCR) James A. L. Fenton, Guy Pratt, and Gareth J. Morgan ................. 275 29 Nonspecific, Nested Suppression PCR Method for Isolation of Unknown Flanking DNA (“Cold-Start Method”) Michael Lardelli .................................................................................. 285 30 Inverse PCR: cDNA Cloning Sheng-He Huang ................................................................................ 293 31 Inverse PCR: Genomic DNA Cloning Ambrose Y. Jong, Anna T’ang, De-Pei Liu, and Sheng-He Huang .................................................................... 301 32 Gene Cloning and Expression Profiling by Rapid Amplification of Gene Inserts with Universal Vector Primers Sheng-He Huang, Hua-Yang Wu, and Ambrose Y. Jong .............. 309 33 The Isolation of DNA Sequences Flanking Tn5 Transposon Insertions by Inverse PCR Vincent J. J. Martin and William W. Mohn ...................................... 315 34 Rapid Amplification of Genomic DNA Sequences Tagged by Insertional Mutagenesis Martina Celerin and Kristin T. Chun ................................................ 325 35 Isolation of Large Terminal Sequences of BAC Inserts Based on Double-Restriction-Enzyme Digestion Followed by Anchored PCR Zhong-Nan Yang and T. Erik Mirkov ............................................... 337 36 A “Step Down” PCR-Based Technique for Walking Into and the Subsequent Direct Sequence Analysis of Flanking Genomic DNA Ziguo Zhang and Sarah Jane Gurr .................................................. 343 PART V. LIBRARY CONSTRUCTION AND SCREENING 37 Use of PCR in Library Screening: An Overview Jinbao Zhu .......................................................................................... 353 38 Cloning of Homologous Genes by Gene-Capture PCR Renato Mastrangeli and Silvia Donini ............................................. 359 39 Rapid and Nonradioactive Screening of Recombinant Libraries by PCR Michael W. King ................................................................................. 377 40 Rapid cDNA Cloning by PCR Screening (RC-PCR) Toru Takumi ....................................................................................... 385 41 Generation and PCR Screening of Bacteriophage λ Sublibraries Enriched for Rare Clones (the “Sublibrary Method”) Michael Lardelli .................................................................................. 391 42 PCR-Based Screening for Bacterial Artificial Chromosome Libraries Yuji Yasukochi ................................................................................... 401 43 A 384-Well Microtiter-Plate-Based Template Preparation and Sequencing Method Lei He and Kai Wang ......................................................................... 411 44 A Microtiter-Plate-Based High Throughput PCR Product Purification Method Ryan Smith and Kai Wang ................................................................ 417 Index ............................................................................................................ 423