The nucleic acid protocols handbook / edited by Ralph Rapley.

Format:

Book

Contributor:

Rapley, Ralph.

Language:

English

Subjects (All):

Nucleic acids--Laboratory manuals.

Nucleic acids.

Polymerase chain reaction--Laboratory manuals.

Polymerase chain reaction.

Gene mapping--Laboratory manuals.

Gene mapping.

Molecular genetics--Laboratory manuals.

Molecular genetics.

Nucleic Acids--isolation & purification.

Chromosome Mapping--methods.

Molecular Biology--methods.

Polymerase Chain Reaction--methods.

Medical Subjects:

Nucleic Acids--isolation & purification.

Chromosome Mapping--methods.

Molecular Biology--methods.

Polymerase Chain Reaction--methods.

Genre:

Laboratory manuals.

Physical Description:

xxii, 1050 pages : illustrations ; 26 cm

Place of Publication:

Totowa, N.J. : Humana Press, [2000]

Contents:

Part I Nucleic Acid Extraction

1 Isolation of High-Molecular-Weight DNA from Animal Cells / lan Garner 3

2 Isolation of mRNA by Affinity Chromatography / Sian Bryant, David L. Manning 9

3 Isolation and Purification of DNA from Plants / Justin Stacey, Peter G. Isaac 13

4 Purification of Uncontaminated, Intact Plant RNA / Shu-Hua Cheng, Brandon D. Moore, Jeffrey R. Seemann 17

5 An Improved Method to Isolate Mitochondrial RNA from Green Plant Tissue / Fei Ye, Ralf Reski 23

6 Isolating Chromosomal DNA from Bacteria / Elisabeth Chachaty, Patrick Saulnier 29

7 Bacterial DNA Extraction for Polymerase Chain Reaction and Pulsed-Field Gel Electrophoresis / Elisabeth Chachaty, Patrick Saulnier 33

8 Isolation of Fungal Nucleic Acids / Surapareddy Sreenivasaprasad 37

9 Total RNA Isolation from Bacteria / John Heptinstall 47

10 Simultaneous RNA and DNA Extraction from Biopsy Material, Culture Cells, Plants, and Bacteria / Udo Dobbeling 53

11 Spectrophotometric Analysis of Nucleic Acids / John Heptinstall, Ralph Rapley 57

Part II Basic Separation and Analysis of DNA

12 Restriction Endonuclease Digestion of DNA / Duncan R. Smith 63

13 Agarose Gel Electrophoresis of Nucleic Acids / D. Ross Williams, Ralph Rapley 67

14 Preparation of RNA Dot Blots / Rachel Hodge 71

15 Native Polyacrylamide Gel Electrophoresis / Adrian J. Harwood 73

16 Southern Blotting of Agarose Gels by Capillary Transfer / Ralph Rapley, Jane Davenport-Jones 77

17 Pulsed-Field Gel Electrophoresis / John Maule 81

18 HPLC of DNA and PCR Products / Elena D. Katz 105

Part III Probe Design, Synthesis, and Labeling

19 End-Labeling of DNA Fragments / Adrian J. Harwood 117

20 Nick Translation and Random Hexamer Labeling of DNA / Jane Davenport-Jones 123

21 Generation of Labeled Probes by Polymerase Chain Reaction / Y. M. Dennis Lo, Shu F. An 127

22 Nonradioactive Oligonucleotide Probe Labeling / Sue Fowler, Ian Durrant 135

23 Preparation of Direct, Enzyme-Labeled DNA Probes / Ian Durrant, Timothy Stone 145

24 Random Prime Labeling of DNA Probes with Fluorescein-Tagged Nucleotides / Bronwen M. Harvey, Claire B. Wheeler, Martin W. Cunningham 149

25 Hybridization and Detection of Fluorescein-Labeled DNA Probes Using Chemiluminescence / Claire B. Wheeler, Bronwen M. Harvey, Martin W. Cunningham 153

26 Hybridization of Enzyme-Labeled Probes and Detection by Chemiluminescence / Timothy Stone, Ian Durrant 157

27 Hybridization and Competition Hybridization of Southern Blots / Rosemary Kelsell 163

28 Autoradiography and Fluorography / Eric Quemeneur 169

Part IV RNA Analysis Techniques

29 Formaldehyde Gel Electrophoresis of Total RNA / Sian Bryant, David L. Manning 177

30 RNA Probes for the Analysis of Gene Expression / Dominique Belin 181

31 Primer Extension Analysis of mRNA / Maggie Walmsley, Mark Leonard, Roger Patient 195

32 S1 Mapping Using Single-Stranded DNA Probes / Stephane Viville, Roberto Mantovani 201

33 Measurements of Rate of Transcription in Isolated Nuclei by Nuclear "Run-Off" Assay / Rai Ajit K. Srivastava, Gustav Schonfeld 207

34 One-Tube RT-PCR with Sequence-Specific RT Primers / Ulrich Pfeffer, Paola Ferro 213

35 Characterization of RNA Using Continuous RT-PCR Coupled with ELOSA / Francois Mallet 219

36 Quantitative Analysis of RNA Species by Polymerase Chain Reaction and Solid-Phase Minisequencing / Anu Suomalainen, Ann-Christine Syvanen 229

37 Nonradioactive Northern Blotting of RNA / Rainer Low 239

38 Analysis of RNA by Northern Blotting Using Riboprobes / Rai Ajit K. Srivastava 249

Part V Gene Library Construction and Screening

39 Production of Double-Stranded cDNA for Gene Library Synthesis / Jane Kirk, Steve Mayall 261

40 Using Rapid Amplification of cDNA Ends (RACE) to Obtain Full-Length cDNAs / Yue Zhang, Michael A. Frohman 267

41 cDNA Library Construction Using Streptavidin-Paramagnetic Beads and PCR / Kris N. Lambert, Valerie M. Williamson 289

42 Rapid (Ligase-Free) Subcloning of Polymerase Chain Reaction Products / Alan R. Shuldiner, Keith Tanner 295

43 Subtraction Hybridization cDNA Libraries / Clifford W. Schweinfest, Peter S. Nelson, Michael W. Graber, Rita I. Demopoulos, Takis S. Papas 305

44 Cloning Polymerase Chain Reaction Products Utilizing the T/A Overhang and a Kit / Melissa Lail-Trecker 319

45 Extraction and Purification of Plasmid DNA / Craig Winstanley, Ralph Rapley 327

46 Biotinylated Probes in Colony Hybridization / Michael J. Haas 333

47 Cloning Long Polymerase Chain Reaction Products / Songrong Ren, J. Michael Ruppert 339

48 Cloning DNA Fragments in M13 Vectors / David Walsh 347

49 cDNA Library Construction for the Lambda ZAP-Based Vectors / Majory A. Snead, Michelle A. Alting-Mees, Jay M. Short 355

50 Expression and Preparation of Fusion Proteins from Recombinant gt11 Phages / Sheng-He Huang, Ambrose Jong 367

51 Antibody Screening of Bacteriophage gt11 DNA Expression Libraries / Peter Jones 373

52 Screening cDNA Libraries by Hybridization with Double-Stranded DNA Probes and Oligonucleotides / Caroline A. Austin 381

53 cDNA Library Screening with the Tetramethylammonium Chloride (TMAC) Technique Using Highly Degenerate Oligoonucleotide Probes / Bent Honore, Peder Madsen 389

54 Screening Recombinant Libraries by Polymerase Chain Reaction / Michael W. King 397

55 Construction and Screening of Cosmid Libraries / Jens Hanke, Jorg D. Hoheisel 405

56 Generation of Large Insert YAC Libraries / Zoia Larin, Anthony P. Monaco, Hans Lehrach 415

57 YAC Library Storage and Transport / John E. Collins, Sheila Hassock, Ian Dunham 425

58 YAC Library Screening: Preparation of Hybridization Filters and Polymerase Chain Reaction Pools / Charlotte G. Cole, John E. Collins, Ian Dunham 431

59 YAC Library Screening: Hybridization and PCR-Based Screening Protocols / Charlotte G. Cole, John E. Collins, Ian Dunham 437

60 Phage-Display Libraries of Murine and Human Antibody Fab Fragments / Jan Engberg, Lene K. Johansen, Michelle Westengaard-Hildinge, Erik S. Riise, Bjarne Albrechtsen 449

Part VI DNA Sequencing

61 Preparation and Analysis of DNA Sequencing Gels / Bimal D. M. Theophilus 481

62 DNA Sequencing of Plasmids / George Murphy 489

63 Sequencing DNA Fragments Cloned into M13 and Phagemid Vectors / Neil Brewis 493

64 Direct cDNA Sequencing Using Sequential Linear/Asymmetric Polymerase Chain Reaction / Ivor J. Mason 499

65 Purification and Enzymatic Sequencing of Polymerase Chain Reaction Products / Frank C. Brosius III, Lawrence B. Holzman, Xinan Cao 505

66 Direct Polymerase Chain Reaction Sequencing with Denaturants / Wei Zhang, Albert B. Deisseroth 515

67 Direct DNA Sequencing of Polymerase Chain Reaction Products Using Magnetic Beads / Joakim Lundeberg, Bertil Pettersson, Mathias Uhlen 523

68 Polymerase Chain Reaction Cycle Sequencing with Degenerate Primers / Zhiyuan Shen, Jingmei Liu, Robert L. Wells, Mortimer M. Elkind 533

69 Direct Automated Cycle Sequencing of Polymerase Chain Reaction Products / Susan E. Daniels 541

70 Affinity-Capture and Solid-Phase Sequencing of Biotinylated Polymerase Chain Reaction Products / Anu Suomalainen, Ann-Christine Syvanen 547

71 DNA Sequencing by the Chemical Method / Eran Pichersky 553

72 One-Step One-Lane Chemical Sequencing of DNA / Giovanna Costanzo, Ernesto Di Mauro, Rodolfo Negri 557

Part VII Basic Polymerase Chain Reaction Methods

73 Polymerase Chain Reaction: Basic Principles and Routine Practice / Lori A. Kolmodin, J. Fenton Williams 569

74 Primer Selection and Design for Polymerase Chain Reaction / Wojciech Rychlik 581

75 One-Step Optimization Using Touchdown and Stepdown Polymerase Chain Reaction / Kenneth H. Roux, Karl H. Hecker 589

76 Cloning Gene Family Members Using Polymerase Chain Reaction with Degenerate Oligonucleotide Primers / Gregory M. Preston 595

77 Construction of Synthetic Genes by Polymerase Chain Reaction / Patrick J. Dillon, Craig A.

Rosen 609

78 Rapid Amplification of cDNA Ends / David Bertioli 613

79 Multiplex Polymerase Chain Reaction / Jerald Radich 619

80 Inverse Polymerase Chain Reaction / Sheng-He Huang 625

81 Long Range Polymerase Chain Reaction / William Waggott 633

Part VIII Analyzing Genes, Mutations, and Protein Interactions

82 Nonradioactive Differential Display of Messenger RNA / Thomas C. G. Bosch, Jan U. Lohmann 645

83 Gene Isolation by Exon Trapping / David B. Krizman 653

84 DNA Rescue by the Vectorette Method / Marcia A. McAleer, Alison Coffey, Ian Dunham 667

85 Random Amplified Polymorphic DNA (RAPDs) / Scott Tingey 675

86 Restriction Fragment Length Polymorphism / Mohammad S. Enayat 679

87 Detection of Mutations in DNA and RNA by Chemical Cleavage / Richard G. H. Cotton 685

88 Mutation Screening Using PCR-SSCP: Silver Staining and Isotopic Protocols / Philip J. Saker 695

89 Detecting Point Mutations by Denaturing-Gradient Gel Electrophoresis / Stephen R. Dlouhy, Patricia Wheeler, James A. Trofatter, Peter J. Stambrook, Jay A. Tischfield 705

90 Analysis of Nucleotide Sequence Variation by Solid-Phase Minisequencing / Anu Suomalainen, Ann-Christine Syvanen 717

91 The Amplification Refractory Mutation System / John M. Old 723

92 DNase I Footprinting / Benoit Leblanc, Tom Moss 729

93 Identification of Protein

DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference / Peter E. Shaw, A. Francis Stewart 737

94 The Gel Shift Assay for the Anmalysis of DNA

Protein Interactions / John D. Taylor, Alison J. Ackroyd, Stephen E. Halford 745

95 Yeast Two-Hybrid Library Screening / Ian G. Cowell 757

96 The Southwestern Assay / Jacques Philippe 773

97 Nonradioactive Methods for the Detection of RNA-Protien Interaction / Asier Echarri, Maria Eugenia Gonzalez, Ivan Ventoso, Luis Carrasco 783

98 Tanscriptional Activation Analysis by the Chloramphenicol Acetyl Transferase (CAT) Enzyme Assay / David R. Hodge, Delores M. Thompson, Alexandra Panayiotakis, Arun Seth 793

Part IX Mutagenesis, Transcription, and Translation In Vitro

99 Generating Nested Deletions with Exonuclease III / George Murphy 807

100 Primer-Directed Site-Specific Mutagenesis / Michael J. O'Donohue, G. Geoff Kneale 815

101 Site-Directed Mutagenesis Using a Uracil-Containing Phagemid Template / Christian Hagemeier 827

102 Site-Directed Mutagenesis Using Double-Stranded Plasmid DNA Templates / Jeffrey Bramam, Carol Papworth, Alan Greener 835

103 Site-Directed Mutagenesis with LA-PCR Technology / Atsushi Shimada, Osamu Takeda 845

104 Recombination and Mutagenesis by Overlap Extension PCR / Robert J. Pogulis, Abbe N. Vallejo, Larry R. Pease 857

105 Site-Directed Mutagenesis and Gene Fusion by Megaprimer PCR / Sailen Barik 865

106 Transcription In Vitro Using Bacteriophage RNA Polymerases / Elaine T. Schenborn 875

107 In Vitro Translation of mRNA in a Rabbit Reticuloctye Lysate Cell-Free System / Louise Olliver, Charles D. Boyd 885

108 In Vitro Translation of mRNA in a Wheat Germ Extract Cell-Free System / Louise Olliver, Anne Grobler-Rabie, Charles D. Boyd 891

109 The Xenopus Egg Extract Translation System / Glenn M. Matthews, Alan Colman 895

110 Manipulation of Baculovirus Vectors / Claire L. Merrington, Mark J. Bailey, Robert D. Possee 907

111 Procedures for the Analysis and Purification of His-Tagged Proteins / Richard E. Kneusel, Joanne Crowe, Melanie Wulbeck, Joachim Ribbe 921

112 Detection and Immobilization of Proteins Containing the 6xHis Tag / Richard E. Kneusel, Melanie Wulbeck, Joachim Ribbe 935

113 Expression and Purification of Recombinant Proteins Using the pET System / Robert C. Mierendorf, Barbara B. Morris, Beth Hammer, Robert E. Novy 947

Part X Gene Localization, Mapping In Situ, and Bioinformatics

114 Preparation of Tissue Sections and Slides for mRNA Hybridization / Giorgio Terenghi 981

115 Use of Digoxigenin-Labeled Probes on Tissue Sections / Giorgio Terenghi 985

116 Gene Mapping by Fish / Rafael Espinosa III, Michelle M. Le Beau 991

117 Oligonucleotide Prins DNA Synthesis / John R. Gosden, Diane Lawson 1011

118 Chromosome-Specific Prins / Jean-Paul Charlieu, Frank Pellestor 1017

119 In Situ PCR Amplification of Intracellular mRNA / Raymond H. Chen, Susan V. Fuggle 1023

120 An Introduction to Bioinformatics / Henry Brzeski 1031.

Notes:

Includes bibliographical references and index.

ISBN:

0896034593

0896038416

OCLC:

39868199