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Tables of Contents for The Nucleic Acids Protocols Handbook
Chapter/Section Title
Page #
Page Count
Preface
v
Contributors
xv
Part I Nucleic Acid Extraction
Isolation of High-Molecular-Weight DNA from Animal Cells
3
6
Ian Garner
Isolation of mRNA by Affinity Chromatography
9
4
Sian Bryant
David L. Manning
Isolation and Purification of DNA from Plants
13
4
Justin Stacey
Peter G. Isaac
Purification of Uncontaminated, Intact Plant RNA
17
6
Shu-Hua Cheng
Brandon D. Moore
Jeffrey R. Seemann
An Improved Method to Isolate Mitochondrial RNA from Green Plant Tissue
23
6
Fei Ye
Ralf Reski
Isolating Chromosomal DNA from Bacteria
29
4
Elisabeth Chachaty
Patrick Saulnier
Bacterial DNA Extraction for Polymerase Chain Reaction and Pulsed-Field Gel Electrophoresis
33
4
Elisabeth Chachaty
Patrick Saulnier
Isolation of Fungal Nucleic Acids
37
10
Surapareddy Sreenivasaprasad
Total RNA Isolation from Bacteria
47
6
John Heptinstall
Simultaneous RNA and DNA Extraction from Biopsy Material, Culture Cells, Plants, and Bacteria
53
4
Udo Dobbeling
Spectrophotometric Analysis of Nucleic Acids
57
6
John Heptinstall
Ralph Rapley
Part II Basic Separation and Analysis of DNA
Restriction Endonuclease Digestion of DNA
63
4
Duncan R. Smith
Agarose Gel Electrophoresis of Nucleic Acids
67
4
D. Ross Williams
Ralph Rapley
Preparation of RNA Dot Blots
71
2
Rachel Hodge
Native Polyacrylamide Gel Electrophoresis
73
4
Adrian J. Harwood
Southern Blotting of Agarose Gels by Capillary Transfer
77
4
Ralph Rapley
Jane Davenport-Jones
Pulsed-Field Gel Electrophoresis
81
24
John Maule
HPLC of DNA and PCR Products
105
12
Elena D. Katz
Part III Probe Design, Synthesis, and Labeling
End-Labeling of DNA Fragments
117
6
Adrian J. Harwood
Nick Translation and Random Hexamer Labeling of DNA
123
4
Jane Davenport-Jones
Generation of Labeled Probes by Polymerase Chain Reaction
127
8
Y. M. Dennis Lo
Shu F. An
Nonradioactive Oligonucleotide Probe Labeling
135
10
Sue Fowler
Ian Durrant
Preparation of Direct, Enzyme-Labeled DNA Probes
145
4
Ian Durrant
Timothy Stone
Random Prime Labeling of DNA Probes with Fluorescein-Tagged Nucleotides
149
4
Bronwen M. Harvey
Claire B. Wheeler
Martin W. Cunningham
Hybridization and Detection of Fluorescein-Labeled DNA Probes Using Chemiluminescence
153
4
Claire B. Wheeler
Bronwen M. Harvey
Martin W. Cunningham
Hybridization of Enzyme-Labeled Probes and Detection by Chemiluminescence
157
6
Timothy Stone
Ian Durrant
Hybridization and Competition Hybridization of Southern Blots
163
6
Rosemary Kelsell
Autoradiography and Fluorography
169
8
Eric Quemeneur
Part IV RNA Analysis Techniques
Formaldehyde Gel Electrophoresis of Total RNA
177
4
Sian Bryant
David L. Manning
RNA Probes for the Analysis of Gene Expression
181
14
Dominique Belin
Primer Extension Analysis of mRNA
195
6
Maggie Walmsley
Mark Leonard
Roger Patient
S1 Mapping Using Single-Stranded DNA Probes
201
6
Stephane Viville
Roberto Mantovani
Measurements of Rate of Transcription in Isolated Nuclei by Nuclear ``Run-Off'' Assay
207
6
Rai Ajit K. Srivastava
Gustav Schonfeld
One-Tube RT-PCR with Sequence-Specific RT Primers
213
6
Ulrich Pfeffer
Paola Ferro
Characterization of RNA Using Continuous RT-PCR Coupled with ELOSA
219
10
Francois Mallet
Quantitative Analysis of RNA Species by Polymerase Chain Reaction and Solid-Phase Minisequencing
229
10
Anu Suomalainen
Ann-Christine Syvanen
Nonradioactive Northern Blotting of RNA
239
10
Rainer Low
Analysis of RNA by Northern Blotting Using Riboprobes
249
12
Rai Ajit K. Srivastava
Part V Gene Library Construction and Screening
Production of Double-Stranded cDNA for Gene Library Synthesis
261
6
Jane Kirk
Steve Mayall
Using Rapid Amplification of cDNA Ends (RACE) to Obtain Full-Length cDNAs
267
22
Yue Zhang
Michael A. Frohman
cDNA Library Construction Using Streptavidin-Paramagnetic Beads and PCR
289
6
Kris N. Lambert
Valerie M. Williamson
Rapid (Ligase-Free) Subcloning of Polymerase Chain Reaction Products
295
10
Alan R. Shuldiner
Keith Tanner
Subtraction Hybridization cDNA Libraries
305
14
Clifford W. Schweinfest
Peter S. Nelson
Michael W. Graber
Rita I. Demopoulos
Takis S. Papas
Cloning Polymerase Chain Reaction Products Utilizing the T/A Overhang and a Kit
319
8
Melissa Lail-Trecker
Extraction and Purification of Plasmid DNA
327
6
Craig Winstanley
Ralph Rapley
Biotinylated Probes in Colony Hybridization
333
6
Michael J. Haas
Cloning Long Polymerase Chain Reaction Products
339
8
Songrong Ren
J. Michael Ruppert
Cloning DNA Fragments in M13 Vectors
347
8
David Walsh
cDNA Library Construction for the Lambda ZAP®-Based Vectors
355
12
Marjory A. Snead
Michelle A. Alting-Mees
Jay M. Short
Expression and Preparation of Fusion Proteins from Recombinant λgt11 Phages
367
6
Sheng-He Huang
Ambrose Jong
Antibody Screening of Bacteriophage λgt11 DNA Expression Libraries
373
8
Peter Jones
Screening cDNA Libraries by Hybridization with Double-Stranded DNA Probes and Oligonucleotides
381
8
Caroline A. Austin
cDNA Library Screening with the Tetramethylammonium Chloride (TMAC) Technique Using Highly Degenerate Oligoonucleotide Probes
389
8
Bent Honore
Peder Madsen
Screening Recombinant Libraries by Polymerase Chain Reaction
397
8
Michael W. King
Construction and Screening of Cosmid Libraries
405
10
Jens Hanke
Jorg D. Hoheisel
Generation of Large Insert YAC Libraries
415
10
Zoia Larin
Anthony P. Monaco
Hans Lehrach
YAC Library Storage and Transport
425
6
John E. Collins
Sheila Hassock
Ian Dunham
YAC Library Screening: Preparation of Hybridization Filters and Polymerase Chain Reaction Pools
431
6
Charlotte G. Cole
John E. Collins
Ian Dunham
YAC Library Screening: Hybridization and PCR-Based Screening Protocols
437
12
Charlotte G. Cole
John E. Collins
Ian Dunham
Phage-Display Libraries of Murine and Human Antibody Fab Fragments
449
32
Jan Engberg
Lene K. Johansen
Michelle Westengaard-Hildinge
Erik S. Riise
Bjarne Albrechtsen
Part VI DNA Sequencing
Preparation and Analysis of DNA Sequencing Gels
481
8
Bimal D. M. Theophilus
DNA Sequencing of Plasmids
489
4
George Murphy
Sequencing DNA Fragments Cloned into M13 and Phagemid Vectors
493
6
Neil Brewis
Direct cDNA Sequencing Using Sequential Linear/Asymmetric Polymerase Chain Reaction
499
6
Ivor J. Mason
Purification and Enzymatic Sequencing of Polymerase Chain Reaction Products
505
10
Frank C. Brosius III
Lawrence B. Holzman
Xinan Cao
Direct Polymerase Chain Reaction Sequencing with Denaturants
515
8
Wei Zhang
Albert B. Deisseroth
Direct DNA Sequencing of Polymerase Chain Reaction Products Using Magnetic Beads
523
10
Joakim Lundeberg
Bertil Pettersson
Mathias Uhlen
Polymerase Chain Reaction Cycle Sequencing with Degenerate Primers
533
8
Zhiyuan Shen
Jingmei Liu
Robert L. Wells
Mortimer M. Elkind
Direct Automated Cycle Sequencing of Polymerase Chain Reaction Products
541
6
Susan E. Daniels
Affinity-Capture and Solid-Phase Sequencing of Biotinylated Polymerase Chain Reaction Products
547
6
Anu Suomalainen
Ann-Christine Syvanen
DNA Sequencing by the Chemical Method
553
4
Eran Pichersky
One-Step One-Lane Chemical Sequencing of DNA
557
12
Giovanna Costanzo
Ernesto Di Mauro
Rodolfo Negri
Part VII Basic Polymerase Chain Reaction Methods
Polymerase Chain Reaction: Basic Principles and Routine Practice
569
12
Lori A. Kolmodin
J. Fenton Williams
Primer Selection and Design for Polymerase Chain Reaction
581
8
Wojciech Rychlik
One-Step Optimization Using Touchdown and Stepdown Polymerase Chain Reaction
589
6
Kenneth H. Roux
Karl H. Hecker
Cloning Gene Family Members Using Polymerase Chain Reaction with Degenerate Oligonucleotide Primers
595
14
Gregory M. Preston
Construction of Synthetic Genes by Polymerase Chain Reaction
609
4
Patrick J. Dillon
Craig A. Rosen
Rapid Amplification of cDNA Ends
613
6
David Bertioli
Multiplex Polymerase Chain Reaction
619
6
Jerald Radich
Inverse Polymerase Chain Reaction
625
8
Sheng-He Huang
Long Range Polymerase Chain Reaction
633
12
William Waggott
Part VIII Analyzing Genes, Mutations, and Protein Interactions
Nonradioactive Differential Display of Messenger RNA
645
8
Thomas C. G. Bosch
Jan U. Lohmann
Gene Isolation by Exon Trapping
653
14
David B. Krizman
DNA Rescue by the Vectorette Method
667
8
Marcia A. McAleer
Alison Coffey
Ian Dunham
Random Amplified Polymorphic DNA (RAPDs)
675
4
Scott Tingey
Restriction Fragment Length Polymorphism
679
6
Mohammad S. Enayat
Detection of Mutations in DNA and RNA by Chemical Cleavage
685
10
Richard G. H. Cotton
Mutation Screening Using PCR-SSCP: Silver Staining and Isotopic Protocols
695
10
Philip J. Saker
Detecting Point Mutations by Denaturing-Gradient Gel Electrophoresis
705
12
Stephen R. Dlouhy
Patricia Wheeler
James A. Trofatter
Peter J. Stambrook
Jay A. Tischfield
Analysis of Nucleotide Sequence Variation by Solid-Phase Minisequencing
717
6
Anu Suomalainen
Ann-Christine Syvanen
The Amplification Refractory Mutation System
723
6
John M. Old
DNase I Footprinting
729
8
Benoit Leblanc
Tom Moss
Identification of Protein---DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference
737
8
Peter E. Shaw
A. Francis Stewart
The Gel Shift Assay for the Analysis of DNA---Protein Interactions
745
12
John D. Taylor
Alison J. Ackroyd
Stephen E. Halford
Yeast Two-Hybrid Library Screening
757
16
Ian G. Cowell
The Southwestern Assay
773
10
Jacques Philippe
Nonradioactive Methods for the Detection of RNA-Protien Interaction
783
10
Asier Echarri
Maria Eugenia Gonzalez
Ivan Ventoso
Luis Carrasco
Tanscriptional Activation Analysis by the Chloramphenicol Acetyl Transferase (CAT) Enzyme Assay
793
14
David R. Hodge
Delores M. Thompson
Alexandra Panayiotakis
Arun Seth
Part IX Mutagenesis, Transcription, and Translation In Vitro
Generating Nested Deletions with Exonuclease III
807
8
George Murphy
Primer-Directed Site-Specific Mutagenesis
815
12
Michael J. O'Donohue
G. Geoff Kneale
Site-Directed Mutagenesis Using a Uracil-Containing Phagemid Template
827
8
Christian Hagemeier
Site-Directed Mutagenesis Using Double-Stranded Plasmid DNA Templates
835
10
Jeffrey Bramam
Carol Papworth
Alan Greener
Site-Directed Mutagenesis with LA-PCR™ Technology
845
12
Atsuhi Shimada
Osamu Takeda
Recombination and Mutagenesis by Overlap Extension PCR
857
8
Robert J. Pogulis
Abbe N. Vallejo
Larry R. Pease
Site-Directed Mutagenesis and Gene Fusion by Megaprimer PCR
865
10
Sailen Barik
Transcription In Vitro Using Bacteriophage RNA Polymerases
875
10
Elaine T. Schenborn
In Vitro Translation of mRNA in a Rabbit Reticuloctye Lysate Cell-Free System
885
6
Louise Olliver
Charles D. Boyd
In Vitro Translation of mRNA in a Wheat Germ Extract Cell-Free System
891
4
Louise Olliver
Anne Grobler-Rabie
Charles D. Boyd
The Xenopus Egg Extract Translation System
895
12
Glenn M. Matthews
Alan Colman
Manipulation of Baculovirus Vectors
907
14
Claire L. Merrington
Mark J. Bailey
Robert D. Possee
Procedures for the Analysis and Purification of His-Tagged Proteins
921
14
Richard E. Kneusel
Joanne Crowe
Melanie Wulbeck
Joachim Ribbe
Detection and Immobilization of Proteins Containing the 6xHis Tag
935
12
Richard E. Kneusel
Melanie Wulbeck
Joachim Ribbe
Expression and Purification of Recombinant Proteins Using the pET System
947
34
Robert C. Mierendorf
Barbara B. Morris
Beth Hammer
Robert E. Novy
Part X Gene Localization, Mapping In Situ, and Bioinformatics
Preparation of Tissue Sections and Slides for mRNA Hybridization
981
4
Giorgio Terenghi
Use of Digoxigenin-Labeled Probes on Tissue Sections
985
6
Giorgio Terenghi
Gene Mapping by FISH
991
20
Rafael Espinosa III
Michelle M. Le Beau
Oligonucleotide PRINS DNA Synthesis
1011
6
John R. Gosden
Diane Lawson
Chromosome-Specific PRINS
1017
6
Jean-Paul Charlieu
Frank Pellestor
In Situ PCR Amplification of Intracellular mRNA
1023
8
Raymond H. Chen
Susan V. Fuggle
An Introduction to Bioinformatics
1031
14
Henry Brzeski
Index
1045