CSH Protocols, Table of Contents
Primary Archive, Section 2

May 2006

Protocols

Analysis of Interacting Proteins with SPR Spectroscopy Using BIAcore • Stage 1: Preparation of the Capture Surface and Test Binding
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3894
Abstract
Full Text

Two-hybrid Systems • Stage 1: Characterization of a Bait-LexA Fusion Protein
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3895
Abstract
Full Text

Identification of Associated Proteins by Coimmunoprecipitation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3898
Abstract
Full Text

Preparation of Plasmid DNA by Alkaline Lysis with SDS: Midipreparation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3901
Abstract
Full Text

Preparation of Plasmid DNA by Small-scale Boiling Lysis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3903
Abstract
Full Text

Preparation of Plasmid DNA: Toothpick Minipreparation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3905
Abstract
Full Text

Preparation of Plasmid DNA by Lysis with SDS
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3906
Abstract
Full Text

Purification of Plasmid DNA by Precipitation with Polyethylene Glycol
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3907
Abstract
Full Text

Preparation of Plasmid DNA by Large-scale Boiling Lysis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3910
Abstract
Full Text

Purification of Closed Circular DNA by Equilibrium Centrifugation in CsCl-Ethidium Bromide Gradients: Discontinuous Gradients
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3913
Abstract
Full Text

Removal of Ethidium Bromide from DNA by Extraction with Organic Solvents
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3914
Abstract
Full Text

Removal of Ethidium Bromide from DNA by Ion-exchange Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3915
Abstract
Full Text

Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Centrifugation through NaCl
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3916
Abstract
Full Text

Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Chromatography through Sephacryl S-1000
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3917
Abstract
Full Text

Removal of Small Fragments of Nucleic Acid from Preparations of Plasmid DNA by Precipitation with Lithium Chloride
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3918
Abstract
Full Text

Directional Cloning into Plasmid Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3919
Abstract
Full Text

Attaching Adaptors to Protruding Termini
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3920
Abstract
Full Text

Blunt-ended Cloning into Plasmid Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3921
Abstract
Full Text

Dephosphorylation of Plasmid DNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3925
Abstract
Full Text

Purification of Plasmid DNA by Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3926
Abstract
Full Text

Purification of Closed Circular DNA by Equilibrium Centrifugation in CsCl-Ethidium Bromide Gradients: Continuous Gradients
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3927
Abstract
Full Text

Ligating Plasmid and Target DNAs in Low-melting-temperature Agarose
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3929
Abstract
Full Text

Preparation and Transformation of Competent E. coli Using Calcium Chloride
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3932
Abstract
Full Text

Transformation of E. coli by Electroporation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3933
Abstract
Full Text

Screening Bacterial Colonies by Hybridization: Small Numbers
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3935
Abstract
Full Text

Screening Bacterial Colonies by Hybridization: Large Numbers
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3937
Abstract
Full Text

Lysing Colonies and Binding of DNA to Filters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3938
Abstract
Full Text

Hybridization of Bacterial DNA on Filters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3939
Abstract
Full Text

Addition of Synthetic Linkers to Blunt-ended DNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3941
Abstract
Full Text

The Hanahan Method for Preparation and Transformation of Competent E. coli: High-efficiency Transformation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3942
Abstract
Full Text

The Inoue Method for Preparation and Transformation of Competent E. Coli: "Ultra-Competent" Cells
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3944
Abstract
Full Text

Screening Bacterial Colonies Using X-gal and IPTG: -Complementation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3945
Abstract
Full Text

Screening Bacterial Colonies by Hybridization: Intermediate Numbers
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3946
Abstract
Full Text

Mapping Protein-binding Sites on DNA by DNase I Footprinting
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3947
Abstract
Full Text

Gel Retardation Assays for DNA-binding Proteins
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3948
Abstract
Full Text

Mapping DNase-I-hypersensitive Sites
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3949
Abstract
Full Text

Measurement of Chloramphenicol Acetyltransferase in Extracts of Mammalian Cells Using Thin-layer Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3951
Abstract
Full Text

Assay for ß-galactosidase in Extracts of Mammalian Cells
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3952
Abstract
Full Text

Transcriptional Run-on Assays
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3956
Abstract
Full Text

Tetracycline as Regulator of Inducible Gene Expression • Stage 2: Stable Transfection of Inducible tTA-expressing NIH-3T3 Cells with Tetracycline-regulated Target Genes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3957
Abstract
Full Text

Tetracycline as Regulator of Inducible Gene Expression • Stage 3: Analysis of Protein Expression in Transfected Cells
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3958
Abstract
Full Text

Probing Protein Interactions Using GFP and FRET • Stage 1: Labeling Proteins with Fluorescent Dyes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3960
Abstract
Full Text

Plating Bacteriophage
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3961
Abstract
Full Text

Picking Bacteriophage Plaques
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3962
Abstract
Full Text

Preparing Stocks of Bacteriophage by Plate Lysis and Elution
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3963
Abstract
Full Text

Large-scale Growth of Bacteriophage : Infection at Low Multiplicity
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3965
Abstract
Full Text

Precipitation of Bacteriophage Particles from Large-scale Lysates
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3966
Abstract
Full Text

Assaying the DNA Content of Bacteriophage Stocks and Lysates by Gel Electrophoresis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3967
Abstract
Full Text

Purification of Bacteriophage Particles by Isopycnic Centrifugation through CsCl Gradients
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3968
Abstract
Full Text

Purification of Bacteriophage Particles by Centrifugation through a Glycerol Step Gradient
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3969
Abstract
Full Text

Purification of Bacteriophage Particles by Pelleting/Centrifugation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3970
Abstract
Full Text

Preparing Stocks of Bacteriophage by Small-scale Liquid Culture
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3971
Abstract
Full Text

Extraction of Bacteriophage DNA from Large-scale Cultures Using Proteinase K and SDS
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3972
Abstract
Full Text

Extraction of Bacteriophage DNA from Large-scale Cultures Using Formamide
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3973
Abstract
Full Text

Preparation of Bacteriophage DNA Cleaved with a Single Restriction Enzyme for Use as a Cloning Vector
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3974
Abstract
Full Text

Alkaline Phosphatase Treatment of Bacteriophage Vector DNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3976
Abstract
Full Text

Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Pilot Reactions
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3978
Abstract
Full Text

Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Preparative Reactions
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3979
Abstract
Full Text

Ligation of Bacteriophage Arms to Fragments of Foreign Genomic DNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3980
Abstract
Full Text

Amplification of Genomic Libraries
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3981
Abstract
Full Text

Transfer of Bacteriophage DNA from Plaques to Filters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3982
Abstract
Full Text

Hybridization of Bacteriophage DNA on Filters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3983
Abstract
Full Text

Rapid Analysis of Bacteriophage Isolates: Purification of  DNA from Plate Lysates
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3984
Abstract
Full Text

Rapid Analysis of Bacteriophage  Isolates: Purification of  DNA from Liquid Cultures
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3985
Abstract
Full Text

Tetracycline as Regulator of Inducible Gene Expression • Stage 1: Stable Transfection of Fibroblasts with pTet-tTAk
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3986
Abstract
Full Text

Preparation of Bacteriophage  DNA Cleaved with Two Restriction Enzymes for Use as a Cloning Vector
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3987
Abstract
Full Text

Rapid Amplification of 5' cDNA Ends (5'-RACE)
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3989
Abstract
Full Text

Purification of Bacteriophage  Arms: Centrifugation through Sucrose Density Gradients
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3990
Abstract
Full Text

Plating Bacteriophage M13
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3993
Abstract
Full Text

Growing Bacteriophage M13 in Liquid Culture
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3994
Abstract
Full Text

Analysis of Recombinant Bacteriophage M13 Clones
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot3996
Abstract
Full Text

Construction of Genomic DNA Libraries in Cosmid Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4000
Abstract
Full Text

Amplification and Storage of a Cosmid Library: Amplification in Liquid Culture
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4001
Abstract
Full Text

Amplification and Storage of a Cosmid Library: Amplification on Filters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4002
Abstract
Full Text

Working with Bacteriophage P1 and Its Cloning Systems
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4003
Abstract
Full Text

Transferring Bacteriophage P1 Clones between E. coli Hosts
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4004
Abstract
Full Text

Isolation of BAC DNA from Small-scale Cultures
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4006
Abstract
Full Text

Isolation of BAC DNA from Large-scale Cultures
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4007
Abstract
Full Text

Isolating the Ends of Genomic DNA Fragments Cloned in High-capacity Vectors: Vectorette Polymerase Chain Reactions
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4009
Abstract
Full Text

Working with Bacterial Artificial Chromosomes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4010
Abstract
Full Text

Phosphorylation of DNA Molecules with Dephosphorylated Blunt Ends or Recessed 5' Termini
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4011
Abstract
Full Text

Phosphorylation of DNA Molecules with Protruding 5' Termini by the Exchange Reaction
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4012
Abstract
Full Text

Screening Recombinant Clones for Site-directed Mutagenesis by Hybridization to Radiolabeled Oligonucleotides
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4013
Abstract
Full Text

Detection of Protein-Protein Interactions Using Far Western with GST Fusion Proteins
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4014
Abstract
Full Text

Analyzing Yeast Colonies by PCR
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4015
Abstract
Full Text

Cloning into Bacteriophage M13 Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4018
Abstract
Full Text

Producing Single-stranded DNA with Phagemid Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4019
Abstract
Full Text

Agarose Gel Electrophoresis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4020
Abstract
Full Text

Detection of DNA in Agarose Gels
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4022
Abstract
Full Text

Recovery of DNA from Agarose and Polyacrylamide Gels: Electroelution into Dialysis Bags
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4023
Abstract
Full Text

Purification of DNA Recovered from Agarose and Polyacrylamide Gels by Anion-exchange Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4024
Abstract
Full Text

Recovery of DNA from Low-melting-temperature Agarose Gels: Organic Extraction
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4025
Abstract
Full Text

Recovery of DNA from Low-melting-temperature Agarose Gels: Enzymatic Digestion with Agarase
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4026
Abstract
Full Text

Alkaline Agarose Gel Electrophoresis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4027
Abstract
Full Text

Neutral Polyacrylamide Gel Electrophoresis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4028
Abstract
Full Text

Detection of DNA in Polyacrylamide Gels by Autoradiography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4029
Abstract
Full Text