DNA Preparation

• Bacterial DNA
• Rapid Bacterial DNA
• "Quick" DNA
• Improved Alcohol Precipitation of DNA
• Bacterial DNA in Agarose Plugs
• Bacterial DNA from Mucoid Strains
• Plasmid Preps - Alkaline Method
• Plasmid Preps - Boiling Method
• Plasmid Preps - CsCl Method
• Plasmid Preps - LiCl Method
• Plasmid Preps - Qiagen Method
• Plasmid Preps - SDS Method
• Plasmid Preps - TELT Method
• Bacteriophage M13 DNA
• Bacteriophage Lambda Particles
• Bacteriophage Lambda DNA
• Mud-P22 DNA
• Blunt-Ended DNA Fragments
• Single Stranded DNA by Exonuclease Digestion
• RNA Preparation - Bacterial RNA

DNA Purification

• DEAE Nitrocellulaose Membranes.
• Freezing Method
• GeneClean
• Spin Dialysis
• Wizard Columns
• Electroelution
• Removal of γ-³²P-ATP from Oligonucleoides
• Manual Detritylation of Oligonucleotides
• Concentration by Butanol Extraction
• Extraction and Precipitation
• Wizard Columns

DNA Reactions

• Standard Taq-Mediated PCR
• Standard Pfu-Mediated PCR
• Cycle Runoffs
• Long PCR
• N Ladders
• Primers
• Primers: Placing in Collection
• Primer Design
• "Universal" Cassettes
• Single Primer ("Semi-Random") PCR
• Terminus PCR
• PCR in Air Cyclers
• Assymetric PCR
• Inverse PCR
• Long Distance PCR
• RNA Reaction - Cycle Runoffs
• Ligation
• Kinasing
• Phosphatasing
• Radiolabeling by Random Priming
• Radiolabeling by Nick Translation
• Polymerase Chain Reaction
• Sequencing Double Stranded Templates - Alkaline Denature
• Sequencing Double Stranded Templates - Nonidet Method
• Sequencing Single Stranded Templates
• Sequencing with Sequenase
• Digestion with Typical Restriction Endonucleases
• Digestion with 4 bp Site Restriction Endonucleases
• Digestion with 8 bp Site Restriction Endonucleases
• Partial Digestion with 4 bp Site Restriction Endonucleases
• Cloning Partial DNA Digests

DNA Electrophoresis

• Agarose Gels for Duplex DNA
• Agarose Gels for Single Stranded DNA
• Polyacrylamide Gels
• Oligonucleotides
• Orienting M13 Bacteriophage Inserts

DNA Transfer

• Southern Method
• Electroblot
• Plaque/Colony Lift
• Dot Blots

DNA Hybridization

• Bacterial DNA
• Kinased Oligonucleotides
• Church Method
• Filter Rinsing
• Removal of Bound DNA

Bacterial Transformations

• Linear Transformation
• Linear Transformation -- Rules for FRT Primers
• CaCl2 Method
• Cohen method
• RuCl Method
• Hanahan Method
• Electroporation Competent Cells
• Electroporation (Preferred)
• Electroporation (Jeff's)
• Colony Electroporation

Microbiology

• Streaking Bacteria for Single Colonies
• Growing Overnight Cultures
• Freezing Bacterial Cultures
• Serial Dilution
• Replica Printing
• Pouring Plates
• Plating in Top Agar
• Using the Anaerobic Chamber
• Maxicells

Genetics

• P22 Phage Stocks
• P22 Phage Lysates
• Quantitation of Bacteriophage P22
• Transduction with Bacteriophage P22
• Use of Bacteriophage P22 with galE Strains
• How Green Plates Work
• Preparation of Bacteriophage P1
• Quantitation of Bacteriophage P1
• Transduction with Bacteriophage P1
• Quantitation of Bacteriophage Lambda
• Amplification of Bacteriophage Lambda
• Preparation of Bacteriophage Mu from Dilysogens
• cis-Transposition of Bacteriophage Mu
• β-Galactosidase Assays
• B12 Bioassays

Mutagenesis

• Bacterial Cells with DES
• Bacteriophage P22 with Hydroxylamine
• Plasmid DNA with Hydroxylamine
• Bochner-Maloy Selection of Tetracycline Sensitivity
• Making Defective-Tn10 Pools in Salmonella
• Making Defective-Mu Pools in Salmonella

Miscellaneous

• Image Room Server
• DNA Quantification - TCA Precipitation
• Molecular Weights of DNA Fragments
• Preparation of Polyacrylamide Gels
• Preparation of DEAE Nitrocellulose Membranes
• Common Prehybridization Solutions
• Common Hybridization Solutions
• Salmonella typhimurium Mud-P22 strains
• International Units of Measurement
• Using Units of Measurement
• 50X E Salts and Derivatives
• Green Indicator Plates
• Lambda Plates
• T2 Buffer
• How to Give a Talk
• Mailing Strains First-Class
• Gene Nomenclature
• Strain Collection
• Strain Collection, Part II: Culture Culture

Old Protocols

DNA

• DNA Electroelution (Method 2)
• DNA from Agarose (Review)
• DNA from P22 Heads (Method 1)
• DNA from P22 Heads (Method 2)
• Magnetic Separation of DNA Strands

Genetic Manipulations

• Bochner Selection
• DES Mutagenesis
• E.coli Genes into Salmonella
• Indicator Plates
• HA Mutagenesis (Method 1)
• HA Mutagenesis (Method 2)
• HA Mutagenesis (Method 3)
• MudP22 Mapping
• P1 Transduction into Salmonella
• P1 Transduction Chart 1
• P1 Transduction Chart 2
• P22 Transduction

Insertion Elements

• Mini Tn10 Pools
• MudA Insertions
• Mud Manipulations
• Mud Nomenclature
• Mud Pools

Phage

• Mu Cloning (In Vitro)
• Mu Cloning (In Vivo)

Proteins

• Beta-Galactosidase Assay
• E.coli Immunoprecipitation

Comprehensive on-line database: Protocol Online

We owe a great debt to Jeff Lawrence, for organizing and systematizing the majority of these protocols. Any errors or mistakes are almost certainly mine, as I was the final editor and webmaster. In some cases, I have appended an earlier version to the main protocol, with appropriate attribution, as this may provide additional information or allow more accurate repeats of critical older experiments.