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Microbial Pathogens Lab

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Last updated on 3/20/00


Molecular Biology Protocols

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--DNA Purification Techniques

  • DNA purification (plasmids, cosmids and p1) using Diatomaceous Earth (Bruce Roe Lab)

  • DNA purification, plasmid mini-preps, diatomaceous earth, contributed by Kyung-Soo Kim and Charles K. Pallaghy 2/10/97
  • DNA purification, bacterial-genomic, triton extraction method
  • DNA purification, bacterial-genomic via Qiagen columns
  • DNA purification, bacterial genomic, specifically Gram positive bacteria
  • DNA isolation from low melting-temperature agarose
  • Low copy plasmid purification using Qiagen Midi columns
  • Plasmid "Miniprep" Isolation: tried and true!
  • Single stranded template from pBluescript phagemid

    --DNA Transformation/Library Preparation

  • Transformation-Competent E. coli preparation

  • Cosmid packaging protocol

    --Southern/Northern Blotting

  • Southern blot-chemiluminescent detection, using Lumigen or Lumiphos (BM "Genius" system)
  • Southern blot-chemiluminescent detection, using CSPD (BM "Genius" system)

    --DNA Sequencing

  • Sequencing gel solutions
  • Sequencing gels: wedge gel performance without pouring wedge gels


  • Oligonucleotide Visualization
  • Oligonucleotide calculator: determine Tm, MW, etc. of your oligonucleotide (requires javascript enabled browser)

    --PCR and Related Methods

  • Core sample PCR: a method to re-PCR unique bands from products of mixed size
  • Cloning PCR-Generated DNA Fragments, contributed by Hugh Griffin, 7/7/95
  • Site-directed Mutagenesis using PCR, contributed by Hugh Griffin, 7/25/95
  • Reverse Transcriptase PCR, contributed by Jim Hutchins 8/25/95
  • Error Rates for Thermal Resistant DNA Polymerases

    --RNA Methods

  • Solublization of RNA in Formamide, contributed by James McCaughern-Carucci, 12/31/96
  • RNAse Protection Assay, contributed by James McCaughern-Carucci, 1/9/97
  • The "Neverfail" Northern Blot Hybridization, contributed by James McCaughern-Carucci, 10/26/97

    --Protein Electrophoresis

  • Tricine-polyacrylamide gels: for high resolution of small proteins
  • SDS-polyacrylamide gels: standard Laemmli protocol
  • Ethanol-based SDS-PAGE Coomassie Blue staining, contributed by Roger Rowlett, 9/5/97
  • Bench protocol for silver staining SDS-polyacrylamide gels, contributed by Melissa Caimano, 3/20/00

    --Protein Purification

  • Preparation of active proteins from inclusion bodies, contributed by Laurent Vuillard and Alasdair Freeman, 3/11/99

    --Autoradiography Tips

  • Intensifying Screens -- their use explained, contributed by John Attwood 12/1/97


  • Generation of Phosgene from Chloroform !

    --Other References

  • Standard Genetic Code

    --Links to other Molecular Biology Protocols and Resources

    Key Resource
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    This list is a work in progress and is part of the Northwest Fisheries Science Center WWW Server. My lab is the Fish Health/Microbiology (Microbial Pathogenesis) group in this Center's Resource Enhancement and Utilization Technologies Division. Feedback, tips, or even submission of your favorite technique is always appreciated. Try out the Molecular Biology Forum.

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