All Protocols

These protocols contain everything you need to know to get started with practical Synthetic Biology. You can learn the basic genetic theory that explains why these protocols work by following this link.

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This is a directory of all the protocols on the site. You can find them organised into a more curated form here;

The Graduate’s Guide to Synthetic Biology

Complete List of Protocols:

1. The Sterile Workspace

2. Host Selection Criteria

3. Culturing Conditions

4. Mixing Media and Pouring Plates

   1. LB Liquid Media

   2. LB-Agar Media

   3. Antibiotic Stock Solution Mixing

5. Sterile Technique

6. DIY Buffer Mixing

   1. Water

   2. Tris-Cl Buffer

   3. Miniprep Buffer Mixing

      1. Buffer P1 (Resuspension Buffer)

      2. Buffer P2 (Lysis Buffer)

      3. Buffer N3 (Neutralisation Buffer)

      4. Buffer PB (Wash Buffer 1)

      5. Buffer PE (Wash Buffer 2)

      6. Elution Buffers (TE, EB, Water)

   4. Agarose Electrophoresis Buffers

      1. TAE Buffer

      2. LAB Buffer

      3. TBE Buffer

   5. Buffer QG (Gel Purification Buffer)

   6. Protein Purification Buffers

      1. Protein Wash Buffer

      2. Protein Elution Buffer

      3. Protein Storage Buffer

   7. SDS-PAGE Buffers

      1. SDS-PAGE 4x Loading Buffer

      2. SDS-PAGE 10x Running Buffer

      3. Coomassie Blue Staining Solution

      4. Destaining Solution

7. DNA101

8. Purification of Genomic DNA

   1. Boil Purification of Genomic DNA

   2. Genomic DNA Extraction with CTAB

9. Plasmids101 - Guide coming soon!

10. Purification of Plasmid DNA (Miniprep aka. Ethanol Lysis)

11. Plasmid Insertion

    1. Preparation of Chemically Competent E.coli cells (Rubidium Chloride) for Heat Shock Transformation

    2. Preparation of Chemically Competent E.coli cells (Calcium Chloride) for Heat Shock Transformation

    3. Heat Shock Transformation of Chemically Competent E. Coli

    4. Preparation of Electrocompetent cells of Pseudomonas or E. coli for Electroporation

    5. Electroporation of Electrocompetent cells of Pseudomonas or E. coli for Electroporation

    6. DIY Gene Gun

12. Agarose Gel Electrophoresis

    1. Buffer QG Gel Purification

    2. Cotton Wool Gel Purification

13. Gel Illumination & Photography

14. Restriction Enzyme Digest of Plasmid & Insert DNA, Optional: Dephosphorylation + Purification

    1. Heat Inactivation of Restriction Enzymes

    2. Column Purification of Restriction Enzyme Digest

15. Ligation & Troubleshooting

    1. Kinase Treatment

16. Polymerase Chain Reaction (PCR)

17. Primer Design

18. Gradient PCR

19. Confirmation of Edits

    1. Patch Plate and Colony PCR (Junction & Spanning PCR)

    2. Restriction Digest Analysis

    3. Preparation for External Sequencing

    4. In-House Sequencing (Oxford Nanopore)

    5. Interpreting Sequencing Results

    6. Preparation of Glycerol Stocks

20. Flanking Sequence Addition

21. Gibson Assembly

22. Golden Gate Assembly

23. Site Directed Mutagenesis

24. GBlock Design

25. Backbone Selection

26. CRISPR/CAS9

27. Proteins101

28. Induction of Protein Expression

29. Cell Lysis

    1. Bead-Beating Lysis

    2. Chloroform Lysis of Periplasm

    3. Chemical Lysis

30. Affinity Tag Purification

    1. His-Tag Protein Purification

       1. Centrifuge & Filter His-Tag Purification

       2. Column Chromatography His-Tag Purification

    2. Car9 Protein Purification

31. SDS-PAGE

32. Antibody Production

33. Aptamer Production

34. Cardinal Blots

    1. Northern Blot

    2. Eastern Blot

    3. Southern Blot

    4. Western Blot

35. ELISA

36. Mass Spec Prep

37. Cell Assays

38. RNA101

39. RNA Purification

40. RT-PCR

41. RT-qPCR

42. In Silica