IGEM:Help/Team experience tutorial

Coming up with a project

Research previous year's projects

1. Go to http://igem2006.com
2. Click on Results
3. Click on Watch the presentations and get the powerpoints
4. Watch team presentations (http://parts.mit.edu/movies/iGEM2006_MIT.mov) and view the slides (http://parts.mit.edu/wiki/images/c/c0/IGEM2006-MIT-Powerpoint.pdf)
5. Go to the team's wiki page by clicking Wiki live
6. Click on Meet the 37 teams
7. Click on 'MIT and read about the project

Let's make a new scent! Vanilla.

Design the system

1. We want a device that takes an input chemical and makes vanilla scent.
2. Need enzymes that synthesize vanilla.

Search the registry

1. Go to the Registry (http://parts.mit.edu)
2. Use the search box to look for existing parts
3. Search for vanilla ... you get no real hits ([1])
4. Search for vanillin ... ([2])
5. No one has made a vanilla synthesizing enzyme ... phew!

Search the literature

1. Visit PubMed
2. Search for vanilla
3. Find a relevant paper
4. Go read the paper
5. Identify the useful components described in the paper
6. You seem to need two gene ech and fcs ... let's grab some sequence
7. Search for Genbank accession numbers
8. Follow the Genbank link

Make a part

Enter a basic part

1. Go back to the Registry
2. Login to the Registry
3. Click on the Add a part
4. Click on the Add a basic part now
   • A basic part is a linear sequence of DNA with a fundamental function like a promoter, terminator, ribosome binding site, CDS etc.
5. Choose Allow edits by your iGEM team
6. Choose the next available part number, or some number within your team's allowed naming range.
7. Enter that number into the Selected Part Name field
8. Choose a part type from the drop down menu.
   • Find out what the different part types are by clicking the Browse Part Types link to the left. The question marks next to each part type give a description of that part type.
9. Enter a short description ... e.g. feruloyl-CoA hydratase for vanillin biosynthesis
10. Enter a long description of the part (you can update this more later)
    • Where species is the enzyme from? Pseudomonas fluorescens
    • What reaction does it catalyze? One of two steps in the bioconversion of ferulic acid to vanillin.
    • Does it work in E. coli? Yes. The authors of the paper have shown that it works already.
    • Does it require any other parts? Yes. Both ech and fcs are needed for vanillin biosynthesis
11. Enter the source of this part
    • Include the species, the GenBank accession number and the paper reference
12. Enter design considerations
    • The stop codon is TGA so we changed it to TAATAA to conform with BioBrick standards
13. Click go on to enter the sequence and add feature annotations
14. Return to the Genbank entry
15. Click on the cds link to get the sequence of the coding region
16. Display it in FASTA format
17. Copy the sequence
18. Paste it into the sequence field and click Save in the upper right
19. Change the TGA stop codon to TAATAA
20. The Registry will automatically check your sequence for BioBricks restriction sites.
    • We will have to remove these in fabricating this part
    • Once the sites have been removed we can edit this information in the Registry
    • See OpenWetWare protocols on site directed mutagenesis
21. Click the Add a feature link
22. Enter the start codon, stop codons and coding region as features. Click Submit to save. And anything else you think is important!

Reviewing your part

Now you can view the part you've created.

1. Go to the Registry main page (http://parts.mit.edu)
2. Click Browse Parts by School (http://parts.mit.edu/registry/index.php/Type:iGEM_2007)
3. Click on your school
4. You should see the part in your sandbox

Make a composite part

Protein coding regions by themselves aren't very useful. We need to make composite parts.

Let's make a protein generator to express our vanilla-scent making enzyme.

Finding existing parts

1. Click Browse parts types on the navigation bar to the left.
2. To express a gene, we need a promoter, RBS, and terminator.
3. Browse the promoters by clicking Regulatory
4. Choose a promoter. The green W indicates that the promoter has been shown to work.
5. Make a