IGEM:Stanford/2009/Project Homeostasis/Helpful Websites

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Project
Research Proposal
Systems Overview
Cloning Plan
Sequences & Primers
Anti-Inflammation
Device Overview
Parts Design
Challenges
Results
Anti-Immunosuppression
Device Overview
Parts Design
Challenges
Results
Protocols
Modeling
Overview
Notebook
Results
Future Work
Archived Work



General Guidelines

1.18-30 nucleotide bases

2. Always end in G or C (for the stronger triple bond)

3. %GC should be 40-65%

4. Melting temp between 52-68C is good

5. Forward Primer:

  • 1. Add TATA at the very beginning
  • 2. After TATA add the proper prefix found on the registry (see below)
  • 3. Check both initial and TATA prefix ratios and melting temps on IDT (see below)

6. Primer 2

  • 1. Take end sequence of proper length then find the reverse complement (Ape see below)
  • 2. Check the reverse complement for %GC and melting temp.
  • 3. Add TATA and suffix to the beginning of the reverse complement strand (parts registry)
  • 4. Check both initial and final sequence on IDT

7. Analyze both strands at NUPACK for hairpins and trouble spots

  • 1. Insert both primer sequences and run the program
  • 2. Shows potential areas for hairpin
  • 3. Red = BAD

8.Both primers should be ready to go

9.Document all papers, gene sequences, and sites