IGEM:Stanford/2009/Project Homeostasis/Helpful Websites

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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