IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-18: Difference between revisions
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*How big does a 2-ply lid need to be to span a 30-helix barrel? | *How big does a 2-ply lid need to be to span a 30-helix barrel? | ||
*Can we use two scaffolds in the design? | *Can we use two scaffolds in the design? | ||
**30-helix bundle with 30*(2*42+12) repeats = 2880 bases | |||
**two-ply-lid: 36 * (2*42+12) = 3456 * 2 = 6912 | |||
**using single scaffold for 2880-base 30hb: 9792 bases total | |||
**30-helix bundle with 30*(3*42+12) repeats = 4140 bases | **30-helix bundle with 30*(3*42+12) repeats = 4140 bases | ||
**two-ply-lid: 36 * (2*42+12) = 3456 * 2 = 6912 | **two-ply-lid: 36 * (2*42+12) = 3456 * 2 = 6912 | ||
**using single scaffold for 4140-base 30hb: 11052 bases total | |||
*Will unused scaffold interfere with proper folding of lid & barrels | *Will unused scaffold interfere with proper folding of lid & barrels | ||
*Should we use two M13-based scaffolds, or try to make {{phix174}} to have less slack? | *Should we use two M13-based scaffolds, or try to make {{phix174}} to have less slack? | ||
Revision as of 08:10, 18 July 2006
Questions
Design 2
- How big does a 2-ply lid need to be to span a 30-helix barrel?
- Can we use two scaffolds in the design?
- 30-helix bundle with 30*(2*42+12) repeats = 2880 bases
- two-ply-lid: 36 * (2*42+12) = 3456 * 2 = 6912
- using single scaffold for 2880-base 30hb: 9792 bases total
- 30-helix bundle with 30*(3*42+12) repeats = 4140 bases
- two-ply-lid: 36 * (2*42+12) = 3456 * 2 = 6912
- using single scaffold for 4140-base 30hb: 11052 bases total
- Will unused scaffold interfere with proper folding of lid & barrels
- Should we use two M13-based scaffolds, or try to make ΦX174 to have less slack?
- Can we easily get ΦX174? fermentas
Protection assay
- Can we digest streptavidin with Qiagen proteinase K and/or Qiagen protease?
- What is our initial protocol?
