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? | ||
**'''2x42bp repeats in barrel'' | **'''2x42bp repeats in barrel''' | ||
**30-helix bundle with 30*(2*42+12) repeats = 2880 bases | **30-helix bundle with 30*(2*42+12) repeats = 2880 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 2880-base 30hb: 9792 bases total = $783.36 | **using single scaffold for 2880-base 30hb: 9792 bases total = $783.36 | ||
**'''3x42bp repeats in barrel'' | **'''3x42bp repeats in barrel''' | ||
**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 |
Revision as of 08:12, 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?
- 2x42bp repeats in barrel
- 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 = $783.36
- 3x42bp repeats in barrel
- 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 = $884.16
- 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?