IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-18

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?