IGEM:Harvard/2006/Container Design 2

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Container 2.0



oligo path

oligo path

Design structure

Double-ply lids, smaller hexagonal cylinder.
  • Barrel: 30 helices @ 84bp each, each side 18.6nm long, widest point 29nm long
  • Lids: double-ply, 26 helices @ 84bp each, 34.2nm long

Notes about designs

  • Calculating coil length: The distance between stacked base pairs is approximately (3.4 nm / turn) / (10.5 bp / turn) = 0.324 nm / bp.
  • Calculating sheet length: The length of a "sheet" can be calculated using simple trigonometry, as demonstrated by the diagram below.
  • The effective diameter of a coil is 3 nm according to Dr. Shih, but I'm not 100% sure that this figure is correct, so I will call it d until we can verify it.

Design details

based on n = 0.324 nm, d = 3.0 nm

Shape Lid ply Cylinder design Lid design Total scaffold length
honeycomb hexagon double 30 tubes (29.0 nm dia) x (84+12)bp long (30.8 nm) 26 tubes (34.2 nm) x (84+12)bp long (30.8 nm) 7872


  • Media:container2barrel.txt
    • (The example hexagonal barrel that William had put up onscreen during the presentation, which is also the one we planned for this design.
  • Media:container2lid.txt
    • Double-ply lid, will need to be fed two different M13 sequence portions, bookending the main barrel's sequence, to be added.

Oligo Sequences (84bp-long helices)

NB: These oligos still seem to be wrong, despite the feeding of p7308 sequence chunks appropriately separated by 12bp linkers.

  • Lid 2: Media: design2oligo_sequenceslid2.txt
    • Oligos for the second lid (program was fed the lid ASCII, 2*42bp per helix, and the third chunk of the p7308 sequence - ie. 84bp*26helices)