# IGEM:Harvard/2006/Container Design 2

## oligo path

### Design structure

• Barrel: 30 helices @ 84bp each, each side 18.6nm long, widest point 29nm long
• Lids: double-ply, 26 helices @ 84bp each, 34.2nm long

• 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

### ASCII Files

• 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.