IGEM:Harvard/2006/Container Design 2

• Project Overview
• Designs
• Notebook
• Protocols
• Presentations
• Literature

• Design 1
• Design 2
• Design 3
• Design 4
• Design 5
• Design 6

ascii

ascii

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

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.

• Lid 1: Media: design2oligo_sequenceslid1.txt
  • Oligos for the first lid (program was fed the lid ASCII, 2*42bp per helix, and the first 84bp*26helices of the p7308 sequence)

• Barrel: Media: design2oligo_sequencesbarrel.txt
  • Oligos for the barrel (program was fed the barrel ASCII, 2*42bp per helix, and the second chunk of the p7308 sequence - ie. 84bp*30helices)

• 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)

• p7308 Sequence Chunk, Lid 1: Media: first84bpx26h.txt
  • Sequence fed for the first lid.

• p7308 Sequence Chunk, Barrel: Media: second84bpx30h.txt
  • Sequence fed for the barrel.

• p7308 Sequence Chunk, Lid 2: Media: third84bpx26h.txt
  • Sequence fed for the second lid.