IGEM:Harvard/2006/Container Design 2

 Project Overview Designs Notebook Protocols Presentations Literature  

 Design 1</li> Design 2</li> Design 3</li> Design 4</li> Design 5</li> Design 6</li> </ul> <br style = "clear:both">

ascii
[[Media:lid_ascii1.txt|ascii]]

oligo path
[[Media:lid1_oligo_path1.txt|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

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

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.