IGEM:Harvard/2006/Container Design 4

Design details

based on n = 0.324 nm, d = 3.0 nm

Shape	Lid ply	Cylinder design	Lid design	Total scaffold length
honeycomb hexagon	single	30 tubes (29.0 nm dia) x (84+12)bp long (30.8 nm) = 2880bp	13 tubes (34.2 nm) x (84+12)bp long (30.8 nm) = 1248bp each	2880+(2*1248) + 6bp + 12bp linkers = 5394

ASCII Files

Lid:

000   002   004   006   008   010   012
   001   003   005   007   009   011   

Barrel:

...   ...   000   002   004   ...   
  ...   029   001   003   005   ...

   ...   028   ...   ...   006   ...
...   027   ...   ...   ...   007   

...   026   ...   ...   ...   008   
   025   ...   ...   ...   ...   009

   024   ...   ...   ...   ...   010
...   023   ...   ...   ...   011   

...   022   ...   ...   ...   012   
   ...   021   ...   ...   013   ...

   ...   020   018   016   014   ...
...   ...   019   017   015   ...   

Sequence Chunks (KV, 6.27.06)

• Media:all chunks.txt
• Oligo Paths and Sequences

Script for generating sequence chunks

#!/usr/bin/python

import string
import sys
import fileinput

def nowhite(s):
  return ''.join([c for c in s if c in string.letters])

seq = ''

# read in sequence
for line in fileinput.input("-"):
  seq = seq + nowhite(line)

lid_1 = 96 * 13
linker_1 = 30
box = 29 * 96
linker_2 = 30
lid_2 = 96 * 14
linker_3 = 200
box_2 = 96

#store first segment up to end of lid 1
lid_1_seq = seq[:lid_1]
#reset sequence to start at end of lid 1
seq = seq[lid_1:]
linker_1_seq = seq[:linker_1]
seq = seq[linker_1:]
box_1_seq = seq[:box]
seq = seq[box:]
linker_2_seq = seq[:linker_2]
seq = seq[linker_2:]
lid_2_seq = seq[:lid_2]
seq = seq[lid_2:]
linker_3_seq = seq[:linker_3]
seq = seq[linker_3:]
box_2_seq = seq[:box_2]
seq = seq[box_2:]
extra_scaffold = seq
barrel = box_1_seq + box_2_seq

#print out the length of each segment and its sequence
print len(lid_1_seq)
print lid_1_seq
print len(linker_1_seq)
print linker_1_seq
print len(barrel)
print barrel
print len(linker_2_seq)
print linker_2_seq
print len(lid_2_seq)
print lid_2_seq
print len(linker_3_seq)
print linker_3_seq

Sequence Chunks (TChan, 6.27.06)

• Media:Chunk1p7308_TC_62706.txt
  • Chunk of p7308 sequence for container4's lid1.

• Media:Chunk2p7308_TC_62706.txt
  • Chunk of p8256 sequence for container4's barrel (skips 6bp after lid1's chunk, 6bp right before lid2, the 96bp*13helices that is lid2, 6bp after lid2, and appends the final helix).

• Media:Chunk3p7308_TC_62706.txt
  • Chunk of p7308 sequence for container4's lid2.

Oligos (TChan, 6.27.06)

• Media:lid1_7308_TC_62706.txt
  • Oligos for lid 1 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices)

• Media:barrel_7308_TC_62706.txt
  • Oligos for barrel (correct wordcount: 74lines, 74words, 2594chars (includes 74 carriage returns) for (96bp-12ssbp)*30helices)

• Media:lid2_7308_TC_62706.txt
  • Oligos for lid 2 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices)