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 1:

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   ...   

Lid 2:

000   002   004   006   008   010   012   ...
   001   003   005   007   009   011   013   

Sequence Chunks (KV, 6.27.06)

• Scaffold Sequence
• Oligo Paths and Sequences
• Oligo Output for 30hb

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

Modifications to William's program to print each oligo number next to what tokens it represents

oligo_num = 0
for oligo in OTP_ra:
        for token in oligo:
                print str(oligo_num) + ": ", token
        oligo_num = oligo_num + 1

Modifications to William's program to print a grid of oligo numbers completely filled in

• add this part to main (AAA or BBB)

####
# generate and print the oligo grid
####

# Initialize the grid with all periods
num_strands = len(TPP_ra)
num_subzones = len(TPP_ra[0])

sub_token_visit_ra = ['.' for subzone_num in range(num_subzones)]
grid_ra = [sub_token_visit_ra[:] for strand_num in range(num_strands)]
        
oligo_num = 0
for oligo in OTP_ra:
        grid_ra = generate_oligo_path(oligo, oligo_num, grid_ra)
        oligo_num = oligo_num + 1
print grid_ra
        
print_all_oligos(grid_ra, num_strands, num_subzones)

• add this part to honeycomb_pointers_v1.py

# The idea here is to have a function that adds the numbers of one oligo path
# to the appropriate places in the big grid array. Eventually this will be printed
# in main. Also it needs to be initialized in main. Oligo_path is the path of
# one oligo, while grid_ra is the grid that is constantly being updated until 
# it is printed in main. oligo_num is number that will be inputed to the grid_ra.
                        
def generate_oligo_path(oligo_path, oligo_num, grid_ra):
        num_path_tokens = len(oligo_path)
                
# Assign visits
        for path_token_num in range(num_path_tokens):
                token = oligo_path[path_token_num]
                strand = token[0]
                subzone = token[1]
                grid_ra[strand][subzone] = oligo_num
        
        
        return grid_ra

def print_all_oligos(grid_ra, num_strands, num_subzones):
        spacer = '   '
        for strand_num in range(num_strands):
                for subzone_num in range(num_subzones):
                        visitor_string = str(grid_ra[strand_num][subzone_num])   
                        sys.stdout.write(visitor_string)
                        sys.stdout.write(spacer[:4 - len(visitor_string)])
                sys.stdout.write('\n')   

honeycomb_pointers_v1.py UPDATED
BBB_make_honeycomb_structure_v1.py UPDATED

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)

Scaffold (TChan, 6.30.06)

• 

  Barrel Plus Oligos

Media:barrel_oligos_TC_63006.ai

Scaffolds (KV, 6.29.06)

• 

  Barrel Plus Lids

• 

  schematic of lid 1 with endpoint aptamers

• 

  schematic of lid 1 with all potential aptamers including looping oligos

• 

  schematic of lid 2 with endpoint aptamers

• 

  Back 3 faces (F,A,B) Inside view. Only in-facing aptamers which come off of oligo endpoints.

• 

  Back 3 faces (F,A,B) Inside view. All in-facing aptamers including those looping off oligos.

• 

  Back 3 faces (F,A,B) Inside view. In and Out aptamers which come off of oligo endpoints.

• 

  Back 3 faces (F,A,B) Inside view. All potential aptamers - in and out, including ones looping off oligos.

• 

  Front 3 faces (C,D,E) Inside view. Only in-facing aptamers which come off of oligo endpoints.

• 

  Front 3 faces (C,D,E) Inside view. All in-facing aptamers including those looping off oligos.

• 

  Front 3 faces (C,D,E) Inside view. In and Out aptamers which come off of oligo endpoints.

• barrel + lid schematic: Media:Barrelpluslids.ai