IGEM:Harvard/2006/Container Design 1

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Contents

Version 1.0

Top view, two lids come up and over
Top view, two lids come up and over
  • This is a top view. Would have two lids (one shown). Lid comes up and over the cylinder.
  • Each tube is 84 turns (or 27.5 nm) long.
  • Notice that the scaffold strand first enters a lid on a positive coil and leaves it on a negative coil (or vice versa).







Dimensions

Shape Lid ply Cylinder design Lid design Total scaffold length
honeycomb hexagonsingle42 tubes (39.4 nm dia) x (84+12) bp long (30.6 nm)16 tubes (~42 nm) x (126+12) bp long (44.3 nm)8256

ASCII representation

Cylinder

...   ...   ...   000   002   004   006   ...   ...
   ...   ...   041   001   003   005   007   ...   ...

   ...   ...   040   ...   ...   ...   008   ...   ... 
...   ...   039   ...   ...   ...   ...   009   ...

...   ...   038   ...   ...   ...   ...   010   ...
   ...   037   ...   ...   ...   ...   ...   011   ...

   ...   036   ...   ...   ...   ...   ...   012   ...
...   035   ...   ...   ...   ...   ...   ...   013

...   034   ...   ...   ...   ...   ...   ...   014
   ...   033   ...   ...   ...   ...   ...   015   ...

   ...   032   ...   ...   ...   ...   ...   016   ...
...   ...   031   ...   ...   ...   ...   017   ...

...   ...   030   ...   ...   ...   ...   018   ...
   ...   ...   029   ...   ...   ...   019   ...   ...

   ...   ...   028   026   024   022   020   ...   ...
...   ...   ...   027   025   023   021   ...   ...

Lid

000   002   004   006   008   010   012   014
   001   003   005   007   009   011   013   015

Program Output using beginning of p8256

The number of tokens visited is 756.
The number of paths with length 2 is 28.
The number of paths with length 6 is 12.
The number of paths with length 314 is 2.
Each token is represented once and only once in the oligo token pointer lists.

ONE PATH ARRAY
.   4   3   .   .   .   .   130 129 .   .   .   .   256 255 .   .   .   
.   5   6   .   .   .   .   131 132 .   .   .   .   257 258 .   .   .   
.   8   7   .   .   .   .   134 133 .   .   .   .   260 259 .   .   .   
.   9   10  .   .   .   .   135 136 .   .   .   .   261 262 .   .   .   
.   12  11  .   .   .   .   138 137 .   .   .   .   264 263 .   .   .   
.   13  14  .   .   .   .   139 140 .   .   .   .   265 266 .   .   .   
.   16  15  .   .   .   .   142 141 .   .   .   .   268 267 .   .   .   
.   17  18  19  20  .   .   143 144 145 146 .   .   269 270 271 272 .   
.   24  23  22  21  .   .   150 149 148 147 .   .   276 275 274 273 .   
.   25  26  27  28  .   .   151 152 153 154 .   .   277 278 279 280 .   
.   32  31  30  29  .   .   158 157 156 155 .   .   284 283 282 281 .   
.   33  34  35  36  .   .   159 160 161 162 .   .   285 286 287 288 .   
.   40  39  38  37  .   .   166 165 164 163 .   .   292 291 290 289 .   
.   41  42  43  44  .   .   167 168 169 170 .   .   293 294 295 296 .   
.   .   .   46  45  .   .   .   .   172 171 .   .   .   .   298 297 .   
.   .   .   47  48  .   .   .   .   173 174 .   .   .   .   299 300 .   
.   .   .   50  49  .   .   .   .   176 175 .   .   .   .   302 301 .   
.   .   .   51  52  .   .   .   .   177 178 .   .   .   .   303 304 .   
.   .   .   54  53  .   .   .   .   180 179 .   .   .   .   306 305 .   
.   .   .   55  56  .   .   .   .   181 182 .   .   .   .   307 308 .   
.   .   .   58  57  .   .   .   .   184 183 .   .   .   .   310 309 .   
.   .   .   59  60  61  62  .   .   185 186 187 188 .   .   311 312 313 
.   .   .   66  65  64  63  .   .   192 191 190 189 .   .   .   .   .   
.   .   .   67  68  69  70  .   .   193 194 195 196 .   .   .   .   .   
.   .   .   74  73  72  71  .   .   200 199 198 197 .   .   .   .   .   
.   .   .   75  76  77  78  .   .   201 202 203 204 .   .   .   .   .   
.   .   .   82  81  80  79  .   .   208 207 206 205 .   .   .   .   .   
.   .   .   83  84  85  86  .   .   209 210 211 212 .   .   .   .   .   
.   .   .   .   .   88  87  .   .   .   .   214 213 .   .   .   .   .   
.   .   .   .   .   89  90  .   .   .   .   215 216 .   .   .   .   .   
.   .   .   .   .   92  91  .   .   .   .   218 217 .   .   .   .   .   
.   .   .   .   .   93  94  .   .   .   .   219 220 .   .   .   .   .   
.   .   .   .   .   96  95  .   .   .   .   222 221 .   .   .   .   .   
.   .   .   .   .   97  98  .   .   .   .   223 224 .   .   .   .   .   
.   .   .   .   .   100 99  .   .   .   .   226 225 .   .   .   .   .   
.   .   .   .   .   101 102 103 104 .   .   227 228 229 230 .   .   .   
.   .   .   .   .   108 107 106 105 .   .   234 233 232 231 .   .   .   
.   .   .   .   .   109 110 111 112 .   .   235 236 237 238 .   .   .   
.   .   .   .   .   116 115 114 113 .   .   242 241 240 239 .   .   .   
.   .   .   .   .   117 118 119 120 .   .   243 244 245 246 .   .   .   
.   .   .   .   .   124 123 122 121 .   .   250 249 248 247 .   .   .   
0   1   2   .   .   125 126 127 128 .   .   251 252 253 254 .   .   .   



Python Scripts

  • any modified script files can go here

Oligos

  • once we generate the oligos, put them here
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