Link to the video lecture
caDNAno is a platform independent, free and open source software for designing three-dimensional DNA origami nanostructures. It was originally created by Shawn Douglas at Harvard. Our tutor this week, William Shih recommended us to use the legacy version, but it was based on Adobe Air, which does not run on Ubuntu, not even under Wine. So I decided to go with caDNAno 2.5 version instead.
Note: This was written for Ubuntu in december 2015. Probably this will be outdated by HTGAA'16. Clone the github repository to you computer. Cloning is recommended vs downloading because caDNAno is under development. In a terminal window, navigate to the folder where you want the caDNAno folder to be placed and type:
git clone https://github.com/cadnano/cadnano2.5.git
Inside that folder cd cadnano2.5 I followed the instructions and executed the check sudo python pyqt5_check.py. But I was getting some errors, so I raised an issue to github and the developers updated the master branch, which solved the problem (If something does not work find out what's the problem. Do not give up). In my case I also had to specify to use python 3 instead of python 2: sudo python3 pyqt5_check.py and install the following packages to make it work:
sudo apt-get install libqt5webkit5-dev
sudo apt-get install python3-pyqt5.qtsvg
sudo apt-get install python3-pyqt5.qtwebkitRunning caDNAno just open a terminal window inside the caDNAno folder and type python3 bin/main.py
As I said before, caDNAno is under active development so expect updates and bugfixes over time. From time to time just open a terminal inside the folder where caDNAno is installed and type git pull. This will update caDNAno.
In 2006 Paul W.K. Rothemund, a Research Professor at Caltech (USA), In 2006, reported a method of creating nanoscale shapes and patterns using DNA. This method is called DNA Origami.
The following image is the output that is obtained and it has been generated from caDNAno exporting to .svg file format. 
You can also download as a .json file.
This is just a matter of exporting the design file. Output: list of sequences in tab delimited text file
Start,End,Sequence,Length,Color
0[87],1[71],CAAGAGTCCACTATTAAAGAACGTACAGGAAA,32,#b8056c
0[119],1[103],AGATAGGGTTGAGTGTTGTTCCAGTTTGACGC,32,#f74308
0[151],1[135],AAAATCCCTTATAAATCAAAAGAACATTGGC,31,#03b6a2
0[183],1[167],AAATCCTGTTTGATGGTGGTTCCGGTAAAGCC,32,#57bb00
0[215],1[199],GCGGTCCACGCTGGTTTGCCCCAGACTCACAT,32,#03b6a2
0[247],1[231],TCACCGCCTGGCCCTGAGAGAGTCTTTCCAG,31,#aaaa00
0[279],1[263],CACCAGTGAGACGGGCAACAGCTGGCATTAAT,32,#007200
1[72],3[71],AACGCTCATTTTTGAATGGCTATTGTATTAAC,32,#f74308
1[104],3[103],TCAATCGTGAAAGCGTAAGAATACGAGAGCCA,32,#f74308
1[136],3[135],AGATTCACTGGCCAACAGAGATTCACCTTG,30,#333333
1[168],3[167],TGGGGTGCGCCGGAAGCATAAAGTGCGCAACT,32,#007200
1[200],3[199],TAATTGCGTTATCCGCTCACAATTGCCTCTTC,32,#03b6a2
1[232],3[231],TCGGGAACATGGTCATAGCTGTGGGATGTG,30,#57bb00
1[264],3[263],GAATCGGCGGATCCCCGGGTACCGACGCCAGG,32,#1700de
2[87],0[88],AGACAATATGGAAATACCTACATTTTGGAA,30,#007200
2[119],0[120],TCTGACCTCTGAAATGGATTATTTATAGCCCG,32,#333333
2[151],0[152],GGGACATTCCAGTCACACGACCAGAAATCGGC,32,#aaaa00
2[183],0[184],ACATACGACTAATGAGTGAGCTACAGGCGA,30,#7300de
2[215],0[216],TGAAATTGTTGCGCTCACTGCCCGTGCAGCAA,32,#57bb00
2[247],0[248],TTCGTAATACCTGTCGTGCCAGCTATTGCCCT,32,#b8056c
2[279],0[280],ACTCTAGACAACGCGCGGGGAGATTCTTTT,30,#b8056c
3[72],5[71],ACCGCCTGTAACAACTAATAGATTTTAATTTT,32,#f74308
3[104],5[103],GCAGCAAAGGAAGGTTATCTAAAATTTGCGGA,32,#f7931e
3[136],5[135],CTGAACCAGTTGGCAAATCAACGAATTATC,30,#b8056c
3[168],5[167],GTTGGGAAATTCGCCATTCAGGCTAACGCCAT,32,#cc0000
3[200],5[199],GCTATTACGCTTCTGGTGCCGGAATCCTGTAG,32,#f74308
3[232],5[231],CTGCAAGAAGATCGCACTCCAGGAGCGAGT,30,#f7931e
3[264],5[263],GTTTTCCCTTTGAGGGGACGACGAGGAACAAA,32,#1700de
4[87],2[88],AGGAGCACCAACAGTGCCACGCTGTGGCAC,30,#1700de
4[119],2[120],GGAATTGATGAAAAATCTAAAGCAAGAACCCT,32,#f74308
4[151],2[152],ATCTGGTCTCAAATATCAAACCCTTAATAAAA,32,#1700de
4[183],2[184],AAAGCGCCGGGCGATCGGTGCGGCCACACA,30,#f74308
4[215],2[216],CCGGCACCGCCAGCTGGCGAAAGGTTCCTGTG,32,#f7931e
4[247],2[248],GCCTCAGGGCGATTAAGTTGGGTAAGCTCGAA,32,#b8056c
4[279],2[280],TCTGCCAGAGTCACGACGTTGTACAGGTCG,30,#57bb00
5[72],7[71],AAAAGTTTAATTATTTGCACGTAATCGCCTGA,32,#f7931e
5[104],7[103],ACAAAGAAATAATGGAAGGGTTAGAATCGCGC,32,#cc0000
5[136],7[135],ATCATATATAATCCTGATTGTTACCTGAGC,30,#f74308
5[168],7[167],CAAAAATATTTTTTAACCAATAGGATTCAACC,32,#f74308
5[200],7[199],CCAGCTTTATTCGCATTAAATTTTGGAGAGGG,32,#b8056c
5[232],7[231],AACAACCTTTAAATTGTAAACGAGGCTATC,30,#b8056c
5[264],7[263],CGGCGGATCCCCAAAAACAGGAAGGCAAACAA,32,#b8056c
6[87],4[88],CATATCAAGAGTAACATTATCATTATCTTT,30,#57bb00
6[119],4[120],ACTTCTGAACCACCAGAAGGAGCGAGTTGAAA,32,#cc0000
6[151],4[152],TCATCAATTCCTGATTATCAGATGCAATCAAT,32,#f7931e
6[183],4[184],TCAGCTCAATTCGCGTCTGGCCTACCAGGC,30,#f74308
6[215],4[216],TTGTTAAACATCAACATTAAATGTCCAGCTTT,32,#57bb00
6[247],4[248],AGCAAATACGTCGGATTCTCCGTGCAGTATCG,32,#cc0000
6[279],4[280],CAGAAAAGTGACCGTAATGGGATCCGTGCA,30,#aaaa00
7[72],9[71],TTGCTTTGTATGTGAGTGAATAACAGTGAATT,32,#007200
7[104],9[103],AGAGGCGATTTTTTAATGGAAACAACTACCTT,32,#cc0000
7[136],9[135],AAAAGAAAATTACATTTAACAATATATAAC,30,#aaaa00
7[168],9[167],GTTCTAGCTCACCATCAATATGATCAATTCTA,32,#57bb00
7[200],9[199],TAGCTATTAAAAGGGTGAGAAAGGCAATAAAT,32,#1700de
7[232],9[231],AGGTCATCAATGCCTGAGTAATCAAAATTA,30,#f7931e
7[264],9[263],GAGAATCGAAAATTTTTAGAACCCAGCTAAAT,32,#03b6a2
8[87],6[88],AATCAATAAATACCAAGTTACAAAACCTAC,30,#f74308
8[119],6[120],GAATTACCATTATTCATTTCAATTTGGATTAT,32,#f7931e
8[151],6[152],ACAAAATTGATGATGAAACAAACAATGGCAAT,32,#333333
8[183],6[184],CAGTCAAATGATAAATTAATGCCTGTTAAA,30,#b8056c
8[215],6[216],AAAGATTCTTTGAGAGATCTACAATTAATATT,32,#333333
8[247],6[248],TTTAAATGTGCCTGAGAGTCTGGAATTGTATA,32,#cc0000
8[279],6[280],CAAGGATAATGAACGGTAATCGTTGATAAT,30,#333333
9[72],11[71],TATCAAAAGGTTTGAAATACCGACACCAGTAT,32,#f74308
9[104],11[103],TTTAACCTAGTTAATTTCATCTTCCTTAATTG,32,#cc0000
9[136],11[135],TATATGTGAACGCGAGAAAACTAACATGTA,30,#f74308
9[168],11[167],CTAATAGTGCTGAAAAGGTGGCATACTCCAAC,32,#aaaa00
9[200],11[199],CATACAGGCTGTTTAGCTATATTTTAATTGCT,32,#333333
9[232],11[231],AGCAATACATTAGATACATTTCCGGATGGC,30,#cc0000
9[264],11[263],CGGTTGTACCAATTCTGCGAACGAATGCTGTA,32,#007200
10[87],8[88],AATTTAATTCATAGGTCTGAGAGGTACATA,30,#f7931e
10[119],8[120],TATATTTTCCGGCTTAGGTTGGGTTTTCATTT,32,#03b6a2
10[151],8[152],AAGACAAAAAATGCTGATGCAAATTCAAGAAA,32,#aaaa00
10[183],8[184],GGGCGCGAAGTAGCATTAACATCCCGGAGA,30,#03b6a2
10[215],8[216],TCAATAACCAAGGCAAAGAATTAGGTGTAGGT,32,#7300de
10[247],8[248],AGTTTGACAAGCCTCAGAGCATAATCATATAT,32,#1700de
10[279],8[280],GTTGATTCCCAAAAACATTATGATTCAACG,30,#aaaa00
11[72],13[71],AAAGCCAAGCTAATGCAGAACGCGTTCCTTAT,32,#333333
11[104],13[103],AGAATCGCGTCCAGACGACGACAACAAGTACC,32,#007200
11[136],13[135],ATTTAGGATAAAGTACCGACAAGTTTTTAT,30,#03b6a2
11[168],13[167],AGGTCAGGACCAGACCGGAAGCAAAGGCTTTT,32,#007200
11[200],13[199],CCTTTTGAATATCGCGTTTTAATTGGTAATAG,32,#f7931e
11[232],13[231],TTAGAGCAAAGATTAAGAGGAACCAATACT,30,#333333
11[264],13[263],GCTCAACAATTATAGTCAGAAGCATGAATCCC,32,#1700de
12[87],10[88],CATGTTCACGCTCAACAGTAGGGTGACCTA,30,#cc0000
12[119],10[120],GTAATTCTCATATTTAACAACGCCTTTTCAAA,32,#333333
12[151],10[152],AAGAGAATCAGAGGCATTTTCGAGCCAATCGC,32,#57bb00
12[182],10[184],AAAGCGAATTAGAGAGTACCTTTCATTTG,29,#b8056c
12[215],10[216],GACTTCAATAAGAGGTCATTTTTGGCAAATGG,32,#b8056c
12[247],10[248],TGCATCAATTAATTGCTGAATATAGTAGATTT,32,#f7931e
12[279],10[280],CCCTGACTTGTTTTAAATATGCATATAACA,30,#f74308
13[72],15[71],CATTCCAAACTTGCGGGAGGTTTTTTTGCCAG,32,#cc0000
13[104],15[103],GCACTCATAAGAACGCGAGGCGTTTTTATCCC,32,#aaaa00
13[136],15[135],TTTCATCAATCAGATATAGAAGGTTTAACG,30,#f7931e
13[168],15[167],GCAAAAGAAAACCAAAATAGCGAGTGAGATGG,32,#03b6a2
13[200],15[199],TAAAATGTATCATAACCCTCGTTTTGAATTAC,32,#7300de
13[232],15[231],GCGGAATAGGAATTACGAGGCACATTATAC,30,#f7931e
13[264],15[263],CCTCAAATACATTCAACTAATGCAATCTACGT,32,#57bb00
14[87],12[88],ACCTCCCGGAACGGGTATTAAACTAAACAA,30,#f74308
14[119],12[120],GGTATTCTCGAGAACAAGCAAGCCAAGGTAAA,32,#f74308
14[151],12[152],AGCAAGCAGTAGGAATCATTACCGCCAGTAAT,32,#aaaa00
14[183],12[183],GACGATAAAGTTTTGCCAGAGGGCGAGCTTC,31,#1700de
14[215],12[216],GCAACACTTTAGACTGGATAGCGTGCCCGAAA,32,#f74308
14[247],12[248],ACGCCAAACGTCATAAATATTCATAAGCGGAT,32,#aaaa00
14[279],12[280],GGAATACCGCTTTAAACAGTTCAGTCTTTA,30,#7300de
15[72],17[71],TTACAAAATAATTGAGCGCTAATAGAAAAGTA,32,#7300de
15[104],17[103],AATCCAAATTAACTGAACACCCTGCAGAAGGA,32,#007200
15[136],17[135],TCAAAAATAAAAACAGGGAAGCGAATACCC,30,#b8056c
15[168],17[167],TTTAATTTAGTAGTAAATTGGGCTGTATCATC,32,#333333
15[200],17[199],CTTATGCGAAGGCTTGCCCTGACGCGCGACCT,32,#03b6a2
15[232],17[231],CAGTCAGTCAACGTAACAAAGCAGGCGCAG,30,#333333
15[264],17[263],TAATAAAATCTTGACAAGAACCGGACTGACCA,32,#1700de
16[87],14[88],TCAGAGGGTAAACAGCCATATTATTAGCGA,30,#f7931e
16[119],14[120],CGGGAGAATAAGAAACGATTTTTTGCTTATCC,32,#007200
16[151],14[152],GAATAACATGAAAATAGCAGCCTTCGCCCAAT,32,#cc0000
16[183],14[184],CCAGAACGCAACTTTAATCATTGACCAGAC,30,#03b6a2
16[215],14[216],CAGTGAATATTTTAAGAACTGGCTTAGTAAGA,32,#f74308
16[247],14[248],TACCCAAAGACGTTGGGAAGAAAAGATACATA,32,#aaaa00
16[279],14[280],AAGAGTAACGAACTAACGGAACAAGATTTA,30,#333333
17[72],19[71],AGCAGATACCACGGAATAAGTTTAACGGAAAT,32,#b8056c
17[104],19[103],AACCGAGGGGTGGCAACATATAAACCGTCACC,32,#f74308
17[136],19[135],AAAAGAATGTTAGCAAACGTAGGCCAGCAA,30,#aaaa00
17[168],19[167],GCCTGATAAGTACAACGGAGATTTGATATATT,32,#1700de
17[200],19[199],GCTCCATGACCCCCAGCGATTATATTAAAGGC,32,#007200
17[232],19[231],ACGGTCAGCAAAAGAATACACTAGCAGCGA,30,#f7931e
17[264],19[263],ACTTTGAACACTACGAAGGCACCAGCAACGGC,32,#cc0000
18[87],16[88],CAAAGACAGCCGAACAAAGTTACAACAAAG,30,#f7931e
18[119],16[120],TACATAAAAAACGCAATAATAACGGCATTAGA,32,#f74308
18[151],16[152],ACGCAGTACTGGCATGATTAAGACTACAGAGA,32,#007200
18[183],16[184],CGAAACAAAATTGTGTCGAAATCAGAAACA,30,#aaaa00
18[215],16[216],CATCTTTGTTACTTAGCCGGAACGTGCTCATT,32,#cc0000
18[247],16[248],CGAAAGAGATCATAAGGGAACCGAATATTCAT,32,#cc0000
18[279],16[280],CGTAATGCAGAGGACAGATGAACCTTCATC,30,#aaaa00
19[72],21[71],TATTCATTTTAGCGTCAGACTGTAACCGCCTC,32,#f74308
19[104],21[103],GACTTGAGGTAATCAGTAGCGACACCGCCACC,32,#7300de
19[136],21[135],AATCACCCGTCACCAATGAAACGCCACCAG,30,#7300de
19[168],21[167],CGGTCGCTTCGCCCACGCATAACCCGATCTAA,32,#57bb00
19[200],21[199],CGCTTTTGCCGATAGTTGCGCCGATAGTAAAT,32,#7300de
19[232],21[231],AAGACAGTTTCGAGGTGAATTTAAACAACT,30,#f74308
19[264],21[263],TACAGAGGGAGCCTTTAATTGTATAATAGAAA,32,#cc0000
20[87],18[88],GTTTGCCTAAAGGTGAATTATCAAGAAACG,30,#1700de
20[119],18[120],GCAGCACCCCATTTGGGAATTAGAAAAATACA,32,#aaaa00
20[151],18[152],GCCGGAAAAGTAGCACCATTACCATCCTTATT,32,#cc0000
20[183],18[184],AACAACCAGAGGCTTGCAGGGAGCCAAGCG,30,#333333
20[215],18[216],GCTTGATACGGGATCGTCACCCTCAAAACACT,32,#1700de
20[247],18[248],CAGCTTGCCATCGGAACGAGGGTAACCTAAAA,32,#aaaa00
20[279],18[280],TCCAAAAGCTTTGAGGACTAAAGTAAAATA,30,#b8056c
21[72],23[71],CCTCAGAGTGGAAAGCGCAGTCTCAGTGCCCG,32,#007200
21[104],23[103],CTCAGAGCACAAACAAATAAATCCCTATTTCG,32,#007200
21[136],23[135],AACCACCGAGGCAGGTCAGACGAGTATTAA,30,#1700de
21[168],23[167],AGTTTTGTCTCATAGTTAGCGTAAGGATTAGG,32,#f74308
21[200],23[199],GAATTTTCCTACAACGCCTGTAGCCAGGCGGA,32,#7300de
21[232],23[231],TTCAACACCGTAACACTGAGTTTAAGTATA,30,#b8056c
21[264],23[263],GGAACAACCAGGGATAGCAAGCCCACTCAGGA,32,#03b6a2
22[87],20[88],AGCCAGAACCGCCACCCTCAGAAGAATCAA,30,#cc0000
22[119],20[120],TGATATTCCACCACCCTCAGAGCCCATCGATA,32,#f74308
22[151],20[152],AGGAGGTTACCAGAGCCGCCGCCATTAGCAAG,32,#b8056c
22[183],20[184],AGACAGCCCGTCTTTCCAGACGTCAATGAC,30,#333333
22[215],20[216],AGTACAAATGTATGGGATTTTGCTCTTAAACA,32,#57bb00
22[247],20[248],CCCATGTAGTTTCAGCGGAGTGAGCGGTTTAT,32,#57bb00
22[279],20[280],CTCATTTTTAAAGGAATTGCGAAAAAAGGC,30,#333333
23[72],22[88],TATAAACAGTTAATGCCCCCTGCTCATTAA,30,#f74308
23[104],22[120],GAACCTATTATTCTGAAACATGAAATTGGCCT,32,#f74308
23[136],22[152],GAGGCTGAGACTCCTCAAGAGAAGCATTGAC,31,#03b6a2
23[168],22[184],ATTAGCGGGGTTTTGCTCAGTACATTCCAC,30,#7300de
23[200],22[216],TAAGTGCCGTCGAGAGGGTTGATATCGTCACC,32,#57bb00
23[232],22[248],GCCCGGAATAGGTGTATCACCGTAATAGGAA,31,#f7931e
23[264],22[280],GGTTTAGTACCGCCACCCTCAGACACCACC,30,#333333Download as a .csv file.
This part of the assignment is slightly independent from the caDNAno one. I hope you have good imagination now. Imagine you have two 96 well plate and you turn them 90ยบ and put them side by side. They will look like this:
In this assignment you have to generate a text file using your favorite text editor representing these two 96 well plates and draw some kind of pattern on it. The ASCII text file below represents a blank 12x16 pixels image (because of decalage looking like pseudo 24x16):
000: ... ... ... ... ... ... ... ... 12
001: ... ... ... ... ... ... ... ... 12
002: ... ... ... ... ... ... ... ... 11
003: ... ... ... ... ... ... ... ... 11
004: ... ... ... ... ... ... ... ... 10
005: ... ... ... ... ... ... ... ... 10
006: ... ... ... ... ... ... ... ... 9
007: ... ... ... ... ... ... ... ... 9
008: ... ... ... ... ... ... ... ... 8
009: ... ... ... ... ... ... ... ... 8
010: ... ... ... ... ... ... ... ... 7
011: ... ... ... ... ... ... ... ... 7
012: ... ... ... ... ... ... ... ... 6
013: ... ... ... ... ... ... ... ... 6
014: ... ... ... ... ... ... ... ... 5
015: ... ... ... ... ... ... ... ... 5
016: ... ... ... ... ... ... ... ... 4
017: ... ... ... ... ... ... ... ... 4
018: ... ... ... ... ... ... ... ... 3
019: ... ... ... ... ... ... ... ... 3
020: ... ... ... ... ... ... ... ... 2
021: ... ... ... ... ... ... ... ... 2
022: ... ... ... ... ... ... ... ... 1
023: ... ... ... ... ... ... ... ... 1
A B C D E F G H A B C D E F G H
<--- 96 well plate ----><--- 96 well plate ---->Where ... represents where a pixel is located. If you leave the ... it will mean that there is no feature (a zero value pixel) and if you replace it with @@@ or XXX or any other symbol it will mean that there is a feature there (a 1 pixel value). So with a litte bit of patience, using mtPaint (sort of GNU version of Microsoft Paint) I created a 16x12 pixels Pacman Ghost, I'm a 80's guy.
From this I transferred it to the 96 well plates.
And finally from the plates to the ASCII art. You know, when I was a teenager I used to spend a lot of time doing things like this when I was bored. I would never had imagined that ASCII art would be useful for building DNA nanostructures.
000: ... ... ... ... ... ... ... ... 12
001: ... ... ... ... ... ... ... ... 12
002: ... ... ... @@@ @@@ @@@ ... ... 11
003: ... ... @@@ @@@ @@@ ... ... ... 11
004: ... ... @@@ @@@ @@@ @@@ @@@ ... 10
005: ... @@@ @@@ @@@ @@@ @@@ ... ... 10
006: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 9
007: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 9
008: ... @@@ ... ... @@@ ... @@@ ... 8
009: ... @@@ ... @@@ ... ... @@@ ... 8
010: ... @@@ @@@ ... @@@ ... @@@ ... 7
011: ... @@@ ... @@@ @@@ ... @@@ ... 7
012: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 6
013: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 6
014: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 5
015: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 5
016: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 4
017: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 4
018: ... @@@ ... @@@ ... @@@ ... ... 3
019: ... @@@ @@@ @@@ @@@ @@@ @@@ ... 3
020: ... @@@ ... @@@ ... @@@ ... ... 2
021: ... ... ... ... ... ... @@@ ... 2
022: ... ... ... ... ... ... ... ... 1
023: ... ... ... ... ... ... ... ... 1
A B C D E F G H A B C D E F G H
<--- 96 well plate ----><--- 96 well plate ---->The next step is to convert the Pacman pattern obtained before into a list of pipetting instructions. If you were actually to create this pattern with DNA you would order all the staple strands, in such a way that the empty strands fit in 2 plates and the dumbbell strands fit in another 2 plates. Below these are the pipetting addresses for well plates 0 and 1 (also called the empty wells), for the pixels with value 0. In the Pacman ghost pattern we will replace the zero values represented as ... with these pipetting addresses.
000: 0AC 0CC 0EC 0GC 1AC 1CC 1EC 1GC C
001: 0BC 0DC 0FC 0HC 1BC 1DC 1FC 1HC C
002: 0AB 0CB 0EB 0GB 1AB 1CB 1EB 1GB B
003: 0BB 0DB 0FB 0HB 1BB 1DB 1FB 1HB B
004: 0AA 0CA 0EA 0GA 1AA 1CA 1EA 1GA A
005: 0BA 0DA 0FA 0HA 1BA 1DA 1FA 1HA A
006: 0A9 0C9 0E9 0G9 1A9 1C9 1E9 1G9 9
007: 0B9 0D9 0F9 0H9 1B9 1D9 1F9 1H9 9
008: 0A8 0C8 0E8 0G8 1A8 1C8 1E8 1G8 8
009: 0B8 0D8 0F8 0H8 1B8 1D8 1F8 1H8 8
010: 0A7 0C7 0E7 0G7 1A7 1C7 1E7 1G7 7
011: 0B7 0D7 0F7 0H7 1B7 1D7 1F7 1H7 7
012: 0A6 0C6 0E6 0G6 1A6 1C6 1E6 1G6 6
013: 0B6 0D6 0F6 0H6 1B6 1D6 1F6 1H6 6
014: 0A5 0C5 0E5 0G5 1A5 1C5 1E5 1G5 5
015: 0B5 0D5 0F5 0H5 1B5 1D5 1F5 1H5 5
016: 0A4 0C4 0E4 0G4 1A4 1C4 1E4 1G4 4
017: 0B4 0D4 0F4 0H4 1B4 1D4 1F4 1H4 4
018: 0A3 0C3 0E3 0G3 1A3 1C3 1E3 1G3 3
019: 0B3 0D3 0F3 0H3 1B3 1D3 1F3 1H3 3
020: 0A2 0C2 0E2 0G2 1A2 1C2 1E2 1G2 2
021: 0B2 0D2 0F2 0H2 1B2 1D2 1F2 1H2 2
022: 0A1 0C1 0E1 0G1 1A1 1C1 1E1 1G1 1
023: 0B1 0D1 0F1 0H1 1B1 1D1 1F1 1H1 1
A B C D E F G H A B C D E F G H
<------- Plate 0 ------><------- Plate 1 ------>The pipetting addresses are coded in the following way: The first character is the plate number (0 or 1 in this case). The second character is the row number of the 96 well-plate (from A to H). The third character represents the column number from 1 to 12 in hexadecimal code (1,2,3,4,5,6,7,8,9,A,B,C).
Now these are the pipetting addresses of pixels with value 1 (plates 2 and 3), represented as @@@ in the Pacman ghost pattern. We will replace values represented as @@@ in the pattern with these addresses.
000: 2AC 2CC 2EC 2GC 3AC 3CC 3EC 3GC C
001: 2BC 2DC 2FC 2HC 3BC 3DC 3FC 3HC C
002: 2AB 2CB 2EB 2GB 3AB 3CB 3EB 3GB B
003: 2BB 2DB 2FB 2HB 3BB 3DB 3FB 3HB B
004: 2AA 2CA 2EA 2GA 3AA 3CA 3EA 3GA A
005: 2BA 2DA 2FA 2HA 3BA 3DA 3FA 3HA A
006: 2A9 2C9 2E9 2G9 3A9 3C9 3E9 3G9 9
007: 2B9 2D9 2F9 2H9 3B9 3D9 3F9 3H9 9
008: 2A8 2C8 2E8 2G8 3A8 3C8 3E8 3G8 8
009: 2B8 2D8 2F8 2H8 3B8 3D8 3F8 3H8 8
010: 2A7 2C7 2E7 2G7 3A7 3C7 3E7 3G7 7
011: 2B7 2D7 2F7 2H7 3B7 3D7 3F7 3H7 7
012: 2A6 2C6 2E6 2G6 3A6 3C6 3E6 3G6 6
013: 2B6 2D6 2F6 2H6 3B6 3D6 3F6 3H6 6
014: 2A5 2C5 2E5 2G5 3A5 3C5 3E5 3G5 5
015: 2B5 2D5 2F5 2H5 3B5 3D5 3F5 3H5 5
016: 2A3 2C3 2E3 2G3 3A3 3C3 3E3 3G3 4
017: 2B3 2D3 2F3 2H3 3B3 3D3 3F3 3H3 4
018: 2A3 2C3 2E3 2G3 3A3 3C3 3E3 3G3 3
019: 2B3 2D3 2F3 2H3 3B3 3D3 3F3 3H3 3
020: 2A2 2C2 2E2 2G2 3A2 3C2 3E2 3G2 2
021: 2B2 2D2 2F2 2H2 3B2 3D2 3F2 3H2 2
022: 2A1 2C1 2E1 2G1 3A1 3C1 3E1 3G1 1
023: 2B1 2D1 2F1 2H1 3B1 3D1 3F1 3H1 1
A B C D E F G H A B C D E F G H
<------- Plate 2 ------><------- Plate 3 ------>There is an isomorphism between the position on the drawing and the position on the plate. You could prepare pipette tip boxes and anywhere you want to get a strand you put a tip there and anywhere you don't want to get the strand you don't put a tip there. And then the pipette tip box actually makes the pattern that you want to draw.
The most interesting feature about DNA nanostructures is that we can create any 2D or 3D shape at the nanometre scale. We still don't know the applications of these structures. But we should keep creating and improving design tools and machines that automate the process of generating these shapes, so that when we find the correct shapes for the correct applications we can quickly create them.
On wednesdays we always have a review session of last week's assignment. Here is the link to this week assignments review.