LabName:Supplementary: Difference between revisions
HaeJoo Kim (talk | contribs) |
HaeJoo Kim (talk | contribs) (→Staple) |
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==Cadnano designs== | ==Cadnano designs== | ||
<gallery widths="450px" heights="300px"> | <gallery widths="450px" heights="300px"> | ||
Image:Brick design.PNG|▲ Cadnano design for | Image:Brick design.PNG|▲ Cadnano design for Brick | ||
Image:connector_design.png|▲ Cadnano design for | Image:connector_design.png|▲ Cadnano design for Connector | ||
</gallery> | </gallery> | ||
<BR> | <BR> | ||
Line 125: | Line 125: | ||
===Staple=== | ===Staple=== | ||
{| class=" | {| class="wikitable" | ||
|- | |- | ||
!colspan="3"|Staple of 4539NT | !colspan="3"|Staple of 4539NT | ||
Line 567: | Line 567: | ||
|- | |- | ||
| 26[127]||25[127]||AACGAGTAGATTTAGTATATAATGCTGTAGCT | | 26[127]||25[127]||AACGAGTAGATTTAGTATATAATGCTGTAGCT | ||
|} | |} | ||
<BR> | <BR> | ||
='''Trials and errors'''= | ='''Trials and errors'''= | ||
== | ==Initial design== | ||
[[Image:early_DNA_silks.png]]<BR> | [[Image:early_DNA_silks.png]]<BR> | ||
▲Initial design of DNA silk<BR> | ▲Initial design of DNA silk<BR> | ||
<BR> | <BR> | ||
-Prepare ssDNA backbone | - Prepare ssDNA backbone via RCR. In it, red parts correspond to amorphous segments of spider silk and blue parts correspond to crystalline segments of spider silk.<br> | ||
- | - To turn DNA strands(blue parts) into a plate where DNA block would be attached, DNA oligos are added. Blue parts unconnected with oligos would form base pair with DNA origami block.<br> | ||
- | - Once DNA origami blocks are added, block-backbone structure is formed.<br> | ||
<br> | <br> | ||
Line 584: | Line 583: | ||
'''Idea 1'''<br> | '''Idea 1'''<br> | ||
[[Image:early1.jpg]]<br> | [[Image:early1.jpg]]<br> | ||
-Connect Plates in each strands after reducing flexibility of DNA silk by attaching ssDNA oligomers<br> | - Connect Plates in each strands after reducing flexibility of DNA silk by attaching ssDNA oligomers<br> | ||
-Then detach ssDNA oligomers using ssDNA oligomers with fully complementary sequence<br> | - Then detach ssDNA oligomers using ssDNA oligomers with fully complementary sequence<br> | ||
<br> | <br> | ||
'''Idea 2'''<br> | '''Idea 2'''<br> | ||
Line 591: | Line 590: | ||
A segment : not attached to DNA origami plate, B segment : attached to DNA origami plate<br> | A segment : not attached to DNA origami plate, B segment : attached to DNA origami plate<br> | ||
<br> | <br> | ||
-Oligomer has 1A'-2A'-3A' sequence in the ordered. In picture, ssDNA 1 from plasmid 1 has 1A-1B-1A-1B and ssDNA 2 from plasmid 2 has 2A-2B-2A-2B....<br> | - Oligomer has 1A'-2A'-3A' sequence in the ordered. In picture, ssDNA 1 from plasmid 1 has 1A-1B-1A-1B and ssDNA 2 from plasmid 2 has 2A-2B-2A-2B....<br> | ||
-By oligomers, each strand connects with | - By oligomers, each strand connects with one another<BR> | ||
<br> | <br> | ||
'''Idea 3'''<br> | '''Idea 3'''<br> | ||
-Make it fabric instead of thread | - Make it as fabric instead of thread. Electrospinning could be used for this process.<br> | ||
<br> | <br> | ||
''' | '''Others'''<br> | ||
[[Image:early4.png]] | |||
[[Image:early5.png|350px]]<br> | [[Image:early5.png|350px]]<br> | ||
<br> | <br> | ||
Line 607: | Line 604: | ||
===Structure of brick=== | ===Structure of brick=== | ||
1. All sides of trigonal prism are made from one scaffold.(composed of 1 strands.)<BR> | |||
1. All | |||
[[Image:Silk_1개_assembly_전.png|500px]] → [[Image:Silk_1개.png|90px]]<BR> | [[Image:Silk_1개_assembly_전.png|500px]] → [[Image:Silk_1개.png|90px]]<BR> | ||
2. 3 | 2. 3 sides made from other 3 scaffold with 1/3 scale.(composed of 3 strands.)<BR> | ||
[[Image:Silk_3개_assembly_전.png|500px]] → [[Image:Silk_3개.png|90px]]<BR> | [[Image:Silk_3개_assembly_전.png|500px]] → [[Image:Silk_3개.png|90px]]<BR> | ||
<BR> | <BR> | ||
'''Idea 1-Rectangular plate(1)''' | '''Idea 1-Rectangular plate(1)'''<BR> | ||
[[Image:hjy141007_1.png|200px]][[Image:hjy141007_2.png|300px]] | |||
<gallery widths="300px" heights="200px"> | |||
[[Image:hjy141007_1.png| | |||
<gallery widths="300px" heights=" | |||
Image:hjy141007_3.png | Image:hjy141007_3.png | ||
</gallery> | </gallery> | ||
6bp * 42 bp * 2layer = 504bp<BR> | 6bp * 42 bp * 2layer = 504bp<BR> | ||
<BR | <BR> | ||
'''Idea 2-Rectangular plate(2)'''<BR> | |||
[[Image:141006yhj_3.png|170px]][[Image:141006yhj_2.png|250px]] | [[Image:141006yhj_3.png|170px]][[Image:141006yhj_2.png|250px]] | ||
<gallery widths="300px" heights=" | <gallery widths="300px" heights="200px"> | ||
Image:141006yhj_1.png | Image:141006yhj_1.png | ||
</gallery> | </gallery> | ||
12bp * 42 bp * 2layer = 1008bp<BR> | 12bp * 42 bp * 2layer = 1008bp<BR> | ||
<BR | <BR> | ||
'''Idea 3-Trigonal prism shaped brick(Honeycomb)'''<BR> | |||
[[Image:141007_DNA_plate(Honeycom)_helix_Hjkim.jpg]][[ | [[Image:141007_DNA_plate(Honeycom)_helix_Hjkim.jpg]][[Image:141007_DNA_plate(honeycom)_Hjkim.jpg]]<BR> | ||
<gallery widths="300px" heights=" | <gallery widths="300px" heights="200px"> | ||
Image:141007_DNA_plate(honeycom)_side1_Hjkim.jpg | Image:141007_DNA_plate(honeycom)_side1_Hjkim.jpg | ||
Image:141007_DNA_plate(honeycom)_front_Hjkim.jpg | Image:141007_DNA_plate(honeycom)_front_Hjkim.jpg | ||
Line 647: | Line 634: | ||
<BR> | <BR> | ||
'''Idea 4-Trigonal prism shaped brick(Square)''' | '''Idea 4-Trigonal prism shaped brick(Square)'''<BR> | ||
< | <gallery widths="300px" heights="200px"> | ||
<gallery widths="300px" heights=" | |||
Image:Rmsf_view1.png | Image:Rmsf_view1.png | ||
Image:Rmsf_view2.png | Image:Rmsf_view2.png | ||
Line 657: | Line 643: | ||
<BR> | <BR> | ||
'''Idea 5-Thick Trigonal prism shaped brick''' | '''Idea 5-Thick Trigonal prism shaped brick'''<BR> | ||
< | <gallery widths="300px" heights="200px"> | ||
<gallery widths="300px" heights=" | |||
Image:20141008KMGthick_tricolumn1.png | Image:20141008KMGthick_tricolumn1.png | ||
Image:20141008KMGthick_tricolumn2.png | Image:20141008KMGthick_tricolumn2.png | ||
Line 668: | Line 653: | ||
===Composition of BCC(Brick-Connector Complex) or Brick complex=== | ===Composition of BCC(Brick-Connector Complex) or Brick complex=== | ||
'''Brick(Red)''' : '''Connector(Blue)''' = '''3''' : '''1'''<BR> | |||
''' | |||
<gallery widths="300px" heights="250px"> | <gallery widths="300px" heights="250px"> | ||
Image:Front_structure_1'.png | Image:Front_structure_1'.png | ||
Line 675: | Line 659: | ||
</gallery> | </gallery> | ||
<BR> | <BR> | ||
''' | '''Brick(Red)''' : '''Connector(Blue)''' = '''3''' : '''3'''<BR> | ||
<gallery widths="300px" heights="250px"> | <gallery widths="300px" heights="250px"> | ||
Image:Front_structure_2.png | Image:Front_structure_2.png | ||
Image:3D_structure_2.png | Image:3D_structure_2.png | ||
</gallery> | </gallery> | ||
<BR | <BR> | ||
''' | '''Brick A(Red)''' : '''Brick B(Blue)''' = '''3''' : '''3'''<BR> | ||
<gallery widths="300px" heights="250px"> | <gallery widths="300px" heights="250px"> | ||
Image:Front_structure_3.png | Image:Front_structure_3.png | ||
Line 693: | Line 677: | ||
2. [[Image:141013-connect2.png|500px]]<BR> | 2. [[Image:141013-connect2.png|500px]]<BR> | ||
3. [[Image:141013-connect3.png|500px]]<BR> | 3. [[Image:141013-connect3.png|500px]]<BR> | ||
'''Red : Brick, Blue : Connector, Yellow : linking staple'''<BR> | ::::'''Red : Brick, Blue : Connector, Yellow : linking staple'''<BR> | ||
We marked where brick and connector are connected by staple(figures above). Scaffold was used to check stability through cando progrem.<br> | |||
<BR> | <BR> |
Latest revision as of 22:12, 25 October 2014
Details of Spider Silk
Cadnano designs
-
▲ Cadnano design for Brick
-
▲ Cadnano design for Connector
Sequence
scaffold
- Scaffold of 4539NT
GATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATT
GGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGT
GATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAG
GAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACT
GACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCT
GGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCT
GGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTT
GATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTC
GCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCC
CAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTT
GTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTT
ATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTT
TCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTG
GGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGC
TTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATG
GCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACT
AATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTG
CTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAAT
GATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAA
CAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGC
TCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAAT
TTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTC
AAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTT
ACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTT
AATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTA
TGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGT
AATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGT
TACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTC
CATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGG
TTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTC
TAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCT
TTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTC
TCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTT
AGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGT
TGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTC
CATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGT
TATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGA
TTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAA
AGCAACCATAGTACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCG
CTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTT
TACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCA
CGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAAC
CACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCC
CGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGT
TTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTA
TGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGG
- Scaffold of 5081NT
AATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCT
AATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACAT
GTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGAC
CTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATC
CGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCA
ATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGC
TATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTT
GAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGT
CCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTT
CTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTG
ATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCC
TCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATA
ATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAA
TGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCC
CGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTAT
CAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAA
AATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTA
CTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAA
CTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGG
GTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAA
ACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTG
TTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACG
GTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCA
ATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTT
CCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGT
CTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTG
CTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCC
TCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCT
TTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGG
TATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGC
TATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGG
TGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGT
TTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATA
AAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAA
TACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCG
GTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTC
TTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTG
TCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTG
TTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAA
CGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTT
GTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATA
AATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGC
AAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATG
TTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTT
ATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAAT
AATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAA
TATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTA
ATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAA
GATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGAT
GCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGT
TCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACG
CTTTCAGGTCAGAAGGGTTCTATCTCTGTTGG
Staple
Staple of 4539NT | ||
---|---|---|
Start | End | Sequence |
1[56] | 3[63] | CAGCAGGCCGAGGTGCGGGCGCTA |
1[90] | 3[95] | AAATCGTGAACCATCGCTGCGC |
1[115] | 3[127] | AAAAGAATAGCCCAAAACCGTAATGCGCC |
2[47] | 4[32] | ACTAAATCGGAACCCTCAAGCGGTAAGAGTCT |
2[79] | 4[64] | TCAAGTTTTTTGGGGTGAAAATCCGTGTTTTT |
2[111] | 4[96] | GCGATGGCCCACTACGGCAAAATCTAGACAGG |
2[143] | 4[128] | CAACGTCAAAGGGCGAGAGATAGGGGAGCTAA |
3[24] | 8[32] | GCGAGAAAGGAAGGGATAGTCTTTCTTGCCTGGACTTTAC |
3[64] | 8[64] | GGGCGCTGACGTGGCACTTGCTGGTAGATAAT |
3[96] | 8[96] | GTAACCACATAGAACCCAGCCATTAGCACTAA |
3[128] | 8[128] | GCTACAGGCAGTAATAATACCTACAATTGAGG |
3[144] | 0[144] | TATGGTTGCTTAACGTGGACTCTTGTTCCAGTTCGTTGCGCTCA |
4[31] | 7[31] | GTCCATCATAACATCAAATGCGCGGAACCACC |
4[63] | 7[63] | ATAATCAGCTATCGGCCAGACAATGCGGTCAG |
4[79] | 0[65] | CCTGAGAATGTTTGATGGTCGGGGAGAGGCGGTTTGC |
4[95] | 7[95] | AACGGTACATTACCGCCTTCTGACCACGCTGA |
4[111] | 0[97] | AGGGATTTCCTTATAAATCGTGCCAGCTGCATTAATG |
4[127] | 7[127] | ACAGGAGGTCATGGAAAAAGGGACAAAGCATC |
4[154] | 6[144] | CCTCGTTAGAAGCTCAATCGTCGATTCACCAGT |
5[16] | 8[16] | ATTAGTAAAACTGATATACCGAACCGACAACT |
5[48] | 2[48] | AACTCAAATGAGGCCAAAAGGAGCCGTAAAGC |
5[80] | 2[80] | AGAACAATGCCAGAATAGCGGTCACACCCAAA |
5[112] | 2[112] | AAAAACGCCCGATTAACCGCGCTTCTATCAGG |
6[47] | 0[33] | ATGGCTATAGAAAGCGCCGAGTAACCACGCTGGGTTTTTCTTTTCAC |
6[143] | 0[129] | CACACGACGCGCGTACTCAGAGCGGTTGAGTGCTGCCCGCTTTCCAG |
7[32] | 5[47] | AGCAGAAGATAAAACAAAGTATTAAGTAGAAG |
7[64] | 5[79] | TATTAACACCGCCTGCGCCGTCAATAATATCC |
7[96] | 5[111] | GAGCCAGCAGCAAATGTCTTTAGGGCAACAGG |
7[128] | 5[143] | ACCTTGCTGAACCTCATTGAAAGGATTTTGAC |
8[31] | 10[40] | AAACAATTTTTAAAAGTTTGAGTAACATTATCGAAACAAT |
8[63] | 10[72] | ACATTTGAGAACAAAGAAACCACCAGAAGGAGAATATACA |
8[87] | 3[79] | AGATTAGAAACAGTGCCTGAAAGCGTAAGAATGCAAGTGT |
8[95] | 10[104] | CAACTAATTCATCATATTCCTGATTATCAGATATTGCGTA |
8[119] | 3[111] | CTAAAATAAAAAATCTATTCTGGCCAACAGAGCACACCCG |
8[127] | 10[136] | AAGGTTATTTCATCAATATAATCCTGATTGTTAAATTATT |
9[16] | 11[23] | TTATTAATTGCTTTGAAGGCGAAT |
9[48] | 6[48] | ATTTTGCGGGATTTAGGAGGTGAGATTTTTGA |
9[144] | 7[154] | TGGATTATACTCAAATCAACAGAATATCAAACC |
10[39] | 15[39] | AACGGATTCAAGACAATTTTTAACAGACGACG |
10[71] | 15[71] | GTAACAGTTATATTTTATTTATCATGCAGAAC |
10[103] | 15[103] | GATTTTCAATTTAATGTAGATTAAAGTCCTGA |
10[135] | 15[143] | TGCACGTAAATAAGGCCCCTTAGAAATTTACGAGCATGTA |
11[40] | 14[40] | CTGAGCAAAGACTACCAGAACGCGTTAGGCAG |
11[72] | 14[72] | AGAAAACAAATAGTGAAGTTAATTAATCGCCA |
11[104] | 14[104] | ATTTGAATCGATAGCTGTTTGAAAAAGCCAAC |
11[136] | 14[136] | ATAAATCATTAATTTTGTTAAATATCATATGC |
12[55] | 10[48] | GGTCTGAGAAGAAGATCATCGGGA |
12[87] | 9[87] | GAAGAGTCAAATTAATGTCAGATGCGGAATTA |
12[119] | 9[119] | AAACATAGTACCTTTTATAAAGAAGATGGCAA |
13[24] | 11[39] | TCCAATCGCGCCTGATTATTCATTTCAATTAC |
13[56] | 11[71] | TTTTCAAAACCTTTTAGATGAAACAAACATCA |
13[88] | 11[103] | TGACCTAAGGTTTAACTACATTTAACAATTTC |
13[120] | 11[135] | GTGTGATAAAACAGAATTAATGGAAACAGTAC |
13[144] | 10[144] | AGAATAAACACGTCGCTATTAAATATATGTGAGCTACCATATCA |
14[39] | 16[32] | AGGCATTTAAGCCTTAGCTTATCC |
14[71] | 16[56] | TATTTAACACCCAGCTGCGCCCAATAGCAAGC |
14[103] | 16[88] | GCTCAACAACGCTAACCCGTTTTTATTTTCAT |
14[135] | 16[120] | GTTATACAGCCAGTTAACCAAGTACCGCACTC |
15[40] | 19[47] | ACAATAAATATAGAAGAATCAAGAAAGTCAGACAATGAAA |
15[72] | 17[79] | GCGCCTGTTCATTACCACAATTTT |
15[104] | 18[104] | ACAAGAAACAAGCAAGGAGCGTCTAGAGAGAA |
16[31] | 13[23] | GGTATTCTAAGAACGCTAAAGTAAGTAATAAGGATGCAAA |
16[55] | 13[55] | AAATCAGACAACATGTCATGTAATAGAAAACT |
16[87] | 13[87] | CGTAGGAATTATCAACTAATTGAGTCATCTTC |
16[119] | 13[119] | ATCGAGAAAATAATATCCAGTATATACCGACC |
16[143] | 19[143] | GGTATTAACAAAATAATTAACGTCTAATAACG |
17[24] | 12[16] | AGGTTTTGTCGAGCCATTCTGTCCCTCCGGCTTAGGTTGG |
17[56] | 12[56] | TATTTTGCAACGCCAATCAGCTAAAAATCATA |
17[88] | 12[88] | TCTTACCAGTAGGGCTAATAGATAGACGCTGA |
17[120] | 12[120] | CCTAATTTAATTCTTACCCATCCTATCCTTGA |
17[144] | 14[144] | ACAGCCATATTTTCCAAGAACGGAAACCAATCACCTGTTTAGTA |
18[79] | 21[79] | TAGACGGGCCTTTTTACACGGAATCACCGACT |
19[16] | 21[23] | AAGCCCAACCAAAGACAGGGAGGG |
19[32] | 17[23] | GCAAGAAAGGGTAATTGAGCGCTAATATCAGACTTGCGGG |
19[64] | 17[55] | ACCGAAGCAGAATTAACTGAACACCCTGAACATTAGTTGC |
19[96] | 17[87] | AGCCGAACTAACATAAAAACAGGGAAGCGCATATCCTGAA |
19[104] | 23[119] | AAAGTTACGGTGGCAAGCAAAATCACCAGTAGCTTTTGATCAGACGAT |
19[128] | 17[119] | AAACGCAAAAAAATGAAAATAGCAGCCTTTACTTCCAGAG |
20[47] | 23[55] | GAAAATTCGAAATTATTCATTAAAGCCCGTATTCAGAGCC |
20[63] | 22[48] | TTTGTCACAATCAATATAGCAATATTTTCATA |
20[87] | 24[72] | AAAGACACAGAAAAGTCGGTCATAGCCCCCTTCCAGAGCCGGGGTCAG |
20[127] | 22[112] | AAAATACATACATAAACAGAAGGAGTCAGACT |
20[143] | 22[144] | ATGTTAGCAAGGCCGGAAACGTCACCATAATCAGTAGC |
20[154] | 18[144] | TATTACGCAGTGAATACCCAAACGATTTTTTGT |
21[32] | 20[24] | TATTGACGATATGGTTTACCAGCG |
21[80] | 23[87] | TGAGCCATGTTTTAACGCCGCCAG |
22[23] | 25[23] | ACCACCGGCCTCAGAATTCGGAACTTAAGAGG |
22[47] | 25[47] | ATCAAAATCACCACCCAAACAGTTGAAGGATT |
22[111] | 24[104] | GTAGCGCGAGGCAGGTGATACAGG |
22[143] | 24[136] | GACAGAATAAACAAATCGTTCCAG |
23[24] | 22[32] | CCGCCACCCTCAGAGCCACCGGAA |
23[56] | 20[64] | GCCACCAGAACCACCAATTAGCGTATCACCGTAAGTTTAT |
23[88] | 20[88] | CATTGACAGGAGGTTGTTTTCATCTAGAGCCACATATAAAAGAAACGC |
23[120] | 20[128] | TGGCCTTGATATTCACCAAGTTTGCCATTAGCAAACGTAG |
23[144] | 26[144] | AAATCCTCATTTCTGAATTTACAGGTTTAGTACCAGAACCGCCA |
25[24] | 26[16] | CTGAGACTGACAGCCCTCATAGTT |
25[32] | 19[31] | CCTCAAGAAATGCCCCCTGCCTATAAGGTAAACCAGAGCCTAATAAGA |
25[64] | 19[63] | TGCTCAGTTGCCTTGAGTAACAGTGGTGAATTTTGCCATCGCTATCTT |
25[72] | 1[55] | ACCAGGCGACTGAGTTTCGTCACCGTATTGGGCGCCAGGGTGTTTGCCC |
25[96] | 19[95] | AGGGTTGAAGTGTACTGGTAATAATTGGGAATGGCATTTTAAGCAGAT |
25[104] | 1[89] | TATAAGTAAGCAAGCCCAATAGGAAATCGGCCAACGCGGGTTCCG |
25[128] | 19[127] | TATCACCGTAAGCGTCATACATGGCACCATTACCTTTAGCAACCGAGG |
25[136] | 0[115] | TACTCAGGCCCTCAGAGCCACCACTCGGGAAACCTGTC |
26[47] | 1[23] | CCTGTAGCATTCCACACAGTGAGACGGGCAACACCTGAGAG |
26[63] | 25[63] | AGTACAAACTACAACGAGGATTAGCGGGGTTT |
26[95] | 25[95] | ACCCATGTACCGTAACGATAAGTGCCGTCGAG |
26[127] | 25[127] | CCTCATTTTCAGGGATTAGCCCGGAATAGGTG |
Staple of 5081NT | ||
---|---|---|
Start | End | Sequence |
1[24] | 4[16] | TTGAATTATTCAAATATATTTTAGTTAATGGTCAGAACGC |
1[56] | 3[63] | AAATCAATCAATCGCATAAATAAG |
1[90] | 3[95] | GTAAATTATATAACTAGAAAAA |
1[115] | 3[127] | TCCCTTAGAATCCACTACCTTTACAAATT |
2[47] | 4[32] | AACGCGAGAAAACTTTCCTTTTTTACATGTTC |
2[79] | 4[64] | AATGCTGATGCAAATCATATGTGAAAGTAATT |
2[111] | 4[96] | CCGGCTTAGGTTGGGTCGTCGCTAAATAAGAG |
2[143] | 4[128] | ATCATAGGTCTGAGAGTTGAAAACTGTAATTT |
3[24] | 8[32] | TTGAAATACCGACCGTAGTTGCTATAATATCCGCAATAGC |
3[64] | 8[64] | AATAAACATGCGGGAGAACCAATCGCCCAATA |
3[96] | 8[96] | GCCTGTTTGAACGCGAATTCCAAGATCAGAGA |
3[128] | 8[128] | CTTACCAGATCAGATAACTCATCGTGAACAAA |
3[144] | 0[144] | CAACGCTCAACAATTTATCAAAAGCTTAGATTAAGTAACAGTAC |
4[31] | 7[31] | AGCTAATGAAGAAAAATTTTGCACGCGTCTTT |
4[63] | 7[63] | CTGTCCAGCATGTAGAGTTTTGAAAAATAAAC |
4[79] | 0[65] | AAAAGGTAGTGAATAACCTATCGCGCAGAGGCGAATT |
4[95] | 7[95] | AATATAAATCCTTATCGGCGTTTTAATAAGAA |
4[111] | 0[97] | GAGCCAGTTTAATTAATTTTCGCCTGATTGCTTTGAA |
4[127] | 7[127] | AGGCAGAGAGTACCGCTAGAAGGCATGAAAAT |
4[154] | 6[144] | ATATTTAACAACAAGCCGTTTTCGCGCCCAATA |
5[16] | 8[16] | TCCTGAACCCAGCTACGCTAACGACGAAGCCC |
5[48] | 2[48] | TTTACGAGACGACGACTAAGGCGTAGACAAAG |
5[80] | 2[80] | GCTGTCTTGTACCGACATAATTACTATATGTA |
5[112] | 2[112] | TTAAACCAGCATTTTCATGCGTTATTTAACCT |
6[47] | 0[33] | TCAAGATTGTGATAAAAATAAACAAATGGAAAGAGCAAAAGAAGATG |
6[143] | 0[129] | GCAAGCAATATAAAGCCGCCAACAATAGCGATCTTTTACATCGGGAG |
7[32] | 5[47] | CCAGAGCCTAATTTGCATGAAATACATCCTAA |
7[64] | 5[79] | AGCCATATTATTTATCTGAGTTAAAATAATCG |
7[96] | 5[111] | ACGATTTTTTGTTTAAGCGCTAATAACGGGTA |
7[128] | 5[143] | AGCAGCCTTTACAGAGGAACACCCAGAACAAG |
8[31] | 10[40] | TATCTTACAGTTACCAGAAGGAAACCGAGGAAAATTATTC |
8[63] | 10[72] | ATAAGAGCATAACGGAATACCCAAAAGAACTGCGATTGAG |
8[87] | 3[79] | ACAAGAATCCAATCCAAGCGAACCTCCCGACTCCGGAATC |
8[95] | 10[104] | GATAACCCAAGACTCCTTATTACGCAGTATGTCCAGCGCC |
8[119] | 3[111] | GTAATTGACGTCAAAATTATCCGGTATTCTAAAGTATCAT |
8[127] | 10[136] | GTCAGAGGGTAGAAAATACATACATAAAGGTGTGTCACAA |
9[16] | 11[23] | CCGAACAACACCGTCAGAGCCAGC |
9[48] | 6[48] | ACGCAATAAAGAAACACAGTTACAGCCTTAAA |
9[144] | 7[154] | GCAACATATAAGAGAATTAACTAGAATAACATA |
10[39] | 15[39] | ATTAAAGGGACGATTGAGAGCCGCGCCCGGAA |
10[71] | 15[71] | GGAGGGAAATCCTCATTCAGAACCGTTTAGTA |
10[103] | 15[103] | AAAGACAACTCTGAATCACCGGAATCAGAACC |
10[135] | 15[143] | TCAATAGAATGGCTTTTTCATAATATTTTCAGGGATAGCA |
11[40] | 14[40] | CCATTACCCCACCCTCGCCTTGATAGGATTAG |
11[72] | 14[72] | AATGAAACCGCCACCCTAAAGCCAAAAGTATT |
11[104] | 14[104] | TAGCGACAAGAGCCACTTACCGTTGCCTATTT |
11[136] | 14[136] | GACTGTAGGCCATCTTTGATGATAAACAGTGC |
12[55] | 10[48] | CAGAGCCAATTAGCAATTGACGGA |
12[87] | 9[87] | CTCAGAGCCATCGATACATTCAACGCATGATT |
12[119] | 9[119] | CCGGAACCGAATCAAGATGGTTTATAGCAAAC |
13[24] | 11[39] | GCAGGTCATGAATTATAAAATCACCAGTAGCA |
13[56] | 11[71] | ACAAATAAGGTAAATAGGCCGGAAACGTCACC |
13[88] | 11[103] | AGCGCAGTAAGGGCGAGCAGCACCGTAATCAG |
13[120] | 11[135] | CGTCATACAAATTCATTTTGCCTTTAGCGTCA |
13[144] | 10[144] | CAGGAGTGTACTATTAGCGTTTCGCGTTTTCATTAAGTTTATTT |
14[39] | 16[32] | GATTAGCGGAATTGCGTGGGATTT |
14[71] | 16[56] | AAGAGGCTATCTCCAACTTTCCAGACGTTAGT |
14[103] | 16[88] | CGGAACCTTAATTGTAATAGTTAGCGTAACGA |
14[135] | 16[120] | CCGTATAAGTGAATTTACAACGCCTGTAGCAT |
15[40] | 19[47] | TAGGTGTATTTCTGTAAATAATAAGAGGGTAGAATGCCAC |
15[72] | 17[79] | CCGCCACCTTTGTCGTAAAAAAGG |
15[104] | 18[104] | GCCACCCTCAGCCCTCTCGGTTTAGCAGGGAG |
16[31] | 13[23] | TGCTAAACAACTTTCAGGTTGATACTCAGTACAGGTTGAG |
16[55] | 13[55] | AAATGAATTCACCGTATCAAGAGAATTCACAA |
16[87] | 13[87] | TCTAAAGTCTCAGAACGAAACATGGAATGGAA |
16[119] | 13[119] | TCCACAGACAGAGCCATGCCCCCTCCAGTAAG |
16[143] | 19[143] | TACAAACTCTTAAACACGCATAACCAAAGTAC |
17[24] | 12[16] | AACTAAAGGGGTTTTGTAAGTATACACCAGAACCACCACC |
17[56] | 12[56] | CGTTGAAAGAGACTCCCTCAGGAGGCCACCCT |
17[88] | 12[88] | GGAGCCTTATTATTCTCGCCACCCCCGCCTCC |
17[120] | 12[120] | CTTTCGAGACAGTTAACCACCCTCCAAAATCA |
17[144] | 14[144] | GCTTGATACCGTTCGTCACCAGAGCCCAATAGGGTGCCTTGAGT |
18[79] | 21[79] | TCACCCTCAAGAGGCACCAACTTTCCCTGACG |
19[16] | 21[23] | TTCCATTAACCTTCATGATATTCA |
19[32] | 17[23] | AAATACGTCAACGGCTACAGAGGCTTTGAGGAAAAGGAAC |
19[64] | 17[55] | TAAAACGAAGCAGCGAAAGACAGCATCGGAACTTTTTTCA |
19[96] | 17[87] | CACTCATCTTAAAGGCCGCTTTTGCGGGATCGCTCCAAAA |
19[104] | 23[119] | TTTGACCCGCAGACGGTTGGGCTTGAGATGGTCAAAAATCGTTTAGAC |
19[128] | 17[119] | GCGCGAAACGATATATTCGGTCGCTGAGGCTTTCAGCTTG |
20[47] | 23[55] | CAGACCAGAACAAAGCTGCTCATTAAGAGGAATAAAAACC |
20[63] | 22[48] | ACAGATGAACGGTGTATACGAAGGATACCACA |
20[87] | 24[72] | CGAACTGAAAAGAATAAGGTAGAAAGATTCATTTTGCAAAAAAGCGGA |
20[127] | 22[112] | TTAGCCGGAACGAGGCCCAGCGATAATAAAAC |
20[143] | 22[144] | ACCTGCTCTCATTGTGAATTACCTTATTACCAGTCAGG |
20[154] | 18[144] | CGAAATCCGCGAACGGAGATTTACCATCGCCCA |
21[32] | 20[24] | ATCAACGTGCGCATAGGCTGGCTG |
21[80] | 23[87] | AGAAACACTCAGAAGCAGAAGTTT |
22[23] | 25[23] | CCAAAAGGCACTATCATTTTAATTGAAGCAAA |
22[47] | 25[47] | TTCAACTAGACGACGAGCCCGAAATTAGAGAG |
22[111] | 24[104] | GAACTAACAGTAAAATAGGTCTTT |
22[143] | 24[136] | ACGTTGGGCTGCGGAACAGAAAAC |
23[24] | 22[32] | TAACCCTCGTTTACCAATGCAGAT |
23[56] | 20[64] | AAAATAGCGAGAGGCTCAGTTGAGAAGGCTTGGAAAGAGG |
23[88] | 20[88] | TGCCAGAGGGGGTAATGGAACAACGTAGTAAATCAATCATAAGGGAAC |
23[120] | 20[128] | TGGATAGCGTCCAATAAAGAAAAAAACTTTAACATGTTAC |
23[144] | 26[144] | TCGTCATAAATTTTAAACAGTTTGCAACTAAAGATATAACAGTT |
25[24] | 26[16] | CTCCAACACATCAATTCTACTAAT |
25[32] | 19[31] | GGTCAGGAGACTTCAAATATCGCGTTACCCAAACATAACGAACGGGTA |
25[64] | 19[63] | TTTTGATATTGCATCAAAAAGATTCAGTGAATATTTAGGACACCAACC |
25[72] | 1[55] | AGAGGTCATAACCTGTTTAGCTATATTCATTTCAATTACCTCAGTACAT |
25[96] | 19[95] | AGAGCTTAACCCTGACTATTATAGCAGAACGAATTATTACCACTAAAA |
25[104] | 1[89] | ATTGCTGATTGACCATTAGATACATACCAAGTTACAAATGCTTCT |
25[128] | 19[127] | CAACATGTGAGAATGACCATAAATTTAATTTCTCTACGTTTATACCAA |
25[136] | 0[115] | TTTAAATAGATTCCCAATTCTGCGAAACAATAACGGAT |
26[47] | 1[23] | CGAGCTGAAAAGGTGGATGAAACAAACATCAAGAATTTCAT |
26[63] | 25[63] | ATTTTCATTTGGGGCGTACCTTTAATTGCTCC |
26[95] | 25[95] | TTTCGCAAATGGTCAATTTTTGCGGATGGCTT |
26[127] | 25[127] | AACGAGTAGATTTAGTATATAATGCTGTAGCT |
Trials and errors
Initial design
▲Initial design of DNA silk
- Prepare ssDNA backbone via RCR. In it, red parts correspond to amorphous segments of spider silk and blue parts correspond to crystalline segments of spider silk.
- To turn DNA strands(blue parts) into a plate where DNA block would be attached, DNA oligos are added. Blue parts unconnected with oligos would form base pair with DNA origami block.
- Once DNA origami blocks are added, block-backbone structure is formed.
Idea to prevent gelation and bonding strands each other
Idea 1
- Connect Plates in each strands after reducing flexibility of DNA silk by attaching ssDNA oligomers
- Then detach ssDNA oligomers using ssDNA oligomers with fully complementary sequence
Idea 2
A segment : not attached to DNA origami plate, B segment : attached to DNA origami plate
- Oligomer has 1A'-2A'-3A' sequence in the ordered. In picture, ssDNA 1 from plasmid 1 has 1A-1B-1A-1B and ssDNA 2 from plasmid 2 has 2A-2B-2A-2B....
- By oligomers, each strand connects with one another
Idea 3
- Make it as fabric instead of thread. Electrospinning could be used for this process.
Others
Idea about crystalline segment
Structure of brick
1. All sides of trigonal prism are made from one scaffold.(composed of 1 strands.)
→
2. 3 sides made from other 3 scaffold with 1/3 scale.(composed of 3 strands.)
→
6bp * 42 bp * 2layer = 504bp
12bp * 42 bp * 2layer = 1008bp
Idea 3-Trigonal prism shaped brick(Honeycomb)
Idea 4-Trigonal prism shaped brick(Square)
About 880bp, height : 80bp
Idea 5-Thick Trigonal prism shaped brick
About 2080bp, height : 80bp
Composition of BCC(Brick-Connector Complex) or Brick complex
Brick(Red) : Connector(Blue) = 3 : 1
Brick(Red) : Connector(Blue) = 3 : 3
Brick A(Red) : Brick B(Blue) = 3 : 3
Connecting location on brick & connector
- Interlocking staple Picture of linking state Linking state by side view
- Red : Brick, Blue : Connector, Yellow : linking staple
- Red : Brick, Blue : Connector, Yellow : linking staple
We marked where brick and connector are connected by staple(figures above). Scaffold was used to check stability through cando progrem.