Biomod/2014/CACGTAATTGACGCCAGCTTTGAAT

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Materials

The chemicals were purchased from Sigma Aldrich, oligonucleotides from MWG Eurofins, yellow green fluorescent beads and 10X BlueJuice™ Gel Loading Buffer from Life Technologies and Pt-nanoparticles from Nanocomposix.



Table 1: Buffer list.

BufferIngredients
1X TE10 mL 1 M Tris-HCl (pH 8)

2 mL 0.5 M EDTA (pH 8)
988 mL water

10X TE100 mL 1 M Tris (pH 8)

20 mL 0.5 M EDTA (pH 8)
880 mL water

PBS8.0 g NaCl

0,2 g KCl
1.42 g Na2HPO4
1.78 Na2HPO4• 2 H2O
0,27 g KH2PO4
1000 mL water

TBE

10.8 g Tris
5.5 g boric acid
0.7 g Na2EDTA
1000 mL water

TAE

4.84 g Tris
1.1 mL acetic acid
2 mL 0.5 M Na2EDTA
997 mL water

Phosphate buffer

400 mL 1 M KH2PO4 solution
500 mL 1 M K2HPO4 solution

LB medium >10 g/L NaCl

10 g/L Bacto-tryptone
5 g/L Yeast extract

in ddH2O, autoclave
DYT medium 16 g/L Bacto-tryptone

10 g/L Yeast extract
5 g/L NaCl

in ddH2O, autoclave
Buffer M1 150 g PEG-8000/500 mL
87.66 g NaCl/500 mL
10mM Tris 121.14 mg Tris base /100 mL
Adjust to pH 8.5 with HCl
Buffer PPB2 1.6 g NaOH/200 mL
2 g SDS/200 mL
Buffer PPB3 58.88 g C2H3KO2/200 mL
Adjust pH to 5.5 with glacial acetic acid


DNA Origami Folding

Supporting information.


Table 2: Staples for Mastermixtures.

MastermixStaples used for the unmodified NanoscooterMastermixStaples used for the Nanoscooter modified for
modified for platinum nanoparticle binding
platinum nanoparticle and bead binding
N1unmodified staples: N1_A1 - N2_E9N3staples modified with 15 adenines: rot1_15A -
orange3_15A
N2unmodified staples: 
rot1_unmod - orange3_unmod
N4unmodified staples N1_A1-N2_E9 without N1_B1,
N1_D8, N1_G9, N1_G11, N2_C7
N5staples modified with 15 adenines: rot1_15A -
orange3_15A and biotin modified staples

The sequences are shown in the attached file (List of staples).

Table 3: Components for DNA origami folding.

Componentsunmodified NanoscooterNanoscooter modified for
platinum nanoparticle binding		Staples used for the Nanoscooter modified for
platinum nanoparticle and bead binding
volume [µL]volume [µL]volume [µL]
Mastermix N13232-
Mastermix N210--
Mastermix N3-10-
Mastermix N4--30
Mastermix N5--10
MgCl2 (100 mM)181818
MilliQ water202022
10x TE buffer101010
Scaffold p8064 (100 nM)101010


Table 4: List of staples.













Oligoname Sequence
N1_A1 CACGTAATTGACGCCAGCTTTGAAT
N1_A2 CCGCTTTTGAGGCTTAGTAAAAGGAT
N1_A3 GTGTACAAGAATCGCAACGCCAACATGT
N1_A4 GGGTCGTAACCTAAGCCCGAAAGACTTC
N1_A5 CAATAGAAAATTCAAGTTTATAAACGTCA
N1_A6 AGCTTGCAGGTAGATTGGTCTTGATACCG
N1_A7 ACGTAACTAACCTCATCTTTGACCCATTA
N1_A8 TCACGGCGGATGGGATAGGTCACGTGGGCGC
N1_A9 GCTTGACCATAACGCCTTTCACATCAAAAAT
N1_A10 ACCGTCACCATTTGCATTACCCCTCAGAGCCG
N1_A11 TACCCAATGAGCATGTAGTCCCTGACGAAACG
N1_A12 AGTCAGGCATTTGTTTTGATACATTAAAATCA
N1_B1 TGCGCGCCTGTTAGCCTTAGAACCCCTCAAAT
N1_B2 TAAACCTTAGGTTGGGTAACACCGATAAATAAG
N1_B3 AGTTTGCAGACTGTAGCGCGTATTTTCGTTCATAA
N1_B4 AGCAACTTCAAAGATTGCTATCGAAACCGTATTAG
N1_B5 AGGGAACTGATTTAGATACGAGACCTTATGCACTG
N1_B6 CAGAGCAATCTAATAGAAACTAAAGTTTGAGTGAA
N1_B7 TTAGCATATTAAATAACAACCAAGAATAGGGTTGA
N1_B8 TACATCATCGAAATTGTGTCGAAATCCGCGACAAC
N1_B9 GACAGCCGCGTAACCCGGCACCGCTTCTGGTGCCC
N1_B10 CTCAAGTGGGACGAGGCCTCAGGAAGATCGCACTC
N1_B11 ATAACGGAAAGATTTTGGCCGTCTCGTCCTCAAGG
N1_B12 GGGCGCCTTCTTTTGAGGTGGAGTTTAAAAATACC
N1_C1 GGTGTGTGTAAACTAACTCTAACGGCATGGTGCCC
N1_C2 AATTACGTGAACCATCAGTTTTTTACCCTAACGAT
N1_C3 CAAAGCGAAAGACAGCAGATCGTCCAAAAGAGAGGG
N1_C4 CTTTCGCGCTTACGTGGTGCTGGAAGTTTCATTCCA
N1_C5 ATAATGATTGCAAGTTACAATCGGCTTTCAAACTGC
N1_C6 AGGCTAATTTACGCTAACGAGCGTCTGTACCGCTCATT
N1_C7 AAAGAATGAACGGTATACCACTGCAGATACATAACATT
N1_C8 TCTCAATCACCAGCTGGCAGCATTTCGGTCTGAAACAT
N1_C9 GCTTTACTTAGCCGGAAGCAGACGTGAAAGAATGAACG
N1_C10 AATATGGTTTAATTTCATTGTGAACCAACTTGTCAATC
N1_C11 ACTAAAGCGCCGTGGCGGAGCTTGACGGGGAAGCACTA
N1_C12 TCGTCTATCAGGGCGATGGCCCACCTCCAAAATAATAA
N1_D1 GGAGCTTTCACACCAGTACAGCTGATTGCCCGGCCCTG
N1_D2 AGAAAGGAGGACTCATTTAAGAGGCGTCGTTAAATCCT
N1_D3 GAACAACGCTCCAATAGGCGAAAAAAATCCGTGCATCTG
N1_D4 TTAGAGCTAAGTTACTCATGAATCCTGTAGCATTCCGCA
N1_D5 GCGTGGTGTACGGTGTGTCATTCACGCTGCGGCCACGAT
N1_D6 AACAGCATGCCCTGCTTTAAACAGTTCAGATGCCAAGTT
N1_D7 GTCAGACGATTGGCCTTGATTATTTGCAAAATAAAAGAT
N1_D8 AATGACAACACGTGGTTCTCACCGGCTTTAGCCACTGCAA
N1_D9 GCCAGTAGACAGGCAAATTTCCATAGGGCTTAATTGGACC
N1_D10 ACAAACTACAACGTTTTACCCATAGGAAGTACCCTCCGCC
N1_D11 TATAACAGTTGATTCCCAATCTCAACAAAAGGGTGGAGACA
N1_D12 ATTCGGTCATCGCCAATACTGCGGAATCTTAGACTTGTTTC
N1_E1 TAATGCGAACCACCACAGGCGCTGCACAGCAGAAGGGTGAGG
N1_E2 CAAAATGTAGCATGAATCGATACAAGGCCTACAACTAAAACA
N1_E3 AAACAGGAGACGGGAGAATTAGAGTAATAGATTCATGTTTTA
N1_E4 ACGCTGCGCGCTGGCGGATCGAGGGCGTCAGTATTGCAACAG
N1_E5 AAGGAAAACAAGAGGTATTAAATTGCCCGTTAACATATTCCT
N1_E6 TGAGTGAAAAACAGATGGATTATTCATTCATTACATTTAACA
N1_E7 CCAGAGCTCATTGCGGAGCAATTTAATTCGGTGCCCTGGGAG
N1_E8 TCTCGTCGAGTTCCGACTTCAATCAAAATCTGGCCCCCCTCA
N1_E9 CGGAGCTAGCGGTTGCGCTCAGCCAACGAGCGCCAACCGGAA
N1_E10 ACAATCGCCTAAAACAGGCCAACGACTCGCCATTAACGAACC
N1_E11 ATATGTTGCAGTTAGCGTTTGGATAAGAATGATGCCACCACC
N1_E12 TAGTTAATACAGCAAACGTTTCAAACTTTAGAGCGCAACCAA
N1_F1 AAAAAATCCCGTAAGGGTAAAGCGGTCCCAGAGCAAACGTCA
N1_F2 AATTAGACAGGAACCCAGAATGTTTTTAGTGAGGCAAGAGTC
N1_F3 GTGATTAAGTTTGTAAAGTGCCAATAACCTCTGTTTACCAGT
N1_F4 CAGAAACAGGATTAAAGGGATTCATACGAGCTTAATTGAGAC
N1_F5 GGAACAAGGTAGAAAGATTCATTTAGGAAATACGAGCCACTC
N1_F6 GGTCAGTACAGTGCCCGCATTGAAGCGTATAAACACCTGCCT
N1_F7 ACTACCTTTTATCAAACGCTGAGAAGAGTGCGATAGCTTAGA
N1_F8 TAAGGCTATCAACGCAAGAACCAAATTCAAAGCCAACGCTCA
N1_F9 GGAAGTTGTAATGTAATTGAGCGCTAATTGAACAATTTTCAT
N1_F10 AGAGAGTTGCAGGTCCGGGCAGAGACGCGCGGTTTGCGTATT
N1_F11 AGCACCGTGCCGGACTTGTAGCATCCTCAATTATCAGAAACC
N1_F12 AGCCCAATGTACCGGAAAGGGCCTCTTCATCCTGTTTCCGAA
N1_G1 ACAGCGGGCATCCCAGATACATTCTGTGCGCGCTCGCAAATG
N1_G2 GTCGGGAGCCAGCTGGAATTTGTTTGATCCCGGGAGAGATAG
N1_G3 AGCCATACAATCCAAATAAGAATGCCGGTATTTTTAAACTCC
N1_G4 GTCAAATATGATATTCATTTTTGGAGCCTCCGTCGGATGGCT
N1_G5 CTGCCAGCACGCGTGCCTGTTCTTCGCGTCCTCACCGTCTCG
N1_G6 AATATGCAACTAAAGCTGGTCTGGGTAAGTGTAGTCAGCAGC
N1_G7 ATCGGCAAAATCCCTTATAAATCAAATAGTCATAACGTCGGA
N1_G8 AAAAATATTATAACCTGAAAATAGCAGCCTTTGTTTAACGTC
N1_G9 TAGTAACCGGTCTGTTATATTTGGCAACAGGAAGATTGTAGT
N1_G10 CTCCGGCGTTTTTTAGTTGAGATGGTCATAGCTGTAAATTGT
N1_G11 CGCCAGGGTGTTAATTTTTTTTCCCAGTCCACCCTGATAGCA
N1_G12 TCACGCAAATTAGGGCCGTTTACCGGGGGTAGTAACACCGTT
N1_H1 ACAGTTTAGAATAGAACAAGCTATTTTCTCTTCCAGACGTTA
N1_H2 CCATAACTAGTATGCATCAGAGAATGCGATCCCACCAACGGC
N1_H3 AGTGAATTTTAACCTCCGGCACGGAATATATGGTTAAAGACAA
N1_H4 TGATAGCGCCTATTAATGGGAAACGTACCGAACGTCGTATCGG
N1_H5 AAAGCTATTACGTCGCGATAATCCAGCTGGCTAACACTACCAGT
N1_H6 ACGATTCCATTACTAAAGACTTTTTAACGAGGTAAAAACAGAGG
N1_H7 CCAGACAGGAGGAAGAATTTTTTTAAAGCCATTTCTTTCCCTGCG
N1_H8 CCAGTTTTGTCGTCTATAATAGCAATATAGAGGTATTCAGGCGTT
N1_H9 TACGGGAGAATCCTGATTGTTTGGTGAATAAAGAACCTAATATTC
N1_H10 AAACTAAATTCAATAGTTACACATTAACAGTACCTTTAATAATCT
N1_H11 GACCAGTAGAGTAGCACGGAATTAGAGCCAGAAAGGTGTAAATAT
N1_H12 GGAGAGTACAGGGCGCGTACTATGGTTACGAGCAGCTTTCCGAAT
N2_A1 TCATATGCGTACTAGAAAAGAATATATATAAATGCTGATGCAAAT
N2_A2 CAGAGCATTAGCAACGGGTTACCCGAGCGGGCGTGGCTGGTAATA
N2_A3 TAATTTAGCGCAAAAACGCGCAACTAAGAATCAAAAAGAAAGCCC
N2_A4 AGGTAATATGCCGTTCCGAGAAGTCCTGAGCTCGAATTTCCACAC
N2_A5 TAAGCCACCACATTAGCAAGCAGCATTAATTAATTTTCCGACATTC
N2_A6 CGGGCGCAAGGGAATGCGGAAACCAGGCGTTGGGAGTGCGGGGGAT
N2_A7 AAGTGTGTTCCTCAGGTCAGGATTAGAGCGGAAGCGAGAGATTATC
N2_A8 TGAGAACTTAAATAGTCTCTGAGTTCTGCTCAGGGTTTTAGGCGGA
N2_A9 GTAGCACTTAGGAAATGTTTTAAGCCGATGGGATTATTGAGGAAGG
N2_A10 TAAGTGCGTTGATATAAGTATAGGTGTATCACCGTTTTAGTAGAAC
N2_A11 CAGAAATCATAATTTAAAGAAAGAGCTACGGATATTAGGCTGAGTA
N2_A12 AAACAAAATTAAAAATCACCAGCAAAAGAAGATGATTCATTTACAG
N2_B1 ATAAGGGCTCCATGCAATAATTGAATTTATACCAGGGGAAGAGATT
N2_B2 AATCGATCCCCGGGTACCGGCAAACGTTAAACGATGCTGCGACATA
N2_B3 GAACAAAATAATCGTTTCCTTATCGCCCTACCGCAATCGTAATGTA
N2_B4 GTAAAACAGGAAGTGGCATAGACTATCATAACCCTACGACGAGTAG
N2_B5 ATTGAATCTTCCTGTCATCAACTTACGAGGAAACCAATTATCCAGGC
N2_B6 CCCGCATTAATGAATCGCTGCCCGACTCACACGGAAGCTCACAATCGT
N2_B7 CAAGATTATAAGCATTGTAAATTATAGTCGGTTTAGGGTAGAAGCAAA
N2_B8 TGTTCCAGCACGACTCCAGCATTAAAAGCCGACTTACAATAAGAGAAT
N2_B9 AAGGGCCTTAGAAATGAAACTGGCAACAACTGGCCTCCTTAAGTCAGA
N2_B10 TAGAGCTTAAGAGGTCAACCGTAAATTAAACGATTGTTACAAAATAAAC
N2_B11 TTAAGAAAGGTAGGTGGTTGATGGGCCAAGCGGTCCACGCTGGTTGGCG
N2_B12 ACAAACAAATAAATAGCGTCAAGCCGCCCAGAGTACAATTACTCGCGCA
N2_C1 CGGCTACTTTGAGGAAACGGGACGTAATAGGCACCAAACGAAAGAGGCA
N2_C2 GCAGGCGTGTACTGTTAACGGGGAACCACCATCTTGTCATAGCCCCCTT
N2_C3 GTGTTGTAACAAGAGTCCACTGTGGACTCCAACGTAAAACCGGTTTATC
N2_C4 TTTTTTCCCCTCAATCGAATTTAAAGAAGTGAGTGCAGCGTGAGTTGAA
N2_C5 GATAAACCGAGAAATAGATATAAAAAAATACATACATAAAGCGTCCTTT
N2_C6 TTGTACCTCATACAGTGGCATCAATTCTGTTTAGCAACGCAATTTTAGA
N2_C7 CTTCAAAGCGAACCATCGCGTACAAGAGTCAATCAGAATCTTTTGCACC
N2_C8 CAGATAGCCGAACAATAGCTAATTGAGTTTTTGCGTTATTTCTATATTT
N2_C9 GCCTGGAGAGGGTAAAGGGAATGGATCTGAATCACCCTCAGACGGATAA
N2_C10 GGCAATTCAGAGTAGCCTTTCTGATGATTCCAGTACCTCATTGAGGCAG
N2_C11 TTAATTTTATTAGGATTAGCGTTTGCCGCGGATCATGAGCTACTTTCCA
N2_C12 TGCTTTTACCCGAAAATGGATACATCACCCTGTAATACTAAGCCCGAGA
N2_D1 CAGCCAGGCGCAGTGTCACTGCACTCTGGCTGGAGGTGTCCAGGTCATT
N2_D2 GCCACGGCCGCCACGCCACCCTCAGAACAGAGCCACACGACGTGGGTAA
N2_D3 GTCAATAGACCATTTCATATAAATGCCTACTGAACAGAGAATAACATAA
N2_D4 GAAAGCTGAGATGATGAAAAAAAGCTATCCGCATAAAGTGTAAAGCTAA
N2_D5 ACGCTGACAAATGAAAGTATCCGACAAATCTAAAGTCACCTTGCTGAAC
N2_D6 TGGACGCTCCGGTATGAGCCGGGTCCCGCCGGTGGCTTTAATATAAACA
N2_D7 CATTCCAGAACCACCACCAATATACTAGGGTTTGGAACAGCGCGGTTGA
N2_D8 GCGGATTCCTGACTACGTTAAAAATTCGTCAACAAAGTCCTGAAGCGGG
N2_D9 CAGCTACAAGGAATAGCCCTTTTATCCTTATGTACAATCAGAATTAAGA
N2_D10 CGGCGAACATTCGCCACGAGTGTGAGTTCAGGCTGCAACGCGTAAGACA
N2_D11 CAGGTCTACGAGAACATTTTTGAACGCCAGAAAAACCCATCCTAGAACC
N2_D12 GCAGAAGGGATAGCTCTCAACGTGAGAATCGACAACCCGATAGATATAA
N2_E1 AACCGATTGAGGGAGTCGCTACCGTAATAGAATCAGGAACCGAATCACC
N2_E2 CTTCTGAATGGTTTCCGTGTGGAGGAAACCGAGGAAACGCAAATACCCA
N2_E3 ACTTTCTCCGTGGTGAAACAGCCAGCAGTTGGGCGGTTGTGTGAAAAAG
N2_E4 TGGTGCCGCACCGTTGTAGCACTTTGATATCACTTGTAGAAGATCGGCC
N2_E5 TCTCGCCCGGATAACCTCCCTACCCTCAGAACCGCTTACCGTACAGGAG
N2_E6 TGTCAAGCGCGAAACAAAGGCTGATTCTATACCAGGCCGAGAATGAAAA
N2_E7 GGAAATGCTCCTTTTGATAATTGCGCTGTAGTCTGCGATTAGTTTACTT
N2_E8 CGCACAGGCGTAGCAGAGGGGCCTTTAGCTTATCCTTATTCCTCAAGAG
N2_E9 AATCGGAGGGGTCGAGGTGCCGTAGAACATTAAAAAAAGATAGCCCGGC






rot1_unmod CATATAAACATCCCTTACAGCCAGTTACCCT
rot2_unmod CCACGGTGCCCAGATGCAATTAAGCAAAATCTCAG
rot3_unmod AACCGCAAGAATGCGCAACCAACTCAATACTGTTGGCTCGTCAAAGCCT
rot4_unmod TCATTTGTGAAAAGGGCAAGGCAAAGAATAAAGCTAAATCGG
rot5_unmod GAGTGGGCCTACTAATATAACATCCAATAAAAAAAACATTATGAT
rot6_unmod AGTGCTGACCTTCATCAATCTTGATAACAAA
gelb1_unmod TCAGATGAGTGCGTGAAATAGCCGCCGCCAG
gelb2_unmod AACCCACAACAGTCAAGCGGATCTTACCGAAGCCCAAGTAAG
gelb3_unmod ACAGTCAAATAATAACAATGAAATAGCAAAGTTAC
orange1_unmod TGACGGAATAACCTTGCTTCTGTAAATCGGGAAGGAATTATC
orange2_unmod AGGCATCGATAGGCCGGTTTGTCACATTGAGCCGACAT
orange3_unmod CAAGACACGCACATCCTTGAAAACATACAGCGCCTACCAAT
rot1_15A CATATAAACATCCCTTACAGCCAGTTACCCTAAAAAAAAAAAAAAA
rot2_15A CCACGGTGCCCAGATGCAATTAAGCAAAATCTCAGAAAAAAAAAAAAAAA
rot3_15A AACCGCAAGAATGCGCAACCAACTCAATACTGTTGGCTCGTCAAAGCCTAAAAAAAAAAAAAAA
rot4_15A TCATTTGTGAAAAGGGCAAGGCAAAGAATAAAGCTAAATCGGAAAAAAAAAAAAAAA
rot5_15A GAGTGGGCCTACTAATATAACATCCAATAAAAAAAACATTATGATAAAAAAAAAAAAAAA
rot6_15A AGTGCTGACCTTCATCAATCTTGATAACAAAAAAAAAAAAAAAAAA
gelb1_15A TCAGATGAGTGCGTGAAATAGCCGCCGCCAGAAAAAAAAAAAAAAA
gelb2_15A AACCCACAACAGTCAAGCGGATCTTACCGAAGCCCAAGTAAGAAAAAAAAAAAAAAA
gelb3_15A ACAGTCAAATAATAACAATGAAATAGCAAAGTTACAAAAAAAAAAAAAAA
orange1_15A TGACGGAATAACCTTGCTTCTGTAAATCGGGAAGGAATTATCAAAAAAAAAAAAAAA
orange2_15A AGGCATCGATAGGCCGGTTTGTCACATTGAGCCGACATAAAAAAAAAAAAAAA
orange3_15A CAAGACACGCACATCCTTGAAAACATACAGCGCCTACCAATAAAAAAAAAAAAAAA






instead of N2_C7, N1_D8, N1_B1, N1_G9, N1_G11
76[77] CTTCAAAGCGAACCATCGCGTACAAGAGTCAATCAGAATCTTTTGCACCB 49 #57bb00 3' Biotin
45[87] AATGACAACACGTGGTTCTCACCGGCTTTAGCCACTGCAATAGTAAC 47 #57bb00
75[70] TTAGCCTTAGAACCCCTCAAAT 22 #57bb00
74[77] CGGTCTGTTATATTTGGCAACAGGAAGATTGTAGTTGCGCGCCTGB 45 #57bb00 3' Biotin
72[56] CGCCAGGGTGTTAATTTTTTTTCCCAGTCCACCCTGATAGCAB 42 #57bb00 3' Biotin

<img src="http://openwetware.org/images/b/b7/Cadnano_Staples.png" width="358" height="1075" >

Figure 1: caDNAno-File of the Nanoscooter.

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