cryo-EM of nanoscale DNA assemblies

REL PDBe PDBe PDBe 2016-04-14 2016-05-04 2016-06-15 2016-07-13 cryo-EM of nanoscale DNA assemblies Zhang K Chiu W Veneziano R Ratanalert S Zhang F Yan H Bathe M Scaffolded DNA origami Veneziano R Ratanalert S Zhang K Zhang F Yan H Chiu W Bathe M Designer nanoscale DNA assemblies programmed from the top down SCIENCE 352 1534 2016 27229143 doi:10.1126/science.aaf4388 DNA icosahedron, 52-bp edge length DNA icosahedron, 52-bp edge length

Monodisperse and pure sample were prepared by overnight folding reaction and purified using centrifugal filter (MWCO 100KDa)

monomer 2 2.07 2.07 Calculation M13mp18 phage genome segment Enterobacteria phage M13 M13mp18 M13 phage 1.01 1.01

amplified using assymetric PCR

TCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTACATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCACCAGATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTCGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAACCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGTTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAAGATCCATTCGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTAGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGC DNA SINGLE STRANDED false Synthetic DNA oligonucleotides synthetic construct 1.06 1.06

CAAGAACCGGATTTTTTATTCATTACGGATCTTCATTTTTTTAAAGCCAGAA CTTGATATTCGTAACAAAGCTGCTCATTCAGAGACGATTGGC ACAAACGAATCCAAATCAAC GATTTTAATAATCATTGTGAATTACAAGAGT AATCTTGACTGGCTGACCTTCATCCTTATGC TGAATAAGGCTTTTTTTGCCCTGACGACGATAAAAACTTTTTCAAAATAGCG AATTACGAGGCTTTTTATAGTAAGAGGAGATGGTTTATTTTTATTTCAACTT ACGAGTAGTAATAACCCTCGTTTACCAGACGAGAACACCAGA AATTGGGCTTCAACACTATC GAATCGTCGACTGGATAGCGTCCACATAACG CCAAAAGGCAACTAATGCAGATAATACTGCG ATATCGCGTTTTTTTTTAATTCGAGCGGGGTAATAGTTTTTTAAAATGTTTA CAAAAGAAGTACCAGACCGGAAGCAAACTCCAGAGGCTTTTG TTTGCCAGAGTTCAAAGCGA GCTCAACATTAATTGCTGAATCTGCCCGAAA GACTTCAAAAGATTAAGAGGAAGGTGCTGTA CGAGCTGAAAATTTTTGGTGGCATCATTTTTGCGGATTTTTTGGCTTAGAGC CTCCTTTTGATAGTAGTAGCATTAGAATAACACCTTTAATTG TAAGAGGTCAATTCTACTAA AGAATTGACTAATATCAGAGAGATTTTTCAT TTGGGGCGACCTGTTTAGCTATAAACCCACA AACAGGTCAGGTTTTTATTAGAGAGTATAAAAACAGGTTTTTGAAGCGCATTGACAGGAGGTTTTTTTGAGGCAGGTC TTAACTGAACACCAGAGCCGCCGCCAGCATTAGACGGGAGAA ACCCTGAACACAGAACCACC ACCGGAACCGCTTTTTCTCCCTCAGACACCACCCTCATTTTTGAGCCGCCAC CTCAGAGCGCCGCCACCCTCAGAACTGAATT TACCGTTCTGGAAAGCGCAGTCTCCGCCACC CGGGATCGTCATTTTTCCCTCAGCAGTTTTAACGGGGTTTTTTCAGTGCCTTCCCTGCCTATTTTTTTTCGGAACCTA TTAATGCCGAGTAACAGTGCCCGTGGAACCA GAGCCACCATAATCAAAATCACCATAAACAG AGGAGTGTACCATCGGAACGAGGGTAGCAACTTTGATGATAC TGGTAATAAGCGAAAGACAG CAGTAAGCGTCTTTTTATACATGGCTGGCTACAGAGGTTTTTCTTTGAGGACTGTACAGACCATTTTTGGCGCATAGG GTCGAAATCCGTTTTTCGACCTGCTCTCAATCATAAGTTTTTGGAACCGAACAACGGGTAAAATTTTTTACGTAATGC TCATGAGGAATGAAAGAGGACAGATGAACGGTAAAGACTTTT GTTTCCATTATGACCAACTT GCAGACGGCATGTTACTTAGCCGGAAAAATC TACGTTAACAGGACGTTGGGAAGAACGAGGC AAGGAATTAGTGAGAATAGAAAGGCGCCTGA TAAATTGTGGAGATTTGTATCATAACAACTA GAACTGGCTCATTTTTTTATACCAGTTAAAACGAACTTTTTTAACGGAACAAGAGATTTAGGATTTTTATACCACATT TGCTAAACAAATGAATTTTCTGTAAAAGATT CATCAGTTCATTATTACAGGTAGTGGGGTTT CCTGTAGCATTTTTTTCCACAGACAAGTCGTCTTTCCTTTTTAGACGTTAGT AAAGTTTTCCCTCATAGTTAGCGTCAGTTCA GAAAACGACTCAAATGCTTTAAAAACGATCT AGGGCGACTGGTTTACCAGCGCTAGTACAAA CTACAACGTGAGTTTCGTCACCAAAGACAAA ATAAATATTCATTTTTTTGAATCCCCGAATGACCATATTTTTAATCAAAAATAGCAAAGCGGATTTTTTTGCATCAAA ATTTTGTCGCAAAGACACCACGGAACTATTA TAGTCAGACAGGTCTTTACCCTGATAAGTTT AAGACTCCTTATTTTTTTACGCAGTAGTGGCAACATATTTTTTAAAAGAAAC ACATAAAGTGTTAGCAAACGTAGAGTTTCAT TCCATGTAGTACGGTGTCTGGAAAAATACAT CCGAAGCCCTTTTTTTTTTAAGAAAAGAAACCGAGGATTTTTAACGCAATAAAAAATCACCAGTTTTTTAGCACCATT ATTTGGGAATCCCAAAAGAACTGGCATGATTCGACTTGAGCC TAGAGCCAGCTAACGGAATA TGTTTTAAATATTTTTTGCAACTAAAACAGTTGATTCTTTTTCCAATTCTGCACATTTCGCAATTTTTATGGTCAATA ACCAGAAGGTAAGCAGATAGCCGAGTTTGAC CATTAGATGAACGAGTAGATTTAACAAAGTT AAGTCAGAGGGTTTTTTAATTGAGCGGTTAAGCCCAATTTTTTAATAAGAGCATTAGCGTTTGTTTTTCCATCTTTTC AAATAGCAATATTTTCGGTCATAGCCCCCTTAAGAAACAATG AGCTATCTTATTTCATCGGC CGCTTTTGTGAGGCTTGCAGGGAGAACCTAA AACGAAAGCACTACGAAGGCACCTTAAAGGC TGAGACTCCTCTTTTTAAGAGAAGGAATAACCGATATTTTTTATTCGGTCGC ACAGCTTGATATTTTTCCGATAGTTGGCGGATAAGTGTTTTTCCGTCGAGAG GGGGTTTTGCGACAACAACCATCGCCCACGCTTAGGATTAGC TCAGTACCAGCGCCGACAAT AGGCGAAAGAATTTTTTACACTAAAAAAGCGCGAAACTTTTTAAAGTACAAC TTTCTTAATTATCAGCTTGCTTTCCCCAGCG ATTATACCCACTCATCTTTGACCGAGGTGAA GAAACCATCGATTTTTTAGCAGCACCTAGCGTCAGACTTTTTTGTAGCGCGT TTTGCCTTGTAATCAGTAGCGACAAAAGTAT TAAGAGGCTTATTCTGAAACATGGAATCAAG TAGGTGTAGGTTGATATAAGTATAGGAAACG TCACCAATACCATTAGCAAGGCCGCCCGGAA AACTTTCAACATTTTTGTTTCAGCGGGCGAATAATAATTTTTTTTTTTCACGGGAACCCATGTTTTTTACCGTAACAC TCACCGTACTCTTTTTAGGAGGTTTAACCGCCACCCTTTTTTCAGAGCCACCGGAGCCTTTAATTTTTTTGTATCGGT CAAAAAAAAATCAGGGATAGCAAGCCCAATATTGAAAATCTC GGCTCCAAAAACCCTCATTT ACAATCAATAGTTTTTAAAATTCATAATTCAACCGATTTTTTTGAGGGAGGGAAGGTGAATTATTTTTTCACCGTCAC CCCTCAGAGTACCGCCACCCTCAGGGAAATT ATTCATTAAAGGTAAATATTGACAACCGCCA

DNA SINGLE STRANDED true singleParticle particle 1.05 8.0

40 mM Tris-HCl, 20 mM acetic acid, 2 mM EDTA

glow-discharged 200-mesh R1.2/1.3 Quantifoil grid

ETHANE 100 FEI VITROBOT MARK IV Blot for 1.5 second before plunging JEOL 2200FS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2 1.5 4.0 25000.0 GATAN LIQUID NITROGEN Objective lens astigmatism was corrected at 80,000 times magnification JEOL

5k * 4k

2015-10-05 DIRECT ELECTRON DE-20 (5k x 3k) 180 63

Every image is the average of 60 frames recorded by the direct electron detecto

The particles were selected manually using EMAN2

each particle

I OTHER 20.0 OTHER EMAN2 3650 emd_3409.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 642.56 642.56 642.56 90.0 90.0 90.0 X Y Z -0.00583043 0.07475706 0.00341404 0.00912775 2.51 2.51 2.51 0.0388 AUTHOR Reconstruction of DNA icosahedron origami

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