Automated Sequence Design and Simulation of DNA Nanostructures

나노구조물의 자동화 시퀀스 설계 및 거동 예측 시뮬레이션

  • 전형민 (전북대학교 기계시스템공학부)
  • Published : 2020.06.05

Abstract

Keywords

References

  1. N. C. Seeman, Nucleic acid junctions and lattices. Journal of Theoretical Biology. 99, 237-247 (1982). https://doi.org/10.1016/0022-5193(82)90002-9
  2. J. Chen, N. C. Seeman, Synthesis from DNA of a molecule with the connectivity of a cube. Nature. 350, 631-633 (1991). https://doi.org/10.1038/350631a0
  3. E. Winfree, F. Liu, L. A. Wenzler, N. C. Seeman, Design and self-assembly of two-dimensional DNA crystals. Nature. 394, 539-544 (1998). https://doi.org/10.1038/28998
  4. P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns. Nature. 440, 297-302 (2006). https://doi.org/10.1038/nature04586
  5. S. M. Douglas, H. Dietz, T. Liedl, B. Hogberg, F. Graf, W. M. Shih, Self-assembly of DNA into nanoscale three-dimensional shapes. Nature. 459, 414-418 (2009). https://doi.org/10.1038/nature08016
  6. H. Dietz, S. M. Douglas, W. M. Shih, Folding DNA into twisted and curved nanoscale shapes. Science. 325, 725-730 (2009). https://doi.org/10.1126/science.1174251
  7. F. Zhang, S. Jiang, S. Wu, Y. Li, C. Mao, Y. Liu, H. Yan, Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nature Nanotechnology. 10, 779-784 (2015). https://doi.org/10.1038/nnano.2015.162
  8. G. Tikhomirov, P. Petersen, L. Qian, Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Nature. 552, 67-71 (2017). https://doi.org/10.1038/nature24655
  9. K. F. Wagenbauer, C. Sigl, H. Dietz, Gigadalton-scale shape-programmable DNA assemblies. Nature. 552, 78-83 (2017). https://doi.org/10.1038/nature24651
  10. L, L, Ong, N. Hanikel, O. K, Yaghi, C. Grun, M. T. Strauss, P. Bron, J. Lai-Kee-Him, F. Schueder, B. Wang, P. Wang, J. Y. Kishi, C. Myhrvold, A. Zhu, R. Jungmann, G. Bellot, Y. Ke, P. Yin, Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. Nature. 552, 72-77 (2017). https://doi.org/10.1038/nature24648
  11. H. T. Maune, S. Han, R. D. Barish, M. Bockrath, W. A. G. Iii, P. W. K. Rothemund, E. Winfree, Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nature Nanotechnology. 5, 61-66 (2010). https://doi.org/10.1038/nnano.2009.311
  12. M. Pilo-Pais, S. Goldberg, E. Samano, T. H. LaBean, G. Finkelstein, Connecting the nanodots: programmable nanofabrication of fused metal shapes on DNA templates. Nano Lett. 11, 3489-3492 (2011). https://doi.org/10.1021/nl202066c
  13. H. Yan, S. H. Park, G. Finkelstein, J. H. Reif, T. H. LaBean, DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science. 301, 1882-1884 (2003). https://doi.org/10.1126/science.1089389
  14. W. Sun, E. Boulais, Y. Hakobyan, W. L. Wang, A. Guan, M. Bathe, P. Yin, Casting inorganic structures with DNA molds. Science. 346, 1258361 (2014). https://doi.org/10.1126/science.1258361
  15. A. Shaw, V. Lundin, E. Petrova, F. Fordos, E. Benson, A. Al-Amin, A. Herland, A. Blokzijl, B. Hogberg, A. I. Teixeira, Spatial control of membrane receptor function using ligand nanocalipers. Nature Methods. 11, 841-846 (2014). https://doi.org/10.1038/nmeth.3025
  16. J. Sharma, R. Chhabra, A. Cheng, J. Brownell, Y. Liu, H. Yan, Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science. 323, 112-116 (2009). https://doi.org/10.1126/science.1165831
  17. Z. Jin, W. Sun, Y. Ke, C.-J. Shih, G. L. C. Paulus, Q. H. Wang, B. Mu, P. Yin, M. S. Strano, Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning. Nature Communications, 4, 1663 (2013). https://doi.org/10.1038/ncomms2690
  18. S. M. Douglas, I. Bachelet, G. M. Church, A logic-gated nanorobot for targeted transport of molecular payloads. Science. 335, 831-834 (2012). https://doi.org/10.1126/science.1214081
  19. S. Li, Q. Jiang, S. Liu, Y. Zhang, Y. Tian, C. Song, J. Wang, Y. Zou, G. J. Anderson, J.-Y. Han, Y. Chang, Y. Liu, C. Zhang, L. Chen, G. Zhou, G. Nie,H. Yan, B. Ding, Y. Zhao, A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nature Biotechnology. 36, 258-264 (2018). https://doi.org/10.1038/nbt.4071
  20. E. Kopperger, J. List, S. Madhira, F. Rothfischer, D. C. Lamb, F. C. Simmel, A self-assembled nanoscale robotic arm controlled by electric fields. Science. 359, 296-301 (2018). https://doi.org/10.1126/science.aao4284
  21. G. P. Acuna, M. Bucher, I. H. Stein, C. Steinhauer, A. Kuzyk, P. Holzmeister, R. Schreiber, A. Moroz, F. D. Stefani, T. Liedl, F. C. Simmel, P. Tinnefeld, Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami. ACS Nano. 6, 3189-3195 (2012). https://doi.org/10.1021/nn2050483
  22. Q. Jiang, C. Song, J. Nangreave, X. Liu, L. Lin, D. Qiu, Z.-G. Wang, G. Zou, X. Liang, H. Yan, B. Ding, DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc. 134, 13396-13403 (2012). https://doi.org/10.1021/ja304263n
  23. S. D. Perrault, W. M. Shih, Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability. ACS Nano. 8, 5132-5140 (2014). https://doi.org/10.1021/nn5011914
  24. E. Benson, A, Mohammed, J. Gardell, S. Masich, E. Czeizler, P. Orponen, B. Hogberg, DNA rendering of polyhedral meshes at the nanoscale. Nature. 523, 441-444 (2015). https://doi.org/10.1038/nature14586
  25. E. Benson, A. Mohammed, A. Bosco, A. I. Teixeira, P. Orponen, B. Hogberg, Computer-aided production of scaffolded DNA nanostructures from flat sheet meshes. Angewandte Chemie International Edition. 55, 8869-8872 (2016). https://doi.org/10.1002/anie.201602446
  26. R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, M. Bathe, Designer nanoscale DNA assemblies programmed from the top down. Science. 352, 1534-1534 (2016). https://doi.org/10.1126/science.aaf4388
  27. H. Jun, F. Zhang, T. Shepherd, S. Ratanalert, X. Qi, H. Yan, M. Bathe, Autonomously designed free-form 2D DNA origami. Science Advances. 5, eaav0655 (2019). https://doi.org/10.1126/sciadv.aav0655
  28. H. Jun, T. R. Shepherd, K. Zhang, W. P, Bricker, S. Li, W, Chiu, M. Bathe, Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. ACS Nano. 13, 2083-2093 (2019). https://doi.org/10.1021/acsnano.8b08671
  29. H. Jun, X. Wang, W. P, Bricker, M. Bathe, Automated sequence design of 2D wireframe DNA origami with honeycomb edges. Nature Communications. 10, 1-9 (2019). https://doi.org/10.1038/s41467-018-07882-8
  30. C. E. Castro, F. Kilchherr, D.-N. Kim, E. L. Shiao, T. Wauer, P. Wortmann, M. Bathe, H. Dietz, A primer to scaffolded DNA origami. Nature Methods. 8, 221-229 (2011). https://doi.org/10.1038/nmeth.1570
  31. D. Wu, N. Sinha, J. Lee, B. P. Sutherland, N. I. Halaszynski, Y. Tian, J. Caplan, H. V. Zhang, J. G. Saven, C. J. Kloxin, D. J. Pochan, Polymers with controlled assembly and rigidity made with click-functional peptide bundles. Nature. 574, 658-662 (2019). https://doi.org/10.1038/s41586-019-1683-4
  32. S. M. Douglas, A. H. Marblestone, S. Teerapittayanon, A. Vazquez, G. M. Church, W. M. Shih, Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001-5006 (2009). https://doi.org/10.1093/nar/gkp436
  33. H. Jun, X. Wang, W. P. Bricker, S. Jackson, M. Bathe, bioRxiv, in press, doi:10.1101/2020.02.09.940320.
  34. O. Henrich, Y. A. Gutierrez Fosado, T. Curk, T. E. Ouldridge, Coarse-grained simulation of DNA using LAMMPS: An implementation of the oxDNA model and its applications. Eur. Phys. J. E. 41, 57 (2018). https://doi.org/10.1140/epje/i2018-11669-8
  35. T. E. Ouldridge, A. A. Louis, J. P. K. Doye, Structural, mechanical, and thermodynamic properties of a coarsegrained DNA model. J. Chem. Phys. 134, 085101 (2011). https://doi.org/10.1063/1.3552946
  36. A. Suma, E. Poppleton, M. Matthies, P. Sulc, F. Romano, A. A. Louis, J. P. K. Doye, C. Micheletti, L. Rovigatti, TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. Journal of Computational Chemistry. 40, 2586-2595 (2019). https://doi.org/10.1002/jcc.26029
  37. K. Pan, D.-N. Kim, F. Zhang, M. R. Adendorff, H. Yan, M. Bathe, Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nature Communications. 5, 5578 (2014). https://doi.org/10.1038/ncomms6578