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Creating complex molecular topologies by configuring DNA four-way junctions

Abstract

The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

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Figure 1: DNA-junction-based strategy for topological construction.
Figure 2: Constructing trefoil knots of both handedness.
Figure 3: Topoisomers of two- and three-component links.
Figure 4: Design and construction of dsDNA knots.
Figure 5: Study of DNA topoisomerase and polymerases with the ssDNA trefoil knot.

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References

  1. Pickover, C. A. The Math Book: From Pythagoras to the 57th Dimension, 250 Milestones in the History of Mathematics (Sterling, 2009).

    Google Scholar 

  2. Adams, C. C. The Knot Book: An Elementary Introduction to the Mathematical Theory of Knots (American Mathematical Society, 2004).

    Google Scholar 

  3. Kauffman, L. H. Knots and Physics 3rd edn (World Scientific, 2001).

    Book  Google Scholar 

  4. Forgan, R. S., Sauvage, J. P. & Stoddart, J. F. Chemical topology: complex molecular knots, links, and entanglements. Chem. Rev. 111, 5434–5464 (2011).

    Article  CAS  Google Scholar 

  5. Ayme, J. F., Beves, J. E., Campbell, C. J. & Leigh, D. A. Template synthesis of molecular knots. Chem. Soc. Rev. 42, 1700–1712 (2013).

    Article  CAS  Google Scholar 

  6. Gil-Ramirez, G., Leigh, D. A. & Stephens, A. J. Catenanes: fifty years of molecular links. Angew. Chem. Int. Ed. 54, 6110–6150 (2015).

    Article  CAS  Google Scholar 

  7. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010).

    Article  CAS  Google Scholar 

  8. Bates, A. D. & Maxwell, A. DNA Topology 2nd edn (Oxford Univ. Press, 2005).

    Google Scholar 

  9. Mueller, J. E., Du, S. M. & Seeman, N. C. Design and synthesis of a knot from single-stranded DNA. J. Am. Chem. Soc. 113, 6306–6308 (1991).

    Article  CAS  Google Scholar 

  10. Du, S. M. & Seeman, N. C. Synthesis of a DNA knot containing both positive and negative nodes. J. Am. Chem. Soc. 114, 9652–9655 (1992).

    Article  CAS  Google Scholar 

  11. Du, S. M., Stollar, B. D. & Seeman, N. C. A synthetic DNA molecule in three knotted topologies. J. Am. Chem. Soc. 117, 1194–1200 (1995).

    Article  CAS  Google Scholar 

  12. Mao, C., Sun, W. & Seeman, N. C. Assembly of Borromean rings from DNA. Nature 386, 137–138 (1997).

    Article  CAS  Google Scholar 

  13. Ciengshin, T., Sha, R. & Seeman, N. C. Automatic molecular weaving prototyped by using single-stranded DNA. Angew. Chem. Int. Ed. 50, 4419–4422 (2011).

    Article  CAS  Google Scholar 

  14. Seeman, N. C. in Molecular Catenanes, Rotaxanes and Knots (eds Sauvage, J.P. & Dietrich-Buchecker, C.) 323–356 (Wiley, 2007).

    Google Scholar 

  15. Chichak, K. S. et al. Molecular Borromean rings. Science 304, 1308–1312 (2004).

    Article  CAS  Google Scholar 

  16. Chen, J. H. & Seeman, N. C. Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991).

    Article  CAS  Google Scholar 

  17. Ackermann, D. et al. A double-stranded DNA rotaxane. Nature Nanotech. 5, 436–442 (2010).

    Article  CAS  Google Scholar 

  18. Schmidt, T. L. & Heckel, A. Construction of a structurally defined double-stranded DNA catenane. Nano Lett. 11, 1739–1742 (2011).

    Article  CAS  Google Scholar 

  19. Han, D., Pal, S., Liu, Y. & Yan, H. Folding and cutting DNA into reconfigurable topological nanostructures. Nature Nanotech. 5, 712–717 (2010).

    Article  CAS  Google Scholar 

  20. Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831 (1983).

    Article  CAS  Google Scholar 

  21. Lilley, D. M. Structures of helical junctions in nucleic acids. Q. Rev. Biophys. 33, 109–159 (2000).

    Article  CAS  Google Scholar 

  22. Seeman, N. C. The design of single-stranded nucleic acid knots. Mol. Eng. 2, 297–307 (1992).

    Article  CAS  Google Scholar 

  23. Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  24. Rodbard, D. & Chrambach, A. Estimation of molecular radius, free mobility, and valence using polyacrylamide gel electrophoresis. Anal. Biochem. 40, 95–134 (1971).

    Article  CAS  Google Scholar 

  25. Bloomfield, V. A., Crothers, D. M. & Tinoco, I. Nucleic Acids: Structures, Properties, and Functions (Univ. Science Books, 2000).

    Google Scholar 

  26. Liu, D., Wang, M., Deng, Z., Walulu, R. & Mao, C. Tensegrity: construction of rigid DNA triangles with flexible four-arm DNA junctions. J. Am. Chem. Soc. 126, 2324–2325 (2004).

    Article  CAS  Google Scholar 

  27. Birac, J. J., Sherman, W. B., Kopatsch, J., Constantinou, P. E. & Seeman, N. C. Architecture with GIDEON, a program for design in structural DNA nanotechnology. J. Mol. Graph. Model. 25, 470–480 (2006).

    Article  CAS  Google Scholar 

  28. Cantrill, S. J., Chichak, K. S., Peters, A. J. & Stoddart, J. F. Nanoscale Borromean rings. Acc. Chem. Res. 38, 1–9 (2005).

    Article  CAS  Google Scholar 

  29. Krasnow, M. A. et al. Determination of the absolute handedness of knots and catenanes of DNA. Nature 304, 559–560 (1983).

    Article  CAS  Google Scholar 

  30. Shaw, S. & Wang, J. Knotting of a DNA chain during ring closure. Science 260, 533–536 (1993).

    Article  CAS  Google Scholar 

  31. Sherman, W. B. HolT Hunter: software for identifying and characterizing low-strain DNA Holliday triangles. J. Comput. Chem. 33, 1393–1405 (2012).

    Article  CAS  Google Scholar 

  32. Baas, N. A., Seeman, N. C. & Stacey, A. Synthesising topological links. J. Math. Chem. 53, 183–199 (2015).

    Article  CAS  Google Scholar 

  33. Chen, S. H., Chan, N. L. & Hsieh, T. S. New mechanistic and functional insights into DNA topoisomerases. Annu. Rev. Biochem. 82, 139–170 (2013).

    Article  CAS  Google Scholar 

  34. Du, S. M., Wang, H., Tse-Dinh, Y.-C. & Seeman, N. C. Topological transformations of synthetic DNA knots. Biochemistry 34, 673–682 (1995).

    Article  CAS  Google Scholar 

  35. Rajendran, A., Endo, M. & Sugiyama, H. Single-molecule analysis using DNA origami. Angew. Chem. Int. Ed. 51, 874–890 (2012).

    Article  CAS  Google Scholar 

  36. Subramani, R. et al. A novel secondary DNA binding site in human topoisomerase I unravelled by using a 2D DNA origami platform. ACS Nano 4, 5969–5977 (2010).

    Article  CAS  Google Scholar 

  37. Niu, J., Hili, R. & Liu, D. R. Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids. Nature Chem. 5, 282–292 (2013).

    Article  CAS  Google Scholar 

  38. Marko, J. F. & Siggia, E. D. Bending and twisting elasticity of DNA. Macromolecules 27, 981–988 (1994).

    Article  CAS  Google Scholar 

  39. Wang, H., Di Gate, R. J. & Seeman, N. C. An RNA topoisomerase. Proc. Natl Acad. Sci. USA 93, 9477–9482 (1996).

    Article  CAS  Google Scholar 

  40. Tkalec, U., Ravnik, M., Copar, S., Zumer, S. & Musevic, I. Reconfigurable knots and links in chiral nematic colloids. Science 333, 62–65 (2011).

    Article  CAS  Google Scholar 

  41. Kleckner, D. & Irvine, W. T. M. Creation and dynamics of knotted vortices. Nature Phys. 9, 253–258 (2013).

    Article  CAS  Google Scholar 

  42. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    Article  CAS  Google Scholar 

  43. Feldkamp, U. CANADA: designing nucleic acid sequences for nanobiotechnology applications. J. Comput. Chem. 31, 660–663 (2010).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank J. Piccirilli and B. Tian for their critical reading of the manuscript, J. Birac for providing the GIDEON software for preparing the DNA structures, W. Sherman for helpful information about the tensegrity-triangle design and T. Witten and G. Zocchi for insightful discussions. D.L. acknowledges the Martha Ann and Joseph A. Chenicek Graduate Research Fund and the HHMI International Student Research Fellowship. This work is supported by the University of Chicago and the NSF CAREER Award (DMR-1555361) to Y.W.

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D.L. and Y.W. conceived the project. D.L. designed the experiments. D.L., G.C. and U.A. performed the research. D.L., G.C. and Y.W. analysed the data and wrote the paper. T.M.C. helped revise the manuscript.

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Correspondence to Yossi Weizmann.

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The authors declare no competing financial interests.

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Liu, D., Chen, G., Akhter, U. et al. Creating complex molecular topologies by configuring DNA four-way junctions. Nature Chem 8, 907–914 (2016). https://doi.org/10.1038/nchem.2564

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