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Cinnamate-based DNA photolithography

Abstract

As demonstrated by means of DNA nanoconstructs1, as well as DNA functionalization of nanoparticles2,3,4 and micrometre-scale colloids5,6,7,8, complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage9. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction10. Here, we show that the substitution of a cinnamate group for a pair of complementary bases provides an efficient, addressable, ultraviolet light-based method to bond complementary DNA covalently. To show the potential of this approach, we wrote micrometre-scale patterns on a surface using ultraviolet light and demonstrated the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multistep, specific binding in self-assembly processes.

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Figure 1: Schematic representation of cinnamate-containing nucleoside and the cycloaddition products.
Figure 2: Efficient and specific crosslinking with cinnamate-based DNA strands, and the application on colloids.
Figure 3: Schematic protocol for DNA photolithography with cinnamate-based DNA strands.
Figure 4: DNA photolithographic patterns on surfaces.
Figure 5: Resolution of DNA photolithography.

References

  1. 1

    Seeman, N. C. DNA in a material world. Nature 421, 427–431 (2003).

    Article  Google Scholar 

  2. 2

    Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).

    CAS  Article  Google Scholar 

  3. 3

    Alivisatos, A. P. et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996).

    CAS  Article  Google Scholar 

  4. 4

    Nykypanchuk, D., Maye, M. M., van der Lelie, D & Gang, O. DNA-guided crystallization of colloidal nanoparticles. Nature 451, 549–552 (2008).

    CAS  Article  Google Scholar 

  5. 5

    Biancaniello, P. L., Kim, A. J. & Crocker, J. C. Colloidal interactions and self-assembly using DNA hybridization. Phys. Rev. Lett. 94, 058302 (2005).

    Article  Google Scholar 

  6. 6

    Valignat, M. P., Theodoly, O., Crocker, J. C., Russel, W. B. & Chaikin, P. M. Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids. Proc. Natl Acad. Sci. USA 102, 4225–4229 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Rogers, P. H. et al. Controllable, and reversible aggregation of polystyrene latex microspheres via DNA hybridization. Langmuir 21, 5562–5569 (2005).

    CAS  Article  Google Scholar 

  8. 8

    Leunissen, M. E. et al. Switchable self-protected attractions in DNA-functionalized colloids. Nature Mater. 8, 590–595 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Wang, T. et al. Self-replication of information-bearing nanoscale patterns. Nature 478, 225–228 (2011).

    CAS  Article  Google Scholar 

  10. 10

    Leunissen, M. E. et al. Towards self-replicating materials of DNA-functionalized colloids. Soft Matter 5, 2422–2430 (2009).

    CAS  Article  Google Scholar 

  11. 11

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

    CAS  Article  Google Scholar 

  12. 12

    Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).

    CAS  Article  Google Scholar 

  13. 13

    Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science 334, 204–208 (2011).

    CAS  Article  Google Scholar 

  14. 14

    Winfree, E., Liu, F. R., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    CAS  Article  Google Scholar 

  15. 15

    Sherman, W. B. & Seeman, N. C. DNA walking biped. Nano Lett. 4, 1203–1207 (2004).

    CAS  Article  Google Scholar 

  16. 16

    Yurke, B., Turberfield, A. J., Mills, A. P. J., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    CAS  Article  Google Scholar 

  17. 17

    Lewin, D. I. DNA computing. Comput. Sci. Eng. 4, 5–8 (2002).

    Google Scholar 

  18. 18

    Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011).

    CAS  Article  Google Scholar 

  19. 19

    Schulman, R. & Winfree, E. Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc. Natl Acad. Sci. USA 104, 15236–15241 (2007).

    CAS  Article  Google Scholar 

  20. 20

    Gu, H., Chao, J., Xiao, S. J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205 (2010).

    CAS  Article  Google Scholar 

  21. 21

    Wassarman, D. & Steitz, J. Interactions of small nuclear RNA’s with precursor messenger RNA during in vitro splicing. Science 257, 1918–1925 (1992).

    CAS  Article  Google Scholar 

  22. 22

    Takasugi, M. et al. Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc. Natl Acad. Sci. USA 88, 5602–5606 (1991).

    CAS  Article  Google Scholar 

  23. 23

    Wu, Q., Christensen, L. A., Legerski, R. J. & Vasquez, K. M. Mismatch repair participates in error-free processing of DNA interstrand cross-links in human cells. EMBO Rep. 6, 551–557 (2005).

    CAS  Article  Google Scholar 

  24. 24

    Yoshimura, Y, Itoa, Y. & Fujimotoa, K. Interstrand photocross-linking of DNA via p-carbamoylvinyl phenol nucleoside. Bioorg. Med. Chem. Lett. 15, 1299–1301 (2005).

    CAS  Article  Google Scholar 

  25. 25

    Yoshimura, Y. & Fujimoto, K. Ultrafast reversible photo-cross-linking reaction: Toward in situ DNA manipulation. Org. Lett. 10, 3227–3230 (2008).

    CAS  Article  Google Scholar 

  26. 26

    Dreyfus, R. et al. Simple quantitative model for the reversible association of DNA coated colloids. Phys. Rev. Lett. 102, 048301 (2009).

    Article  Google Scholar 

  27. 27

    Xu, Q., Feng, L., Sha, R., Seeman, N. C. & Chaikin, P. M. Subdiffusion of a sticky particle on a surface. Phys. Rev. Lett. 106, 228102 (2011).

    CAS  Article  Google Scholar 

  28. 28

    Xia, D., Yan, J. & Hou, S. Fabrication of nanofluidic biochips with nanochannels for applications in DNA analysis. Small 8, 2787–2801 (2012).

    CAS  Article  Google Scholar 

  29. 29

    Maalouf, A., Gadonna, M. & Bosc, D. An improvement in standard photolithography resolution based on Kirchhoff diffraction studies. J. Phys. D 42, 015106 (2009).

    Article  Google Scholar 

  30. 30

    Gorzolnik, B., Mela, P. & Möller, M. Nano-structured micropatterns by combination of block copolymer self-assembly and UV photolithography. Nanotechnology 17, 5027–5032 (2006).

    CAS  Article  Google Scholar 

  31. 31

    Varghese, B. et al. Size selective assembly of colloidal particles on a template by directed self-assembly technique. Langmuir 22, 8248–8252 (2006).

    CAS  Article  Google Scholar 

  32. 32

    Naiser, T., Mai, T., Michel, W. & Ott, A. Versatile maskless microscope projection photolithography system and its application in light-directed fabrication of DNA microarrays. Rev. Sci. Instrum. 77, 063711 (2006).

    Article  Google Scholar 

  33. 33

    Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610–614 (1996).

    CAS  Article  Google Scholar 

  34. 34

    Liu, Q. H. et al. DNA computing on surfaces. Nature 403, 175–179 (2000).

    CAS  Article  Google Scholar 

  35. 35

    Pregibon, D. C., Toner, M. & Doyle, P. S. Multifunctional encoded particles for high-throughput biomolecule analysis. Science 315, 1393–1396 (2007).

    CAS  Article  Google Scholar 

  36. 36

    Jiang, S. et al. Janus particle synthesis and assembly. Adv. Mater. 22, 1060–1071 (2010).

    CAS  Article  Google Scholar 

  37. 37

    Caruthers, M. H. Gene synthesis machines: DNA chemistry and its uses. Science 230, 281–85 (1985).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This research has been partially supported by the MRSEC Program of the National Science Foundation under Award Number DMR-0820341 for the cinnamate-functionalized phosphoramidite, NASA NNX08AK04G for microscopy, and DOE-BES-DE-SC0007991 to P.C. for data acquisition and analysis, as well as by the following grants to N.C.S. for DNA synthesis and characterization: GM-29554 from the National Institute of General Medical Sciences, CTS-0608889 and CCF-0726378 from the National Science Foundation, 48681-EL and W911NF-07-1-0439 from the Army Research Office, and N000140910181 and N000140911118 from the Office of Naval Research. J. Romulus acknowledges support through the Margaret Strauss Kramer Graduate Student Fellowship in Chemistry.

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Contributions

L.F. designed and performed experiments, analysed data and wrote the paper; J. Romulus and M.L. synthesized the cinnamate-containing phosphoramidite and wrote the paper; R.S. incorporated the cinnamate in the DNA strands, performed gel experiments, analysed data and wrote the paper; J. Royer performed experiments, analysed data and wrote the paper; K-T.W. performed experiments, analysed data and wrote the paper; Q.X. performed experiments and analysed data; N.C.S. initiated and directed the project, designed experiments, analysed data and wrote the paper; M.W. initiated and directed the project, designed experiments and wrote the paper; P.C. initiated and directed the project, designed experiments, analysed data and wrote the paper.

Corresponding authors

Correspondence to Lang Feng, Nadrian C. Seeman, Marcus Weck or Paul Chaikin.

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The authors declare no competing financial interests.

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Feng, L., Romulus, J., Li, M. et al. Cinnamate-based DNA photolithography. Nature Mater 12, 747–753 (2013). https://doi.org/10.1038/nmat3645

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