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Electrically induced bonding of DNA to gold

Abstract

The development of single-molecule techniques has afforded many new methods for the observation and assembly of supramolecular structures and biomolecular networks. We previously reported a method, known as the single-molecule cut-and-paste approach, to pick up and deposit individual DNA strands on a surface. This, however, required pre-functionalization of the surface with DNA strands complementary to those that were to be picked up and then deposited. Here we show that single molecules of double-stranded DNA, bound to the tip of an atomic force microscope, can be deposited on a bare gold electrode using an electrical trigger (surface potential cycling). The interactions between the DNA and the electrode were investigated and we found that double-stranded DNA chemisorbs to the gold electrode exclusively at its end through primary amine groups. We corroborated this finding in experiments in which only a single adenosine nucleotide on a polyethylene glycol spacer was ‘electrosorbed’ to the gold electrode.

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Figure 1: Electrically induced chemical bonding of a dsDNA strand to gold through its terminal end.
Figure 2: Electrochemistry of DNA-gold bonding.
Figure 3: Nucleotide specificity of DNA–gold electrosorption.
Figure 4: Coordination bond rupture of individual nucleotides.

References

  1. Duwez, A. S. et al. Mechanochemistry: targeted delivery of single molecules. Nature Nanotech. 1, 122–125 (2006).

    Article  CAS  Google Scholar 

  2. Kufer, S. K., Puchner, E. M., Gumpp, H., Liedl, T. & Gaub, H. E. Single-molecule cut-and-paste surface assembly. Science 319, 594–596 (2008).

    Article  CAS  Google Scholar 

  3. Puchner, E. M., Kufer, S. K., Strackharn, M., Stahl, S. W. & Gaub, H. E. Nanoparticle self-assembly on a DNA-scaffold written by single-molecule cut-and-paste. Nano Lett. 8, 3692–3695 (2008).

    Article  CAS  Google Scholar 

  4. Kufer, S. K. et al. Optically monitoring the mechanical assembly of single molecules. Nature Nanotech. 4, 45–49 (2009).

    Article  CAS  Google Scholar 

  5. Boon, E. M., Ceres, D. M., Drummond, T. G., Hill, M. G. & Barton, J. K. Mutation detection by electrocatalysis at DNA-modified electrodes. Nature Biotechnol. 18, 1096–1100 (2000).

    Article  CAS  Google Scholar 

  6. Wang, J. From DNA biosensors to gene chips. Nucleic Acids Res. 28, 3011–3016 (2000).

    Article  CAS  Google Scholar 

  7. McKendry, R. et al. Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array. Proc. Natl Acad. Sci. USA 99, 9783–9788 (2002).

    Article  CAS  Google Scholar 

  8. Kershner, R. J. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotech. 4, 557–561 (2009).

    Article  CAS  Google Scholar 

  9. Braun, E., Eichen, Y., Sivan, U. & Ben-Yoseph, G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775–778 (1998).

    Article  CAS  Google Scholar 

  10. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Marszalek, P. E., Greenleaf, W. J., Li, H. B., Oberhauser, A. F. & Fernandez, J. M. Atomic force microscopy captures quantized plastic deformation in gold nanowires. Proc. Natl Acad. Sci. USA 97, 6282–6286 (2000).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. Tao, N. J., Derose, J. A. & Lindsay, S. M. Self-assembly of molecular superstructures studied by in situ scanning tunneling microscopy—DNA bases on Au(111). J. Phys. Chem. 97, 910–919 (1993).

    Article  CAS  Google Scholar 

  15. Wang, J. et al. Sequence-specific electrochemical biosensing of M-tuberculosis DNA. Anal. Chim. Acta 337, 41–48 (1997).

    Article  CAS  Google Scholar 

  16. Daniel, M. C. & Astruc, D. Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem. Rev. 104, 293–346 (2004).

    Article  CAS  Google Scholar 

  17. Fan, F. R. F. & Bard, A. J. STM on wet insulators—electrochemistry or tunneling. Science 270, 1849–1851 (1995).

    Article  CAS  Google Scholar 

  18. Drummond, T. G., Hill, M. G. & Barton, J. K. Electrochemical DNA sensors. Nature Biotechnol. 21, 1192–1199 (2003).

    Article  CAS  Google Scholar 

  19. Murphy, L. Biosensors and bioelectrochemistry. Curr. Opin. Chem. Biol. 10, 177–184 (2006).

    Article  CAS  Google Scholar 

  20. Frederix, P. et al. Atomic force bio-analytics. Curr. Opin. Chem. Biol. 7, 641–647 (2003).

    Article  CAS  Google Scholar 

  21. Rief, M., Clausen-Schaumann, H. & Gaub, H. E. Sequence-dependent mechanics of single DNA molecules. Nature Struct. Biol. 6, 346–349 (1999).

    Article  CAS  Google Scholar 

  22. Angersteinkozlowska, H., Conway, B. E., Hamelin, A. & Stoicoviciu, L. Elementary steps of electrochemical oxidation of single-crystal planes of Au .1. chemical basis of processes involving geometry of anions and the electrode surfaces. Electrochim. Acta 31, 1051–1061 (1986).

    Article  CAS  Google Scholar 

  23. Hansma, H. G., Laney, D. E., Bezanilla, M., Sinsheimer, R. L. & Hansma, P. K. Applications for atomic-force microscopy of DNA. Biophys. J. 68, 1672–1677 (1995).

    Article  CAS  Google Scholar 

  24. Anselmetti, D. et al. Biological-materials studied with dynamic force microscopy. J. Vac. Sci. Technol. B 12, 1500–1503 (1994).

    Article  CAS  Google Scholar 

  25. Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. Entropic elasticity of lambda-phage DNA. Science 265, 1599–1600 (1994).

    Article  CAS  Google Scholar 

  26. Marko, J. F. & Siggia, E. D. Stretching DNA. Macromolecules 28, 8759–8770 (1995).

    Article  CAS  Google Scholar 

  27. Smith, S. B., Cui, Y. J. & Bustamante, C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–799 (1996).

    Article  CAS  Google Scholar 

  28. Christie, J. H. & Lingane, P. J. Theory of staircase voltammetry. J. Electroanal. Chem. 10, 176–182 (1965).

    CAS  Google Scholar 

  29. Hamelin, A., Sottomayor, M. J., Silva, F., Chang, S. C. & Weaver, M. J. Cyclic voltammetric characterization of oriented monocrystalline gold surfaces in aqueous alkaline-solution. J. Electroanal. Chem. 295, 291–300 (1990).

    Article  CAS  Google Scholar 

  30. Pastre, D. et al. Adsorption of DNA to mica mediated by divalent counterions: a theoretical and experimental study. Biophys. J. 85, 2507–2518 (2003).

    Article  CAS  Google Scholar 

  31. Andreatta, D. et al. Ultrafast dynamics in DNA: ‘fraying’ at the end of the helix. J. Am. Chem. Soc. 128, 6885–6892 (2006).

    Article  CAS  Google Scholar 

  32. Every, A. E. & Russu, I. M. Influence of magnesium ions on spontaneous opening of DNA base pairs. J. Phys. Chem. B 112, 15261–15261 (2008).

    Article  CAS  Google Scholar 

  33. Shirahata, S. et al. Electrolyzed-reduced water scavenges active oxygen species and protects DNA from oxidative damage. Biochem. Biophys. Res. Commun. 234, 269–274 (1997).

    Article  CAS  Google Scholar 

  34. Xu, B. Q. & Tao, N. J. J. Measurement of single-molecule resistance by repeated formation of molecular junctions. Science 301, 1221–1223 (2003).

    Article  CAS  Google Scholar 

  35. Chen, F., Li, X. L., Hihath, J., Huang, Z. F. & Tao, N. J. Effect of anchoring groups on single-molecule conductance: comparative study of thiol-, amine-, and carboxylic-acid-terminated molecules. J. Am. Chem. Soc. 128, 15874–15881 (2006).

    Article  CAS  Google Scholar 

  36. Venkataraman, L., Klare, J. E., Nuckolls, C., Hybertsen, M. S. & Steigerwald, M. L. Dependence of single-molecule junction conductance on molecular conformation. Nature 442, 904–907 (2006).

    Article  CAS  Google Scholar 

  37. Grunder, S. et al. New cruciform structures: toward coordination induced single molecule switches. J. Org. Chem. 72, 8337–8344 (2007).

    Article  CAS  Google Scholar 

  38. Strunz, T., Oroszlan, K., Schafer, R. & Guntherodt, H. J. Dynamic force spectroscopy of single DNA molecules. Proc. Natl Acad. Sci. USA 96, 11277–11282 (1999).

    Article  CAS  Google Scholar 

  39. Morfill, J. et al. B–S transition in short oligonucleotides. Biophys. J. 93, 2400–2409 (2007).

    Article  CAS  Google Scholar 

  40. Ho, D. et al. Force-driven separation of short double stranded DNA. Biophys. J. 97, 3158–3167 (2009).

    Article  CAS  Google Scholar 

  41. Herne, T. M. & Tarlov, M. J. Characterization of DNA probes immobilized on gold surfaces. J. Am. Chem. Soc. 119, 8916–8920 (1997).

    Article  CAS  Google Scholar 

  42. Storhofff, J. J., Elghanian, R., Mirkin, C. A. & Letsinger, R. L. Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir 18, 6666–6670 (2002).

    Article  Google Scholar 

  43. Bilic, A., Reimers, J. R., Hush, N. S. & Hafner, J. Adsorption of ammonia on the gold(111) surface. J. Chem. Phys. 116, 8981–8987 (2002).

    Article  CAS  Google Scholar 

  44. Lambropoulos, N. A., Reimers, J. R. & Hush, N. S. Binding to gold(0): Accurate computational methods with application to AuNH3 . J. Chem. Phys. 116, 10277–10286 (2002).

    Article  CAS  Google Scholar 

  45. Demers, L. M. et al. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 124, 11248–11249 (2002).

    Article  CAS  Google Scholar 

  46. Rapino, S. & Zerbetto, F. Modeling the stability and the motion of DNA nucleobases on the gold surface. Langmuir 21, 2512–2518 (2005).

    Article  CAS  Google Scholar 

  47. Manohar, S. et al. Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy. Nano Lett. 8, 4365–4372 (2008).

    Article  CAS  Google Scholar 

  48. Israelachvili, J. van der Waals Forces between Surfaces 2nd edn, II (Academic, 2003).

    Google Scholar 

  49. Ostblom, M., Liedberg, B., Demers, L. M. & Mirkin, C. A. On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study. J. Phys. Chem. B 109, 15150–15160 (2005).

    Article  Google Scholar 

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Acknowledgements

The authors thank K. Gottschalk, D. Ho, W. Schuhmann and U. Sivan for helpful discussions. This work was supported by the German Science Foundation (SFB 486) and the Nanosystems Initiative Munich (NIM). A.F. thanks the Alexander von Humboldt Foundation for generous support.

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M.E., A.F. and H.E.G. conceived and designed the experiments and co-wrote the paper. M.E. performed the experiments and analysed the data. R.D. contributed the dsDNA and provided the tip and electrode functionalization. All authors discussed the results and commented on the manuscript.

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Correspondence to Ann R. Fornof.

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Erdmann, M., David, R., Fornof, A. et al. Electrically induced bonding of DNA to gold. Nature Chem 2, 745–749 (2010). https://doi.org/10.1038/nchem.722

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