Skip to main content

Journal for Biophysical Chemistry

Biointerphases Cover Image

Sum-frequency-generation spectroscopy of DNA films in air and aqueous environments

Abstract

Understanding the organization and orientation of surface-immobilized single stranded DNA (ssDNA) in aqueous environments is essential for optimizing and further developing the technology based on oligonucleotide binding. Here the authors demonstrate how sum-frequency-generation (SFG) spectroscopy can be used to compare the structure and orientation of model monolayers of ssDNA on gold in air, D2O, and phosphate buffered saline (PBS) solution. Films of adenine and thymine homo-oligonucleotides showed significant conformational changes in air versus aqueous environments in the CH stretching region. The thymine films showed changes between D2O and PBS solution, whereas the SFG spectra of adenine films under these conditions were largely similar, suggesting that the thymine films undergo greater conformational changes than the adenine films. Examination of thymine films in the amide I vibrational region revealed that molecules in films of nonthiolated DNA were lying down on the gold surface whereas molecules in films of thiol-linked DNA were arranged in a brushlike structure. Comparison of SFG spectra in the amide I region for thiol-linked DNA films in air and D2O also revealed substantial conformational changes.

References

  1. 1

    S. Cosnier and P. Mailley, Analyst (Cambridge, U.K.) 133, 984 (2008).

    Article  CAS  Google Scholar 

  2. 2

    B. Kasemo, Surf. Sci. 500, 656 (2002).

    Article  CAS  Google Scholar 

  3. 3

    D. G. Castner and B. D. Ratner, Surf. Sci. 500, 28 (2002).

    Article  CAS  Google Scholar 

  4. 4

    R. Levicky and A. Horgan, Trends Biotechnol. 23, 143 (2005).

    Article  CAS  Google Scholar 

  5. 5

    H. J. Lee, T. T. Goodrich, and R. M. Corn, Anal. Chem. 73, 5525 (2001).

    Article  CAS  Google Scholar 

  6. 6

    A. W. Peterson, R. J. Heaton, and R. M. Georgiadis, Nucleic Acids Res. 29, 5163 (2001).

    Article  CAS  Google Scholar 

  7. 7

    R. Georgiadis, K. P. Peterlinz, and A. W. Peterson, J. Am. Chem. Soc. 122, 3166 (2000).

    Article  CAS  Google Scholar 

  8. 8

    A. B. Steel, R. L. Levicky, T. M. Herne, and M. J. Tarlov, Biophys. J. 79, 975 (2000).

    Article  CAS  Google Scholar 

  9. 9

    C. Y. Lee, P. Gong, G. M. Harbers, D. W. Grainger, D. G. Castner, and L. J. Gamble, Anal. Chem. 78, 3316 (2006).

    Article  CAS  Google Scholar 

  10. 10

    D. Y. Petrovykh, H. Kimura-Suda, M. J. Tarlov, and L. J. Whitman, Langmuir 20, 429 (2004).

    Article  CAS  Google Scholar 

  11. 11

    D. Y. Petrovykh, V. Perez-Dieste, A. Opdahl, H. Kimura-Suda, J. M. Sullivan, M. J. Tarlov, F. J. Himpsel, and L. J. Whitman, J. Am. Chem. Soc. 128, 2 (2006).

    Article  CAS  Google Scholar 

  12. 12

    A. Opdahl, D. Y. Petrovykh, H. Kimura-Suda, M. J. Tarlov, and L. J. Whitman, Proc. Natl. Acad. Sci. U.S.A. 104, 9 (2007).

    Article  Google Scholar 

  13. 13

    J. Wang, S. H. Lee, and Z. Chen, J. Phys. Chem. B 112, 2281 (2008).

    Article  CAS  Google Scholar 

  14. 14

    J. Wang, Z. Paszti, M. L. Clarke, X. Y. Chen, and Z. Chen, J. Phys. Chem. B 111, 6088 (2007).

    Article  CAS  Google Scholar 

  15. 15

    X. Y. Chen, M. L. Clarke, J. Wang, and Z. Chen, Int. J. Mod. Phys. B 19, 691 (2005).

    Article  CAS  Google Scholar 

  16. 16

    R. L. York, O. Mermut, D. C. Phillips, K. R. McCrea, R. S. Ward, and G. A. Somorjai, J. Phys. Chem. C 111, 8866 (2007).

    Article  CAS  Google Scholar 

  17. 17

    D. C. Phillips, R. L. York, O. Mermut, K. R. McCrea, R. S. Ward, and G. A. Somorjai, J. Phys. Chem. C 111, 255 (2007).

    Article  CAS  Google Scholar 

  18. 18

    O. Mermut, D. C. Phillips, R. L. York, K. R. McCrea, R. S. Ward, and G. A. Somorjai, J. Am. Chem. Soc. 128, 3598 (2006).

    Article  CAS  Google Scholar 

  19. 19

    J. Wang, M. A. Even, X. Y. Chen, A. H. Schmaier, J. H. Waite, and Z. Chen, J. Am. Chem. Soc. 125, 9914 (2003).

    Article  CAS  Google Scholar 

  20. 20

    I. Rocha-Mendoza, D. R. Yankelevich, M. Wang, K. M. Reiser, C. W. Frank, and A. Knoesen, Biophys. J. 93, 4433 (2007).

    Article  CAS  Google Scholar 

  21. 21

    S. Y. Jung, S. M. Lim, F. Albertorio, G. Kim, M. C. Gurau, R. D. Yang, M. A. Holden, and P. S. Cremer, J. Am. Chem. Soc. 125, 12782 (2003).

    Article  CAS  Google Scholar 

  22. 22

    X. Chen, L. B. Sagle, and P. S. Cremer, J. Am. Chem. Soc. 129, 15104 (2007).

    Article  CAS  Google Scholar 

  23. 23

    C. Howell, M. Diesner, M. Grunze, and P. Koelsch, Langmuir 24, 13819 (2008).

    Article  CAS  Google Scholar 

  24. 24

    Y. R. Shen, Nature (London) 337, 519 (1989).

    Article  CAS  Google Scholar 

  25. 25

    G. Y. Stokes, J. M. Gibbs-Davis, F. C. Boman, B. R. Stepp, A. G. Condie, S. T. Nguyen, and F. M. Geiger, J. Am. Chem. Soc. 129, 7492 (2007).

    Article  CAS  Google Scholar 

  26. 26

    Y. Sartenaer, G. Tourillon, L. Dreesen, D. Lis, A. A. Mani, P. A. Thiry, and A. Peremans, Biosens. Bioelectron. 22, 2179 (2007).

    Article  CAS  Google Scholar 

  27. 27

    H. Asanuma, H. Noguchi, K. Uosaki, and H.-Z. Yu, J. Am. Chem. Soc. 130, 8016 (2008).

    Article  CAS  Google Scholar 

  28. 28

    G. W. H. Wurpel, M. Sovago, and M. Bonn, J. Am. Chem. Soc. 129, 8420 (2007).

    Article  CAS  Google Scholar 

  29. 29

    N. T. Samuel, C.-Y. Lee, L. J. Gamble, D. A. Fischer, and D. G. Castner, J. Electron Spectrosc. Relat. Phenom. 152, 134 (2006).

    Article  CAS  Google Scholar 

  30. 30

    C. D. Bain, J. Chem. Soc., Faraday Trans. 91, 1281 (1995).

    Article  CAS  Google Scholar 

  31. 31

    M. Himmelhaus, F. Eisert, M. Buck, and M. Grunze, J. Phys. Chem. B 104, 576 (2000).

    Article  CAS  Google Scholar 

  32. 32

    S. G. Ray, H. Cohen, R. Naaman, and Y. Rabin, J. Am. Chem. Soc. 127, 17138 (2005).

    Article  CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Howell, C., Schmidt, R., Kurz, V. et al. Sum-frequency-generation spectroscopy of DNA films in air and aqueous environments. Biointerphases 3, FC47–FC51 (2008). https://doi.org/10.1116/1.3064107

Download citation