Skip to main content
Biointerphases

Journal for Biophysical Chemistry

Download PDF

Mixed DNA/oligo (ethylene glycol) functionalized gold surfaces improve DNA hybridization in complex media

Biointerphases volume 1, pages 82–92 (2006)Cite this article

Abstract

Reliable, direct “sample-to-answer” capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo (ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results #followed by monitoring the N 1s → π* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein adsorption, facilitating detection of small DNA target sequences from these undiluted, unpurified complex biological mixtures unachievable with previously reported, analogous ssDNA/11-mercapto-1-undecanol monolayer surfaces [P. Gong, C.-Y. Lee, L. J. Gamble, D. G. Castner, and D.W. Grainger, Anal. Chem. 78, 3326 (2006)].

References

  1. 1

    S. Hahn, S. Mergenthaler, B. Zimmermann, and W. Holzgreve, Bioelectrochemistry 67, 151 (2005).

    Article  Google Scholar 

  2. 2

    P. A. E. Piunno and U. J. Krull, Anal. Bioanal. Chem. 381, 1004 (2005).

    Article  Google Scholar 

  3. 3

    P. Gong, C.-Y. Lee, L. J. Gamble, D. G. Castner, and D. W. Grainger, Anal. Chem. 78, 3326 (2006).

    Article  Google Scholar 

  4. 4

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

    Article  Google Scholar 

  5. 5

    M. Lochhead, C. A. Greef, P. Gong, and D. W. Grainger, in Microarrays: Methods and Protocols (Methods in Molecular Biology), 2nd ed. (Humana Press, Totowa, NJ, in press).

  6. 6

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

    Article  Google Scholar 

  7. 7

    A. W. Peterson, R. J. Heaton, and R. Georgiadis, J. Am. Chem. Soc. 122, 7837 (2000).

    Article  Google Scholar 

  8. 8

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

    Article  Google Scholar 

  9. 9

    A. W. Peterson, L. K. Wolf, and R. M. Georgiadis, J. Am. Chem. Soc. 124, 14601 (2002).

    Article  Google Scholar 

  10. 10

    B. P. Nelson, T. E. Grimsrud, M. R. Liles, R. M. Goodman, and R. M. Corn, Anal. Chem. 73, 1 (2001).

    Article  Google Scholar 

  11. 11

    Y. K. Cho, S. Kim, Y. A. Kim, H. K. Lim, K. Lee, D. S. Yoon, G. Lim, Y. E. Pak, T. H. Ha, and K. Kim, J. Colloid Interface Sci. 278, 44 (2004).

    Article  Google Scholar 

  12. 12

    F. Caruso, E. Rodda, D. N. Furlong, and V. Haring, Sens. Actuators B 41, 189 (1997).

    Article  Google Scholar 

  13. 13

    R. Levicky, T. M. Herne, M. J. Tarlov, and S. K. Satija, J. Am. Chem. Soc. 120, 9787 (1998).

    Article  Google Scholar 

  14. 14

    T. M. Herne and M. J. Tarlov, J. Am. Chem. Soc. 119, 8916 (1997).

    Article  Google Scholar 

  15. 15

    H. J. Lee, Y. Li, A. W. Wark, and R. M. Corn, Anal. Chem. 77, 5096 (2005).

    Article  Google Scholar 

  16. 16

    T. T. Goodrich, H. J. Lee, and R. M. Corn, J. Am. Chem. Soc. 126, 4086 (2004).

    Article  Google Scholar 

  17. 17

    L. K. Ista, H. Y. Fan, O. Baca, and G. P. Lopez, FEMS Microbiol. Lett. 142, 59 (1996).

    Article  Google Scholar 

  18. 18

    K. L. Prime and G. M. Whitesides, J. Am. Chem. Soc. 115, 10714 (1993).

    Article  Google Scholar 

  19. 19

    K. Bergstrom, K. Holmberg, A. Safranj, A. S. Hoffman, M. J. Edgell, A. Kozlowski, B. A. Hovanes, and J. M. Harris, J. Biomed. Mater. Res. 26, 779 (1992).

    Article  Google Scholar 

  20. 20

    C. Palegrosdemange, E. S. Simon, K. L. Prime, and G. M. Whitesides, J. Am. Chem. Soc. 113, 12 (1991).

    Article  Google Scholar 

  21. 21

    C. Boozer, J. Ladd, S. F. Chen, Q. Yu, J. Homola, and S. Y. Jiang, Anal. Chem. 76, 6967 (2004).

    Article  Google Scholar 

  22. 22

    C. Y. Lee, H. E. Canavan, L. J. Gamble, and D. G. Castner, Langmuir 21, 5134 (2005).

    Article  Google Scholar 

  23. 23

    K. E. Nelson, L. Gamble, L. S. Jung, M. S. Boeckl, E. Naeemi, S. L. Golledge, T. Sasaki, D. G. Castner, C. T. Campbell, and P. S. Stayton, Langmuir 17, 2807 (2001).

    Article  Google Scholar 

  24. 24

    J. L. Lenhart, R. L. Jones, E. K. Lin, C. L. Soles, W. L. Wu, D. A. Fischer, S. Sambasivan, D. L. Goldfarb, and M. Angelopoulos, J. Vac. Sci. Technol. B 20, 2920 (2002).

    Article  Google Scholar 

  25. 25

    J. Stohr, NEXAFS Spectroscopy (Springer, New York, 1992).

    Book  Google Scholar 

  26. 26

    L. S. Jung, C. T. Campbell, T. M. Chinowsky, M. N. Mar, and S. S. Yee, Langmuir 14, 5636 (1998).

    Article  Google Scholar 

  27. 27

    P. G. Wu, B. S. Fujimoto, L. Song, and J. M. Schurr, Biophys. Chem. 41, 217 (1991).

    Article  Google Scholar 

  28. 28

    R. E. Harrington, J. Am. Chem. Soc. 92, 6957 (1970).

    Article  Google Scholar 

  29. 29

    J. E. Darnell and H. Lodish, Molecular Cell Biology (Scientific American, New York, 1990).

    Google Scholar 

  30. 30

    J. Mandel, The Statistical Analysis of Experimental Data (Dover, New York, 1984).

    Google Scholar 

  31. 31

    C. J. May, H. E. Canavan, and D. G. Castner, Anal. Chem. 76, 1114 (2004).

    Article  Google Scholar 

  32. 32

    G. Beamson and D. Briggs, High Resolution XPS of Organic Polymers (Wiley, West Sussex, 1992).

    Google Scholar 

  33. 33

    D. G. Castner, K. Hinds, and D. W. Grainger, Langmuir 12, 5083 (1996).

    Article  Google Scholar 

  34. 34

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

    Article  Google Scholar 

  35. 35

    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  Google Scholar 

  36. 36

    J. N. Crain, A. Kirakosian, J. L. Lin, Y. D. Gu, R. R. Shah, N. L. Abbott, and F. J. Himpsel, J. Appl. Phys. 90, 3291 (2001).

    Article  Google Scholar 

  37. 37

    A. G. Shard, J. D. Whittle, A. J. Beck, P. N. Brookes, N. A. Bullett, R. A. Talib, A. Mistry, D. Barton, and S. L. McArthur, J. Phys. Chem. B 108, 12472 (2004).

    Article  Google Scholar 

  38. 38

    M. Zwahlen, D. Brovelli, W. Caseri, and G. Hahner, J. Colloid Interface Sci. 256, 262 (2002).

    Article  Google Scholar 

  39. 39

    M. Zharnikov, Y. Ouchi, M. Hasegawa, and A. Scholl, J. Phys. Chem. B 108, 859 (2004).

    Article  Google Scholar 

  40. 40

    M. G. Samant, J. Stohr, H. R. Brown, T. P. Russell, J. M. Sands, and S. K. Kumar, Macromolecules 29, 8334 (1996).

    Article  Google Scholar 

  41. 41

    G. Hahner, M. Kinzler, C. Thummler, C. Woll, and M. Grunze, J. Vac. Sci. Technol. A 10, 2758 (1992).

    Article  Google Scholar 

  42. 42

    D. A. Outka, J. Stohr, J. P. Rabe, and J. D. Swalen, J. Chem. Phys. 88, 4076 (1988).

    Article  Google Scholar 

  43. 43

    N. L. Anderson and N. G. Anderson, Mol. Cell Proteomics 1, 845 (2002).

    Article  Google Scholar 

  44. 44

    N. L. Rosi and C. A. Mirkin, Chem. Rev. (Washington, D.C.) 105, 1547 (2005).

    Article  Google Scholar 

Download references

Author information

Affiliations

  1. National ESCA and Surface Analysis Center for Biomedical Problems Department of Chemical Engineering, University of Washington, Box 351750, 98195-1750, Seattle, Washington

    Chi-Ying Lee

  2. National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington, Box 351750, 98195-1750, Seattle, Washington

    Lara J. Gamble

  3. Department of Chemistry, Colorado State University, 80523-1872, Fort Collins, Colorado

    David W. Grainger

  4. National ESCA and Surface Analysis Center for Biomedical Problems Departments of Bioengineering and Chemical Engineering, University of Washington, Box 351750, 98195-1750, Seattle, Washington

    David G. Castner

Authors
  1. Chi-Ying Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lara J. Gamble
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David W. Grainger
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David G. Castner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David G. Castner.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lee, CY., Gamble, L.J., Grainger, D.W. et al. Mixed DNA/oligo (ethylene glycol) functionalized gold surfaces improve DNA hybridization in complex media. Biointerphases 1, 82–92 (2006). https://doi.org/10.1116/1.2219110

Download citation