Voltammetric procedure for examining DNA-modified surfaces: Quantitation, cationic binding activity, and electron-transfer kinetics

Analytical Chemistry

Volumn 75, Issue 15, 2003, Pages 3902-3907

  Yu, Hua Zhong ^a   Luo, Chuan Yun ^a   Sankar, Carlo G ^a   Sen, Dipankar ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROLYTES; ELECTROSTATICS; OXIDATION; POSITIVE IONS; RATE CONSTANTS; REDUCTION; SURFACE TREATMENT; TRANSITION METALS;

BINDING ACTIVITIES;

DNA;

METAL ION;

ARTICLE; BINDING AFFINITY; DNA MODIFICATION; DNA PROBE; ELECTRODE; ELECTRON TRANSPORT; KINETICS; OXIDATION; POTENTIOMETRY; REDUCTION;

CATIONS; DNA; ELECTROCHEMISTRY; ELECTRON TRANSPORT; ELECTROSTATICS; KINETICS; OLIGODEOXYRIBONUCLEOTIDES; RUBIDIUM;

EID: 0041561078     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac034318w     Document Type: Article

References (46)

1. For recent reviews of DNA chips, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. (b) Blohm, D. H.; Guiseppi-Elie, A. Curr. Opin. Biotechnol. 2001, 12, 41. (c) Wang, J. Nucleic Acids Res. 2000, 28, 3011. (d) Freeman, W. M.; Robertson, D. J.; Vrana, K. E. Biotechniques 2000, 29, 1042. (e) Niemeyer, C. M.; Blohm, D. H. Angew. Chem., Int. Ed. 1999, 38, 2865.
2. For recent reviews of DNA chips, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. (b) Blohm, D. H.; Guiseppi-Elie, A. Curr. Opin. Biotechnol. 2001, 12, 41. (c) Wang, J. Nucleic Acids Res. 2000, 28, 3011. (d) Freeman, W. M.; Robertson, D. J.; Vrana, K. E. Biotechniques 2000, 29, 1042. (e) Niemeyer, C. M.; Blohm, D. H. Angew. Chem., Int. Ed. 1999, 38, 2865.
3. For recent reviews of DNA chips, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. (b) Blohm, D. H.; Guiseppi-Elie, A. Curr. Opin. Biotechnol. 2001, 12, 41. (c) Wang, J. Nucleic Acids Res. 2000, 28, 3011. (d) Freeman, W. M.; Robertson, D. J.; Vrana, K. E. Biotechniques 2000, 29, 1042. (e) Niemeyer, C. M.; Blohm, D. H. Angew. Chem., Int. Ed. 1999, 38, 2865.
4. For recent reviews of DNA chips, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. (b) Blohm, D. H.; Guiseppi-Elie, A. Curr. Opin. Biotechnol. 2001, 12, 41. (c) Wang, J. Nucleic Acids Res. 2000, 28, 3011. (d) Freeman, W. M.; Robertson, D. J.; Vrana, K. E. Biotechniques 2000, 29, 1042. (e) Niemeyer, C. M.; Blohm, D. H. Angew. Chem., Int. Ed. 1999, 38, 2865.
5. For recent reviews of DNA chips, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. (b) Blohm, D. H.; Guiseppi-Elie, A. Curr. Opin. Biotechnol. 2001, 12, 41. (c) Wang, J. Nucleic Acids Res. 2000, 28, 3011. (d) Freeman, W. M.; Robertson, D. J.; Vrana, K. E. Biotechniques 2000, 29, 1042. (e) Niemeyer, C. M.; Blohm, D. H. Angew. Chem., Int. Ed. 1999, 38, 2865.
6. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
7. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
8. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
9. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
10. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
11. For examples of studies of DNA-modified surfaces, see: (a) Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 8916. (b) Kelley, S. O.; Jackson, N. M.; Hill, M. G.; Barton, J. K. Angew. Chem., Int. Ed. 1999, 38, 941. (c) Yu, C. J.; Wan, Y. J.; Yowanto, H.; Li, J.; Tao, C. L.; James, M. D.; Tan, C. L.; Blackburn, G. F.; Meade, T. J. J. Am. Chem. Soc. 2001, 123, 11155. (d) Kertesz, V.; Whittemore, N. A.; Chambers, J. Q.; McKinney, M. S.: Baker, D. C. J. Electroanal. Chem. 2000, 493, 28. (e) Hartwich, G.; Caruana, D. J.; de Lumley-Woodyear, T.; Wu, Y. B.; Campbell, C. N.; Heller, A. J. Am. Chem. Soc. 1999, 121, 10803. (f) Pike, A. R.; Lie, L. H.; Eagling, R. A.; Ryder, L. C.; Patole, S. N.; Connolly, B. A.; Horrocks, B. R.; Houlton, A. Angew. Chem., Int. Ed. 2002, 41, 615.
12. For examples, see: (a) Peterlinz, K. A.; Georgiadis, R. M.; Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119, 3401.
13. (b) Kelley, S. O.; Barton, J. K. Bioconjugate Chem. 1997, 8, 31.
14. (c) Brewer, S. H.; Anthireya, S. J.; Lappi, S. E.; Drapcho, D. L.; Franzen, S. Langmuir 2002, 18, 4460.
15. (d) Demers, L. M.; Mirkin, C. A.; Mucic, R. C.; Reynolds, R. A., III; Letsinger, R. L.; Elghanian, R.; Viswanadham, G. Anal. Chem. 2000, 72, 5535.
16. Whittemore, N. A.; Mullenix, A. N.; Inamati, G. B.; Manoharan, M.; Cook, P. D.; Tuinman, A. A.; Baker, D. C.; Chambers, J. Q. Bioconjugate Chem. 1999, 10, 261.
17. (a) Steel, A. B.; Herne, T. M.; Tarlov, M. J. Anal. Chem. 1998, 70, 4670.
18. (b) Steel, A. B.; Herne, T. M.; Tarlov, M. J. Bioconjugate Chem. 1999, 10, 419.
19. (a) Patolsky, F.; Weizmann, Y.; Willner, I. J. Am. Chem. Soc. 2002, 124. 770.
20. (b) Patolsky, F.; Katz, E.; Willner, I. Angew. Chem., Int. Ed. 2002, 41, 3398.
21. (a) Carter, M. T.; Bard, A. J. J. Am. Chem. Soc. 1987, 109, 7528.
22. (b) Carter, M. T.; Rodriguez, M.; Bard, A. J. J. Am. Chem. Soc. 1989, 111, 8901.
23. Millan, K. M.; Mikkelsen, S. R. Anal. Chem. 1993, 65, 2317.
24. Wang, J.; Cai, X.; Rivas, G.; Shiraishi, H.; Faria, P. A. M.; Donta, N. Anal. Chem. 1996, 68, 2629.
25. Holmlin, R. E.; Stemp, E. D. A.; Barton, J. K. J. Am. Chem. Soc. 1996, 118, 5236.
26. (a) Pang, D. W.; Abruña, H. D. Anal. Chem. 1998, 70, 3162.
27. (b) Pang, D. W.; Abruña, H. D. Anal. Chem. 2000, 72, 4700.
28. (a) Horrocks, B. R.; Mirkin, M. V. Anal. Chem. 1998, 70, 4653.
29. (b) Aslanoglu, M.; Isaac, C. J.; Houlton, A.; Horrocks, B. R. Analyst 2000, 125, 1791.
30. Fahlman, R. P.; Sen, D. J. Am. Chem. Soc. 2002, 124, 4610 and references therein.
31. (a) Oyama, N.; Anson, F. C. Anal. Chem. 1980, 52, 1192.
32. (b) Peerce, P. J.; Bard, A. J. J. Electroanal. Chem. 1980, 112, 97.
33. (c) Schneider, J. R.; Murray, R. W. Anal. Chem. 1982, 54, 1508.
34. (d) Guadalupe, A. R.; Abruña, H. D. Anal. Chem. 1985, 57, 142.
35. 2), which would exhibit a considerably lower hybridization ratio as result of spatial hindrance. The other method, as demonstrated in this work (see also ref 3b), is to prepare a dsDNA-modified surface first and then remove the complementary strand, which naturally produces an ssDNA-modified surface with optimal surface coverage for hybridization.
36. Bard, A. J.; Faulkner, L. R. Electrochemical Methods: Fundamentals and Applications, 2nd ed.; John Wiley & Sons: New York, 2001.
37. To be more accurate, at these relatively high concentrations (Figure 2), the area of the left half of the peak (with negligible contribution from the diffusing peaks) was measured and multiplied by 2.
38. 2), within the experimental uncertainties. This could be due to incomplete heterogeneous denaturation of the duplex or to imperfect hybridization when the duplex was prepared in solution before self-assembly on the electrode surfaces. These are challenging topics in DNA chip technology for which further investigations are in progress in our laboratory.
39. Laviron, E. J. Electroanal. Chem. 1979, 101, 19.
40. (a) Kelley, S. O.; Barton, J. K.; Jackson, N. M.; McPherson, L. D.; Potter, A. B.; Spain, E. M.; Allen, M. J.; Hill, M. G. Langmuir 1998, 14, 6781.
41. (b) Sam, M.; Boon, E. M.; Barton, J. K.; Hill, M. G.; Spain, E. M. Langmuir 2001, 17, 5727.
42. For recent reviews of charge transport in DNA, see: (a) Giese, B.; Spichty, M. Chem Phys Chem 2000, I, 195. (b) Schuster, G. B. Acc. Chem. Res. 2000, 33, 253.
43. For recent reviews of charge transport in DNA, see: (a) Giese, B.; Spichty, M. Chem Phys Chem 2000, I, 195. (b) Schuster, G. B. Acc. Chem. Res. 2000, 33, 253.
44. Sistare, M. F.; Codden, S. J.; Heimlich, G.; Thorp, H. H. J. Am. Chem. Soc. 2000, 122, 4742.
45. In the determination of adsorbed reactants by chronocoulometry, reactants arrive at the diffusion-limited rate: Anson, F. C.; Osteryoung, R. A. J. Chem. Educ. 1083, 60, 293. Heterogeneous kinetic data can be obtained by using a step potential that is insufficiently extreme to enforce diffusion-controlled electrolysis throughout the experimental time domain and analyzed by appropriate theoretical considerations: Christie, J. H.; Lauer, G.; Osteryoung, R. J. Electroanal. Chem. 1064, 7, 60. It is not easy to measure kinetic parameters of the adsorbed reactant in the presence of diffusing reactants at concentrations high enough to contribute significantly to the measured charges.
46. For an example, see: Badia, A.; Lennox, R. B.; Reven, L. Acc. Chem. Res. 2000, 33, 475.