Hybridization of mismatched or partially matched DNA at surfaces

Journal of the American Chemical Society

Volumn 124, Issue 49, 2002, Pages 14601-14607

  Peterson, Alexander W ^a   Wolf, Lauren K ^a   Georgiadis, Rosina M ^a  

^a BOSTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MISMATCHED SEQUENCES;

ADSORPTION; ISOTHERMS; REACTION KINETICS; SPECTROSCOPY; SURFACE CHEMISTRY;

DNA;

DNA; OLIGONUCLEOTIDE;

ADSORPTION; ARTICLE; BASE MISPAIRING; DNA BINDING; DNA HYBRIDIZATION; DNA PROBE; DNA SEQUENCE; GENETIC HETEROGENEITY; IMMOBILIZATION; ISOTHERM; MOLECULAR MODEL; PROTEIN TARGETING; STEREOCHEMISTRY; SURFACE PLASMON RESONANCE; TEMPERATURE;

BASE PAIR MISMATCH; DNA; HEATING; KINETICS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; OLIGONUCLEOTIDES;

EID: 0037065343     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0279996     Document Type: Article

References (51)

1. Lockhart, D. J.; Dong, H. L.; Byme, M. C.; Follettie, M. T.; Gallo, M. V.; Chee, M. S.; Mittmann, M.; Wang, C. W.; Kobayashi, M.; Horton, H.; Brown, E. L. Nat. Biotechnol. 1996, 14, 1675-1680.
2. Southern, E.; Mir, K.; Shchepinov, M. Nature Genet. 1999, 21, 5-9.
3. Mir, K. U.; Southern, E. M. Nat. Biotechnol. 1999, 17, 788-792.
4. Tillib, S. V.; Mirzabekov, A. Curr. Opin. Biotechnol. 2001, 12, 53-58.
5. Lipshutz, R. J.; Fodor, S. P. A.; Gingeras, T. R.; Lockhart, D. J. Nature Genet. 1999, 21, 20-24.
6. Hughes, T. R.; Mao, M.; Jones, A. R.; Burchard, J.; Marton, M. J.; Shannon, K. W.; Lefkowitz, S. M.; Ziman, M.; Schelter, J. M.; Meyer, M. R.; Kobayashi, S.; Davis, C.; Dai, H. Y.; He, Y. D. D.; Stephaniants, S. B.; Cavet, G.; Walker, W. L.; West, A.; Coffey, E.; Shoemaker, D. D.; Stoughton, R.; Blanchard, A. P.; Friend, S. H.; Linsley, P. S. Nat. Biotechnol. 2001, 19, 342-347.
7. Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. Nature 1996, 382, 607-609.
8. Alivisatos, A. P.; Johnsson, K. P.; Peng, X. G.; Wilson, T. E.; Loweth, C. J.; Bruchez, M. P.; Schultz, P. G. Nature 1996, 382, 609-611.
9. Winfree, E.; Liu, F. R.; Wenzler, L. A.; Seeman, N. C. Nature 1998, 394, 539-544.
10. Park, S. J.; Lazarides, A. A.; Mirkin, C. A.; Letsinger, R. L. Angew. Chem.-Int. Edit. 2001, 40, 2909-2912.
11. Seeman, N. C. Nano Lett. 2001, 1, 22-26.
12. Gerion, D.; Parak, W. J.; Williams, S. C.; Zanchet, D.; Micheel, C. M.; Alivisatos, A. P. J. Am. Chem. Soc. 2002, 124, 7070-7074.
13. Bloomfield, V. A.; Crothers. D. M.; Tinoco, I. Nucleic Acids Structures, Properties, and Functions; University Science Books: Sausalito, 2000.
14. Forman, J. E.; Walton, I. D.; Stern, D.; Rava, R. P.; Trulson, M. O. In Molecular Modeling of Nucleic Acids; AMER CHEMICAL SOC: Washington, 1998; Vol. 682, pp 206-228.
15. Liebermann, T.; Knoll, W.; Sluka, P.; Herrmann, R. Colloid Surf. A-Physicochem. Eng. Asp. 2000, 169, 337-350.
16. Guo, Z.; Guilfoyle, R. A.; Thiel, A. J.; Wang, R. F.; Smith, L. M. Nucleic Acids Res. 1994, 22, 5456-5465.
17. Shchepinov, M. S.; CaseGreen, S. C.; Southern, E. M. Nucleic Acids Res. 1997, 25, 1155-1161.
18. Steel, A. B.; Herne, T. M.; Tarlov, M. J. Anal. Chem. 1998, 70, 4670-4677.
19. Chudin, E.; Walker, R.; Kosaka, A.; Wu, S. X.; Rabert, D.; Chang, T. K.; Kreder, D. E. Genome Biol 2001, 3, 5000-5010.
20. Naef, F.; Lim, D. A.; Patil, N.; Magnasco. M. Phys. Rev. E 2002, 65, 040901-040904.
21. Peterson, A. W.; Heaton, R. J.; Georgiadis. R. J. Am. Chem. Soc 2000, 122, 7837-7838.
22. Peterson, A. W.; Heaton. R. J.; Georgiadis, R. M. Nucleic Acids Res. 2001, 29, 5163-5168.
23. SantaLucia, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460-1465.
24. Peyret, N.; Seneviratne, P. A.; Allawi, H. T.; SantaLucia, J. Biochem. 1999, 38, 3468-3477.
25. 2 and a volume fraction of 7%. On the basis of solution-phase data, the diameter of each cylinder is expected to be ∼20 Å for duplex DNA; a concentric sheath of condensed counterions would increase the effective diameter slightly at the high solution ionic strength (IM) used.
26. Levicky, R.; Herne, T. M.; Tarlov, M. J.; Satija, S. K. J. Am. Chem. Soc. 1998, 120, 9787-9792.
27. Mathews, C. K.; van Holde. K. E. Biochemistry: Benjamin/Cummings: Redwood City, 1990.
28. Peterlinz, K. A.; Georgiadis, R. Opt. Commun. 1996, 130, 260-266.
29. Georgiadis, R.; Peterlinz, K. P.; Peterson, A. W. J. Am. Chem. Soc. 2000, 122, 3166-3173.
30. Heaton, R. J.; Peterson, A. W.; Georgiadis. R. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98. 3701-3704.
31. Demers, L. M.; Mirkin, C. A.; Mucic, R. C.; Reynolds, R. A.; Letsinger, R. L.; Elghanian R.; Viswanadham, G. Anal. Chem. 2000, 72, 5535-5541.
32. Peterlinz, K. A.; Georgiadis, R. M. J. Am. Chem. Soc. 1997, 119, 3401-3402.
33. Peterlinz, K. A.; Georgiadis, R. Langmuir 1996, 12, 4731 -4740.
34. Mbindyo, J. K. N.; Reiss, B. D.; Martin, B. R.; Keating, C. D.; Natan, M. J.; Mallouk, T. E. Adv. Mater. 2001, 13, 249-254.
35. Herne, T. M.; Tarlov, M. J. J. Am. Chem. Soc. 1997, 119. 8916-8920.
36. Caspersson, T. Nature 1938, 141, 122-122.
37. Wilkins, M. H. F.; Gosling, R. G.; Seeds, W. E. Nature 1951, 167, 759-760.
38. Weidlich, T.; Lindsay, S. M.; Rupprecht, A. Biopolymers 1987, 26, 439-453.
39. Craig, M. E.; Crothers, D. M.; Doty, P. J. Mol. Bio. 1971, 62, 383-401.
40. Cantor, C. R.; Schimmel, P. Biophysical Chemistry, Part 1; WH Freeman: New York, 1980.
41. The steady state for each target is reached rather quickly (< 1/2 h) and remains constant for many hours. Careful fitting (not shown) at short times (< 1/2 h) indicates that a first-order Langmuir model cannot sufficiently describe the kinetics.
42. Hook, F.; Ray, A.; Norden, B.; Kasemo, B. Langmuir 2001, 17, 8305-8312.
43. Hansen, K. M.; Ji, H. F.; Wu, G. H.; Datar, R.; Cote, R.; Majumdar, A.; Thundat, T. Anal. Chem. 2001, 73, 1567-1571.
44. Fritz, J.; Baller, M. K.; Lang, H. P.; Rothuizen, H.; Vettiger, P.; Meyer, E.; Guntherodt, H. J.; Gerber, C.; Gimzewski, J. K. Science 2000, 288, 316-318.
45. Wu, G. H.; Ji, H. F.; Hansen, K.; Thundat, T.; Datar, R.; Cote, R.; Hagan, M. F.; Chakraborty, A. K.; Majumdar, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 1560-1564.
46. Pease, A. C.; Solas, D.; Sullivan, E. J.; Cronin, M. T.; Holmes, C. P.; Fodor, S. P. A. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5022-5026.
47. Watterson, J. H.; Piunno, P. A. E.; Wust, C. C.; Krull, U. J. Langmuir 2000, 16, 4984-4992.
48. Sips, R. J. Chem. Phys. 1948, 16, 490-495.
49. Vijayendran, R. A.; Leckband, D. E. Anal. Chem. 2001, 73, 471-480.
50. Nelson, B. P. Grimsrud, T. E.; Liles, M. R.; Goodman. R. M.; Corn, R. M. Anal. Chem. 2001, 73, 1-7.
51. Jensen, K. K.; Orum, H.; Nielsen, P. E.; Norden, B. Biochem. 1997, 36, 5072-5077.