Discrimination of DNA hybridization using chemical force microscopy

Biophysical Journal

Volumn 76, Issue 6, 1999, Pages 2922-2933

  Mazzola, Laura T ^a   Frank, Curtis W ^a,b   Fodor, Stephen P A ^c   Mosher, Curtis ^d   Lartius, Raj ^d   Henderson, Eric ^d  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c Thermo Fisher Scientific   (United States)

^d Bioforce Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOMIC FORCE MICROSCOPY; DNA HYBRIDIZATION; DNA PROBE; IMAGE ANALYSIS; MOLECULAR RECOGNITION;

EID: 0033063510     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77447-3     Document Type: Article

References (59)

1. Albrecht, T. R., M. M. Dovek, C. A. Lang, P. Grütter, C. F. Quate, S. W. J. Kuan, C. W. Frank, and R. F. W. Pease. 1988. Imaging and modification of polymers by scanning tunneling and atomic force microscopy. J. Appl. Phys. 64:1178-1184.
2. Atkinson, T., and M. Smith. 1984. Solid phase synthesis of oligodeoxyri-bonucleotides by the phosphite-triester method. In Oligonucleotide Synthesis: A Practical Approach. M. J. Gait, editor. IRL Press, Oxford, England. 35-81.
3. Bely, V. A., A. I. Sviridenok, M. I. Petrokovets, and V. G. Savkin. 1982. Structure and frictional properties. In Friction and Wear in PolymerBased Materials. Pergamon Press, Oxford. 187-193.
4. Binnig, G., and C. F. Quate. 1986. Atomic force microscope. Phys. Rev. Lett. 56:930-933.
5. Boland, T., and B. D. Ratner. 1995. Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy. Proc. Natl. Acad. Sci. USA. 92:5297-5301.
6. Breslauer, K. J., R. Frank, H. Blöcker, and L. A. Marky. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA. 83:3746-3750.
7. Burnham, N. A., D. D. Dominguez, R. L. Mowery, and R. J. Colton. 1990. Probing the surface forces of monolayer films with an atomic force microscope. Phys. Rev. Lett. 64:1931-1934.
8. Butt, H.-J. 1991. Electrostatic interaction in atomic force microscopy. Biophys. J. 60:777-785.
9. Chen, Y. L., C. A. Helm, and J. N. Israelachvili. 1991. Molecular mechanisms associated with adhesion and contact angle hysteresis of monolayer surfaces. J. Phys. Chem. 95:10736-10747.
10. Chilkoti, A., T. Boland, B. D. Ratner, and P. S. Stayton. 1995. The relationship between ligand-binding thermodynamics and protein-ligand interaction forces measured by atomic force microscopy. Biophys. J. 69:2125-2130.
11. Dammer, U., O. Popescu, P. Wagner, D. Anselmetti, H.-J. Güntherodt, and G. N. Misevic. 1995. Binding strength between cell adhesion proteoglycans measured by atomic force microscopy. Science. 267:1173-1175.
12. Ducker, W. A., T. J. Senden, and R. M. Pashley. 1991. Direct measurement of colloidal forces using an atomic force microscope. Nature. 353: 239-241.
13. Florin, E.-L., V. T. Moy, and H. E. Gaub. 1994. Adhesion forces between individual ligand-receptor pairs. Science. 264:415-417.
14. Florin, E.-L., M. Rief, H. Lehmann, M. Ludwig, C. Dornmair, V. Moy, and H. E. Gaub. 1995. Sensing specific molecular interactions with the atomic force microscope. Biosens. Bioelectron. 10:895-901.
15. Fodor, S. P. A., J. L. Read, M. C. Pirrung, L. Stryer, A. T. Lu, and D. Solas. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science. 251:767-773.
16. Forman, J. E., I. D. Walton, D. Stern, R. P. Rava, and M. O. Trulson. 1998. Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. In Molecular Modeling of Nucleic Acids, ACS Symposium Series 682. 206-228.
17. Frisbie, C. D., L. F. Rozsnyai, A. Noy, M. S. Wrighton, and C. M. Lieber. 1994. Functional group imaging by chemical force microscopy. Science. 265:2071-2074.
18. Fujihira, M., D. Aoki, Y. Okabe, H. Takano, H. Hokari, J. Frommer, Y. Nagatani, and F. Sakai. 1996. Effect of capillary force on friction force microscopy: a scanning hydrophilicity microscope. Chem. Lett. 7:499-500.
19. Grafström, S., M. Neitzert, T. Hagen, J. Ackermann, R. Neumann, O. Probst, and M. Wörtge. 1993. The role of topography and friction for the image contrast in lateral force microscopy. Nanotechnology. 4:143-151.
20. Green, J.-B. D., M. T. McDermott, M. D. Porter, and L. M. Siperko. 1995. Nanometer-scale mapping of chemically distinct domains at well-defined organic interfaces using frictional force microscopy. J. Phys. Chem. 99:10960-10965.
21. Hähner, G., A. Marti, and N. D. Spencer. 1997. The influence of pH on friction between oxide surfaces in electrolytes, studied with lateral force microscopy: application as a nanochemical imaging technique. Tribol. Lett. 3:359-365.
22. Hansma, H. G., K. J. Kim, D. E. Laney, R. A. Garcia, M. Argaman, M. J. Allen, and S. M. Parsons. 1997. Properties of biomolecules measured from atomic force microscope images: a review. J. Struct. Biol. 119: 99-108.
23. Hansma, P. K., V. B. Elings, O. Marti, and C. E. Bracker. 1988. Scanning tunneling microscopy and atomic force microscopy: application to biology and technology. Science. 242:209-216.
24. Henderson, E., C. C. Hardin, S. K. Walk, I. J. Tinoco, and E. H. Blackburn. 1987. Telomeric DNA oligonucleotides from novel intramolecular structures containing quanine-guanine base pairs. Cell. 51:899-908.
25. Hinterdorfer, P., W. Baumgartner, H. J. Gruber, K. Schilcher, and H. Schindler. 1996. Detection and localization of individual antibody-antigen recognition events by atomic force microscopy. Proc. Natl. Acad. Sci. USA. 93:3477-3481.
26. Hoh, J. H., J. P. Cleveland, C. B. Prater, J.-P. Revel, and P. K. Hansma. 1992. Quantized adhesion detected with the atomic force microscope. J. Am. Chem. Soc. 114:4917-4918.
27. Israelachvili, J. 1992. Adhesion. In Intermolecular and Surface Forces, 2nd Ed. Academic Press, London. 312-337.
28. Johnson, K. L., K. Kendall, and A. D. Roberts. 1971. Surface energy and contact of elastic solids. Proc. R. Soc. Lond. A. 324:301-313.
29. Knapp, H. F., W. Wiegräbe, M. Heim, R. Eschrich, and R. Guckenberger. 1995. Atomic force microscope measurements and manipulation of Langmuir-Blodgett films with modified tips. Biophys. J. 69:708-715.
30. Lee, G. U., L. A. Chrisey, and R. J. Colton. 1994a. Direct measurement of the forces between complementary strands of DNA. Science. 266: 771-773.
31. Lee, G. U., D. A. Kidwell, and R. J. Colton. 1994b. Sensing discrete streptavidin-biotin interactions with atomic force microscopy. Langmuir. 10:354-357.
32. Li, Y. Q., N. J. Tao, J. Pan, A. A. Garcia, and S. M. Lindsay. 1993. Direct measurement of interaction forces between colloidal particles using the scanning force microscope. Langmuir. 9:637-641.
33. Liu, Y., T. Wu, and D. F. Evans. 1994. Lateral force microscopy study on the shear properties of self-assembled monolayers of dialkylammonium surfactant on mica. Langmuir. 10:2241-2245.
34. Mate, C. M., G. M. McClelland, R. Erlandsson, and S. Chiang. 1987. Atomic-scale friction of a tungsten tip on a graphite surface. Phys. Rev. Lett. 59:1942-1945.
35. Mazzola, L. T., and S. P. A. Fodor. 1995. Imaging biomolecule arrays by atomic force microscopy. Biophys. J. 68:1653-1660.
36. McGall, G. H., A. D. Barone, M. Diggelmann, S. P. A. Fodor, E. Gentalen, and N. Ngo. 1997. The efficiency of light-directed synthesis of DNA arrays on glass substrates. J. Am. Chem. Soc. 119:5081-5090.
37. Nakagawa, T., K. Ogawa, T. Kurumizawa, and S. Ozaki. 1993. Discriminating molecular length of chemically adsorbed molecules using an atomic force microscope having a tip covered with sensor molecules. Jpn. J. Appl. Phys. 32:294-296.
38. Neumeister, J. M., and W. A. Ducker. 1994. Lateral, normal, and longitudinal spring constants of atomic force microscopy cantilevers. Rev. Sci. Instrum. 65:2527-2531.
39. Noy, A., C. D. Frisbie, L. F. Rozsnyai, M. S. Wrighton, and C. M. Lieber. 1995. Chemical force microscopy: exploiting chemically-modified tips to quantify adhesion, friction, and functional group distributions in molecular assemblies. J. Am. Chem. Soc. 117:7943-7951.
40. Noy, A., D. V. Vezenov, and C. M. Lieber. 1997. Chemical force microscopy. Annu. Rev. Mater. Sci. 27:381-421.
41. Orosz, J. M., and J. G. Wetmur. 1977. DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions. Biopolymers. 16:1183-1199.
42. Overney, R. M., E. Meyer, J. Frommer, D. Brodbeck, R. Lüthi, L. Howald, H.-J. Güntherodt, M. Fujihira, H. Takano, and Y. Gotoh. 1992. Friction measurements on phase-separated thin films with a modified atomic force microscope. Nature. 359:133-135.
43. Overney, R. M., E Meyer, J. Frommer, H.-J. Güntherodt, M. Fujihira, H. Takano, and Y. Gotoh. 1994. Force microscopy study of friction and elastic compliance of phase-separated organic thin films. Langmuir. 10:1281-1286.
44. Pease, A. C., D. Solas, E. J. Sullivan, M. T. Cronin, C. P. Holmes, and S. P. A. Fodor. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA. 91:5022-5026.
45. Perry, R. H. 1992. Physical and chemical data. In Perry's Chemical Engineers' Handbook, 6th Ed. D. W. Green and J. O. Maloney, editors. McGraw-Hill, New York. 8-63.
46. Pollock, H. M. 1992. Surface forces and adhesion. In Fundamentals of Friction: Macroscopic and Microscopic Processes. NATO ASI Series, E. I. L. Singer and H. M. Pollock, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 25-34.
47. Rabinovich, Y. I., and R.-H. Yoon. 1994. Use of atomic force microscope for the measurements of hydrophobic forces between silanated silica plate and glass sphere. Langmuir. 10:1903-1909.
48. Ruan, J.-A., and B. Bhushan. 1994. Atomic-scale friction measurements using friction force microscopy. Part I. General principles and new measurement techniques. J. Tribol. 116:378-388.
49. Saenger, W. 1988. Principles of Nucleic Acid Structure. Springer-Verlag, New York.
50. Savkoor, A. R. 1992. Models of friction based on contact and fracture mechanics. In Fundamentals of Friction: Macroscopic and Microscopic Processes. NATO ASI Series, E. I. L. Singer and H. M. Pollock, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 111-113.
51. Singer, I. L. 1992. Solid lubrication processes. In Fundamentals of Friction: Macroscopic and Microscopic Processes. NATO ASI Series, E. I. L. Singer and H. M. Pollock, editors. Kluwer Academic Publishers, Dordrecht, The Netherlands. 237-261.
52. Stuart, J. K., and V. Hlady. 1995. Effects of discrete protein-surface interactions in scanning force microscopy adhesion force measurements. Langmuir. 11:1368-1374.
53. Thomas, R. C., J. E. Houston, R. M. Crooks, T. Kim, and T. A. Michalske. 1995. Probing adhesion forces at the molecular scale. J. Am. Chem. Soc. 117:3830-3834.
54. van der Vegte, E. W., and G. Hadziioannou. 1997. Scanning force microscopy with chemical specificity: an extensive study of chemically specific tip-surface interactions and the chemical imaging of surface functional groups. Langmuir. 13:4357-4368.
55. Wang, D. G., J. Fan, C. Siao, A. Berno, P. Young, R. Sapolsky, G. Ghanour, N. Perkins, E. Winchester, J. Spencer, L. Kruglyak, L. Stein, L. Hsie, T. Topaloglou, E. Hubbell, E. Robinson, M. Mittmann, M. Morris, N. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. Hudson, R. Lipshutz, M. Chee, and E. Lander. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. 1998. Science. 280:1077-1082.
56. Warmack, R. J., X.-Y. Zheng, T. Thundat, and D. P. Allison. 1994. Friction effects in the deflection of atomic force microscope cantilevers. Rev. Sci. Instrum. 65:394-399.
57. Weisenhom, A. L., P. Maivald, H.-J. Butt, and P. K. Hansma. 1992. Measuring adhesion, attraction, and repulsion between surfaces in liquids with an atomic force microscope. Phys. Rev. B. 45:11226-11232.
58. Wilbur, J. L., H. A. Biebuyck, J. C. MacDonald, and G. M. Whitesides. 1995. Scanning force microscopies can image patterned self-assembled monolayers. Langmuir. 11:825-831.
59. Yang, G., J. P. Vesenka, and C. J. Bustamante. 1996. Effects of tip-sample forces and humidity on the imaging of DNA with a scanning force microscope. Scanning. 18:344-350.