Discrimination of DNA hybridization using chemical force microscopy (original) (raw)

Abstract

Atomic force microscopy (AFM) can be used to probe the mechanics of molecular recognition between surfaces. In the application known as "chemical force" microscopy (CFM), a chemically modified AFM tip probes a surface through chemical recognition. When modified with a biological ligand or receptor, the AFM tip can discriminate between its biological binding partner and other molecules on a heterogeneous substrate. The strength of the interaction between the modified tip and the substrate is governed by the molecular affinity. We have used CFM to probe the interactions between short segments of single-strand DNA (oligonucleotides). First, a latex microparticle was modified with the sequence 3'-CAGTTCTACGATGGCAAGTC and epoxied to a standard AFM cantilever. This DNA-modified probe was then used to scan substrates containing the complementary sequence 5'-GTCAAGATGCTACCGTTCAG. These substrates consisted of micron-scale, patterned arrays of one or more distinct oligonucleotides. A strong friction interaction was measured between the modified tip and both elements of surface-bound DNA. Complementary oligonucleotides exhibited a stronger friction than the noncomplementary sequences within the patterned array. The friction force correlated with the measured strength of adhesion (rupture force) for the tip- and array-bound oligonucleotides. This result is consistent with the formation of a greater number of hydrogen bonds for the complementary sequence, suggesting that the friction arises from a sequence-specific interaction (hybridization) of the tip and surface DNA.

Full Text

The Full Text of this article is available as a PDF (466.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Binnig G, Quate CF, Gerber C. Atomic force microscope. Phys Rev Lett. 1986 Mar 3;56(9):930–933. doi: 10.1103/PhysRevLett.56.930. [DOI] [PubMed] [Google Scholar]
  2. Boland T., Ratner B. D. Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5297–5301. doi: 10.1073/pnas.92.12.5297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burnham NA, Dominguez DD, Mowery RL, Colton RJ. Probing the surface forces of monolayer films with an atomic-force microscope. Phys Rev Lett. 1990 Apr 16;64(16):1931–1934. doi: 10.1103/PhysRevLett.64.1931. [DOI] [PubMed] [Google Scholar]
  5. Butt H. J. Electrostatic interaction in atomic force microscopy. Biophys J. 1991 Oct;60(4):777–785. doi: 10.1016/S0006-3495(91)82112-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chilkoti A., Boland T., Ratner B. D., Stayton P. S. The relationship between ligand-binding thermodynamics and protein-ligand interaction forces measured by atomic force microscopy. Biophys J. 1995 Nov;69(5):2125–2130. doi: 10.1016/S0006-3495(95)80083-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dammer U., Popescu O., Wagner P., Anselmetti D., Güntherodt H. J., Misevic G. N. Binding strength between cell adhesion proteoglycans measured by atomic force microscopy. Science. 1995 Feb 24;267(5201):1173–1175. doi: 10.1126/science.7855599. [DOI] [PubMed] [Google Scholar]
  8. Florin E. L., Moy V. T., Gaub H. E. Adhesion forces between individual ligand-receptor pairs. Science. 1994 Apr 15;264(5157):415–417. doi: 10.1126/science.8153628. [DOI] [PubMed] [Google Scholar]
  9. Fodor S. P., Read J. L., Pirrung M. C., Stryer L., Lu A. T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991 Feb 15;251(4995):767–773. doi: 10.1126/science.1990438. [DOI] [PubMed] [Google Scholar]
  10. Frisbie C. D., Rozsnyai L. F., Noy A., Wrighton M. S., Lieber C. M. Functional group imaging by chemical force microscopy. Science. 1994 Sep 30;265(5181):2071–2074. doi: 10.1126/science.265.5181.2071. [DOI] [PubMed] [Google Scholar]
  11. Hansma H. G., Kim K. J., Laney D. E., Garcia R. A., Argaman M., Allen M. J., Parsons S. M. Properties of biomolecules measured from atomic force microscope images: a review. J Struct Biol. 1997 Jul;119(2):99–108. doi: 10.1006/jsbi.1997.3855. [DOI] [PubMed] [Google Scholar]
  12. Hansma P. K., Elings V. B., Marti O., Bracker C. E. Scanning tunneling microscopy and atomic force microscopy: application to biology and technology. Science. 1988 Oct 14;242(4876):209–216. doi: 10.1126/science.3051380. [DOI] [PubMed] [Google Scholar]
  13. Henderson E., Hardin C. C., Walk S. K., Tinoco I., Jr, Blackburn E. H. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 1987 Dec 24;51(6):899–908. doi: 10.1016/0092-8674(87)90577-0. [DOI] [PubMed] [Google Scholar]
  14. Hinterdorfer P., Baumgartner W., Gruber H. J., Schilcher K., Schindler H. Detection and localization of individual antibody-antigen recognition events by atomic force microscopy. Proc Natl Acad Sci U S A. 1996 Apr 16;93(8):3477–3481. doi: 10.1073/pnas.93.8.3477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Knapp H. F., Wiegräbe W., Heim M., Eschrich R., Guckenberger R. Atomic force microscope measurements and manipulation of Langmuir-Blodgett films with modified tips. Biophys J. 1995 Aug;69(2):708–715. doi: 10.1016/S0006-3495(95)79946-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lee G. U., Chrisey L. A., Colton R. J. Direct measurement of the forces between complementary strands of DNA. Science. 1994 Nov 4;266(5186):771–773. doi: 10.1126/science.7973628. [DOI] [PubMed] [Google Scholar]
  17. Mate CM, McClelland GM, Erlandsson R, Chiang S. Atomic-scale friction of a tungsten tip on a graphite surface. Phys Rev Lett. 1987 Oct 26;59(17):1942–1945. doi: 10.1103/PhysRevLett.59.1942. [DOI] [PubMed] [Google Scholar]
  18. Mazzola L. T., Fodor S. P. Imaging biomolecule arrays by atomic force microscopy. Biophys J. 1995 May;68(5):1653–1660. doi: 10.1016/S0006-3495(95)80394-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Orosz J. M., Wetmur J. G. DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions. Biopolymers. 1977 Jun;16(6):1183–1199. doi: 10.1002/bip.1977.360160603. [DOI] [PubMed] [Google Scholar]
  20. Pease A. C., Solas D., Sullivan E. J., Cronin M. T., Holmes C. P., Fodor S. P. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5022–5026. doi: 10.1073/pnas.91.11.5022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Wang D. G., Fan J. B., Siao C. J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998 May 15;280(5366):1077–1082. doi: 10.1126/science.280.5366.1077. [DOI] [PubMed] [Google Scholar]
  22. Weisenhorn AL, Maivald P, Butt H, Hansma PK. Measuring adhesion, attraction, and repulsion between surfaces in liquids with an atomic-force microscope. Phys Rev B Condens Matter. 1992 May 15;45(19):11226–11232. doi: 10.1103/physrevb.45.11226. [DOI] [PubMed] [Google Scholar]