Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis

Journal of Molecular Biology

Volumn 264, Issue 5, 1996, Pages 919-932

  Rivetti, Claudio ^a,b   Guthold, Martin ^a   Bustamante, Carlos ^a  

^a UNIVERSITY OF OREGON   (United States)

^b UNIVERSITY OF PARMA   (Italy)

Author keywords

DNA deposition; DNA persistence length; Excluded volume effects; Mica; Scanning force microscopy

Indexed keywords

DNA FRAGMENT; HORSERADISH PEROXIDASE; HYBRID PROTEIN; POLYMER; STREPTAVIDIN;

ARTICLE; DIFFUSION; DNA DETERMINATION; DNA TRANSFER; ION EXCHANGE; KINETICS; PRIORITY JOURNAL; PROPRIOCEPTION; SCANNING FORCE MICROSCOPY; STATISTICS; SURFACE PROPERTY;

EID: 0030596081     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0687     Document Type: Article

References (41)

1. Bednar, J., Furrer, P., Katritch, V., Stasiak, A. Z., Dubochet, J. & Stasiak, A. (1995). Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J. Mol. Biol. 254, 579-594.
2. Bettini, A., Pozzan, M. R., Valdevit, E. & Frontali, C. (1980). Microscopic persistence length of DNA: Its relation to average molecular dimensions. Biopolymers, 19, 1689-1694.
3. Bezanilla, M., Drake, B., Nudler, E., Kashlev, M., Hansma, P. K. & Hansma, H. G. (1994). Motion and enzymatic degradation of DNA in the atomic force microscope. Biophys. J. 67, 2454-2459.
4. Binnig, G., Quate, C. F. & Gerber, C. H. (1986). Atomic force microscope. Phys. Rev. Letters, 56, 930-933.
5. Bustamante, C. & Keller, D. (1995). Scanning force microscopy in biology. Physics Today, 48, 32-38.
6. Bustamante, C. & Rivetti, C. (1996). Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu. Rev. Biophys. Biomol. Struct. 25, 395-429.
7. Bustamante, C., Vesenka, J., Tang, C. L., Rees, W., Guthold, M. & Keller, R. (1992). Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry, 3, 22-26.
8. Bustamante, C., Keller, D. & Yang, G. (1993). Scanning force microscopy of nucleic acids and nucleoprotein assemblies. Curr. Opin. Struct. Biol. 3, 363-372.
9. Bustamante, C., Erie, D. A. & Keller, D. (1994a). Biochemical and structural applications of scanning force microscopy. Curr. Opin. Struct. Biol. 4, 750-760.
10. Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. (1994b). Entropic elasticity of λ-phage DNA. Science, 265, 1599-1600.
11. Crothers, D. M. & Zimm, B. H. (1965). Viscosity and sedimentation of the DNA from bacteriophages T2 and T7 and the relation to molecular weight. J. Mol. Biol. 12, 525-536.
12. Erie, D. A., Hajiseyedjavadi, O., Young, M. C. & von Hippel, P. H. (1993). Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science, 262, 867-873.
13. Erie, D. A., Yang, G., Schultz, H. C. & Bustamante, C. (1994). DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science, 266, 1562-1566.
14. Flory, P. J. (1969). Statistical Mechanics of Chain Molecules, Interscience Publishers, New York.
15. Frontali, C. (1988). Excluded-volume effect on the bidimensional conformation of DNA molecules adsorbed to protein films. Biopolymers, 27, 1329-1331.
16. Frontali, C., Dore, E., Ferrauto, A., Gratton, E., Bettini, A., Porzzan, M. R. & Valdevit, E. (1979). An absolute method for the determination of the persistence length of native DNA from electron micrographs. Biopolymers, 18, 1353-1373.
17. Griffith, J. D., Makhov, A., Zawel, L. & Reinberg, D. (1995). Visualization of TBP oligomers binding and bending the HIV-1 and adeno promoters. J. Mol. Biol. 246, 576-584.
18. Grosberg, A. Y. & Khokhlov, A. R. (1994). Statistical Physics of Macromolecules, API Press, Woodbury, NY.
19. Hagerman, P. J. (1988). Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17, 265-286.
20. Hansma, H. G. & Hoh, J. (1994). Biomolecular imaging with atomic force microscope. Annu. Rev. Biophys. Biomol. Struct. 23, 115-139.
21. Hansma, H. G., Browne, K. A., Bezanilla, M. & Bruice, T. C. (1994). Bending and straightening of DNA induced by the same ligand: characterization with the atomic force microscope. Biochemestry, 33, 8436-8441.
22. Joanicot, M. & Revet, B. (1987). DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality. Biopolymers, 26, 315-326.
23. Kratky, O. & Porod, G. (1949). Röntgenuntersuchung aufgelöster Fadenmoleküle. Recueil, 68, 1106-1122.
24. Landau, L. D. & Lifshitz, E. M. (1980). Statistical Physics, Part 1. 3rd edit, Pergamon Press, Oxford, NY.
25. Landau, L. D. & Lifshitz, E. M. (1986). Theory of Elasticity, Pergamon Press, Oxford, NY.
26. Lang, D. & Coates, P. (1968). Diffusion coefficient of DNA in solution at "zero" concentration as measured by electron microscopy. J. Mol. Biol. 36, 137-151.
27. Lang, D., Bujard, H., Wolff, B. & Russell, D. (1967). Electron microscopy of size and shape of viral DNA in solutions of different ionic strengths. J. Mol. Biol. 23, 163-181.
28. Lindsay, S. M., Tao, N. J., DeRose, J. A., Oden, P. I. & Lyubchenko, L. Y. (1992). Potentiostatic deposition of DNA for scanning probe microscopy. Biophys. J. 61, 1570-1584.
29. Lyubchenko, L. Y., Lindsay, S. M., DeRose, J. A. & Thundat, T. (1991). A technique for stable adhesion of DNA to a modified graphite surface for imaging by scanning tunneling microscopy. J. Vac. Sci. Technol. 9, 1288-1290.
30. Lyubchenko, Y. L., Shlyakhtenko, L. S., Harrington, R. E., Oden, P. I. & Lindsay, S. M. (1993). Atomic force microscopy of long DNA: imaging in air and under water. Proc. Natl Acad. Sci. USA, 90, 2137-2140.
31. Namork, E. & Johansen, B. V. (1982). Surface activation of carbon film supports for biological electron microscopy. Ultramicroscopy, 7, 321-330.
32. Nishimura, S., Biggs, S., Scales, P. J., Healy, T. W., Tsunematsu, K. & Tateyama, H. (1994). Molecular-scale structure of the cation modified muscovite mica basal plane. Langmuir, 10, 4554-4559.
33. Nishimura, S., Scales, P. J., Tateyama, H., Tsunematsu, K. & Healy, T. W. (1995). Cationic modification of muscovite mica: an electrokinetic study. Langmuir, 11, 291-295.
34. Porschke, D. (1991). Persistence length and bending dynamics of DNA from electrooptical measuraments at high salt concentrations. Biophys. Chem. 40, 169-179.
35. Rabke, C. E., Wenzler, L. A. & Beebe, T. P. J. (1994). Electron spectroscopy and atomic force microscopy studies of DNA adsorption on mica. Scanning Microsc. 8, 471-478.
36. Rees, W. A., Keller, R. W., Vesenka, J. P., Yang, G. & Bustamante, C. (1993). Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science, 260, 1646-1649.
37. Schaper, A., Pietrasanta, L. I. & Jovin, T. M. (1993). Scanning force microscopy of circular and linear plasmid DNA spread on mica with a quaternary ammonium salt. Nucl. Acids Res. 21, 6004-6009.
38. Schellman, J. A. (1974). Flexibility of DNA. Biopolymers, 13, 217-226.
39. Thundat, T., Allison, D. P., Warmack, R. J., Brown, G. M., Jacobson, K. B., Schrick, J, J. & Ferrell, T. L. (1992). Atomic force microscopy of DNA on mica and chemically modified mica. Scanning Microsc. 6, 911-918.
40. Vesenka, J., Guthold, M., Tang, C. L., Keller, D., Delaine, E. & Bustamante, C. (1992). Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy, 42-44, 1243-1249.
41. Wyman, C., Grotkopp, E., Bustamante, C. & Nelson, H. C. M. (1995). Determination of heat-shock transcription factor 2 stoichiometry at looped DNA complexes using scanning force microscopy. EMBO J. 14, 117-123.