Sample Preparation for SFM Imaging of DNA, Proteins, and DNA–Protein Complexes

Methods in Molecular Biology

Volumn 783, Issue , 2011, Pages 213-231

  Ristic, Dejan ^a   Sanchez, Humberto ^a   Wyman, Claire ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Atomic force microscopy; Combining fluorescence and topography; DNA protein complexes; Scanning force microscopy; Single molecule imaging

Indexed keywords

DNA; PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; METHODOLOGY;

DNA; MICROSCOPY, ATOMIC FORCE; PROTEINS;

EID: 80054759778     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-282-3_12     Document Type: Chapter

References (15)

1. Janicijevic, A., Ristic, D. and Wyman, C. (2003) The molecular machines of DNA repair: scanning force microscopy analysis of their architecture. J Microsc. 212, 264–72.
2. Dame, R.T., Wyman, C. and Goosen, N. (2003) Insights into the regulation of transcription by scanning force microscopy. J Microsc. 212, 244–53.
3. Erie, D.A., Yang, G., Schultz, H. C. and Bustamante, C. (1994) DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science 266, 1562–6.
4. Ristic, D., Modesti, M., van der Heijden, T., van Noort, J., Dekker, C., Kanaar, R. and Wyman, C. (2005) Human Rad51 filaments on double-and single-stranded DNA: correlating regular and irregular forms with recombination function. Nucleic Acids Res. 33, 3292–302.
5. Bustamante, C., Vesenka, J., Tang, C. L., Rees, W., Guthold, M. and Keller, R. (1992) Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry 31, 22–6.
6. Vesenka, J., Guthold, M., Tang, C. L., Keller, D., Delaine, E. and Bustamante, C. (1992) Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy 42–44, 1243–9.
7. Hansma, H.G. and Laney, D.E. (1996) DNA binding to mica correlates with cationic radius: assay by atomic force microscopy. Biophys J. 70, 1933–9.
8. Han, W., Lindsay, S. M., Dlakic, M. and Harrington, R. E. (1997) Kinked DNA. Nature 386, 563.
9. Rivetti, C., Guthold, M. and Bustamante, C. (1996) Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol. 264, 919–32.
10. Beerens, N., Hoeijmakers, J. H., Kanaar, R., Vermeulen, W. and Wyman, C. (2005) The CSB protein actively wraps DNA. J Biol Chem. 280, 4722–9.
11. Ratcliff, G.C. and Erie, D.A. (2001) A novel single-molecule study to determine protein– protein association constants. J Am Chem Soc. 123, 5632–5.
12. Wyman, C., Rombel, I., North, A. K., Bustamante, C. and Kustu, S. (1997) Unusual olig-omerization required for activity of NtrC, a bacterial enhancer-binding protein. Science 275, 1658–61.
13. van der Linden, E., Sanchez, H., Kinoshita, E., Kanaar, R. and Wyman, C. (2009) RAD50 and NBS1 form a stable complex functional in DNA binding and tethering. Nucleic Acids Res. 37, 1580–8.
14. Janicijevic, A., Sugasawa, K., Shimizu, Y., Hanaoka, F., Wijgers, N., Djurica, M., Hoeijmakers, J. H. and Wyman, C. (2003) DNA bending by the human damage recognition complex XPC-HR23B. DNA Repair (Amst). 2, 325–36.
15. Dame, R.T., van Mameren, J., Luijsterburg, M. S., Mysiak, M. E., Janicijevic, A., Pazdzior, G., van der Vliet, P. C., Wyman, C. and Wuite, G. J. (2005) Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res. 33, e68.