Correcting for AFM tip induced topography convolutions in protein-DNA samples

Ultramicroscopy

Volumn 121, Issue , 2012, Pages 8-15

  Winzer, A T ^a   Kraft, C ^b   Bhushan, S ^b   Stepanenko, V ^c   Tessmer, I ^b  

^a Bosch Solar Thin Film GmbH   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

AFM tip evaluation; Atomic force microscopy (AFM); Geometrical models; Image convolutions; Protein DNA

Indexed keywords

AFM IMAGING; AFM TIP; FINITE SIZE; GEOMETRICAL MODELS; IMAGE CONVOLUTION; LATERAL CALIBRATION; LATERAL DIMENSION; MECHANICAL IMAGING; PROTEIN ASSEMBLY; PROTEIN-DNA; PROTEIN-DNA COMPLEXES; SIZE EVALUATION;

ATOMIC FORCE MICROSCOPY; CALIBRATION; CONVOLUTION; GEOMETRY; NANOPROBES; NANOTUBES; PROTEINS;

DNA;

BACTERIAL PROTEIN; DNA; PROTEIN; PROTEIN BAX; PROTEIN BAX1; PROTEIN UVRB; UNCLASSIFIED DRUG;

ARTICLE; ATOMIC FORCE MICROSCOPY; CALIBRATION; GEOMETRY; IMAGE PROCESSING; IMAGE QUALITY; MATHEMATICAL MODEL; PROTEIN DNA INTERACTION;

BACILLUS; BACTERIAL PROTEINS; CALIBRATION; DNA; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; THERMOPLASMA;

EID: 84865058391     PISSN: 03043991     EISSN: 18792723     Source Type: Journal    
DOI: 10.1016/j.ultramic.2012.07.002     Document Type: Article

References (25)

1. Ratcliff G.C., Erie D.A. A novel single-molecule study to determine protein-protein association constants. Journal of the American Chemical Society 2001, 123(24):5632-5635.
2. Markiewicz P., Goh M.C. Atomic-force microscopy probe tip visualisation and improvement of images using a simple deconvolution procedure. Langmuir 1994, 10(1):5-7.
3. Odin C., et al. Tip finite-size effects on atomic-force microscopy in the contact mode-simple geometrical considerations for rapid estimation of apex radius and tip angle based on the study of polystyrene latex balls. Surface Science 1994, 317(3):321-340.
4. Rowlen K.L., Ramirez-Aguilar K.A. Tip characterization from AFM images of nanometric spherical particles. Langmuir 1998, 14(9):2562-2566.
5. Onishi K., Fujita D. Novel tip shape reconstruction method for restoration of AFM topography images using nano-structures with given shapes. Analytical Sciences 2011, 27(2):157-161.
6. Xu S., Arnsdorf M.F. Calibration of the scanning (atomic) force microscope with gold particles. Journal of Microscopy 1994, 173(Pt 3):199-210.
7. Wang Y., Chen X. Carbon nanotubes: a promising standard for quantitative evaluation of AFM tip apex geometry. Ultramicroscopy 2007, 107(4-5):293-298.
8. Allen M.J., et al. Tip-radius-induced artifacts in AFM images of protamine-complexed DNA fibres. Ultramicroscopy 1992, 42-44(Pt B):1095-1100.
9. Bustamante C., et al. Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry 1992, 31(1):22-26.
10. Vesenka J., et al. Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy 1992, 42-44(Pt B):1243-1249.
11. Jiao Y., Schaffer T.E. Accurate height and volume measurements on soft samples with the atomic force microscope. Langmuir 2004, 20(23):10038-10045.
12. Vesenka J., et al. Humidity effects on atomic force microscopy of gold-labeled DNA on mica. Scanning Microscopy 1993, 7(3):781-788.
13. Tang J., et al. Enhancement of resolution of DNA on silylated mica using atomic force microscopy. Journal of Vacuum Science and Technology B 2000, 18(4):1858-1860.
14. Lyubchenko Y.L., et al. Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. Nucleic Acids Research 1993, 21(5):1117-1123.
15. Thomson N.H., et al. Reversible binding of DNA to mica for AFM imaging. Langmuir 1996, 12(24):5905-5908.
16. Moreno-Herrero F., Colchero J., Baro A.M. DNA height in scanning force microscopy. Ultramicroscopy 2003, 96(2):167-174.
17. Watson J.D., Crick F.H.C. The structure of DNA. Cold Spring Harbor Symposia on Quantitative Biology 1953, 18:123-131.
18. Mandelkern M., et al. The dimensions of DNA in solution. Journal of Molecular Biology 1981, 152(1):153-161.
19. Margeat E., Le Grimellec C., Royer C.A. Visualisation of trp repressor and its complexes with DNA by atomic force microscopy. Biophysical Journal 1998, 75(6):2712-2720.
20. Severin N., et al. Replication of single macromolecules with graphene. Nano Letters 2011, 11:2436-2439.
21. Garcia V.J., et al. Probe Microscopy 1997, 1:107.
22. Koehne J.E., et al. Using carbon nanotube probes for high-resolution three-dimensional imaging of cells. Ultramicroscopy 2011, 111(8):1155-1162.
23. Theis K., et al. Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. The EMBO Journal 1999, 18(24):6899-6907.
24. Roth H.M., et al. Bax1 is a novel endonuclease: implications for archaeal nucleotide excision repair. The Journal of Biological Chemistry 2009, 284(47):32272-32278.
25. Orren D.K., Sancar A. The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex. Proceedings of the National Academy of Sciences of the United States of America 1989, 86(14):5237-5241.