AFM imaging of DNA, DNA-drug complexes, DNA-protein complexes, nanotubes and other nanomaterials

Lambda DNA

AFM image of Lambda DNA (~ 16 micrometers long)

We are AFM imaging DNA, various protein-DNA, drug-DNA complexes and other nanomaterials to determine their structural properties.  This work is done in collaboration with the Wake Forest University Chemistry and Cancer Biology departments. 

AFM imaging specific publications:

  1. Ghosh, S., Dutta, S., Gomes, E., Carroll, D., D’Agostino, Jr., R., Olson, J. Guthold, M., Gmeiner, W. H. “Increased Heating Efficiency and Selective Thermal Ablation of Malignant Tissue with DNA-Encased Multiwalled Carbon Nanotubes”, ACS Nano (2009) 3, 2667-73.
  2. Wong, O.-K., Guthold, M., Erie, D. A., Gelles, J. (2008) “Interconvertable lactose repressor-DNA looped complexes revealed by single-molecule experiments”  PLOS Biology 6(9):e232, 2028-2042.
  3. Liu, W., Bonin, K. Guthold, M. (2007) “An easy and direct method for calibrating AFM lateral force measurements” Review of Scientific Instruments 78, 063707 (7 pages)
  4. Guthold, M., Liu, W., Stephens, B. J., Lord, S. T., Hantgan, R. R., Erie, D. A., Taylor, R. M., Superfine, R. (2004) “Visualization and Mechanical Manipulations of Individual Fibrin Fibers Suggest that Fiber Cross-Section has Fractal Dimension 1.3”  Biophys. J. 87, 4226-36
  5. Rivetti, C. & Guthold, M. (2003) “Single DNA molecule analysis of transcription complexes” Method. Enzymol. 371, 34-50
  6. Dwyer, C., Guthold, M., Falvo, M., Washburn, S., Superfine, R., Erie, D. (2002) DNA-functionalized single-walled carbon nanotubes. Nanotechnology 13, 601-604
  7. Guthold, M., Zhu, X., Rivetti, C., Yang, G., Thomson, N. H., Kasas, S., Hansma, H. G., Smith, B., Hansma, P. K. & Bustamante, C. (1999). Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys. J. 77, 2284-2294
  8. Bustamante, C., Guthold, M., Zhu, X. & Yang, G. (1999). Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in liquid. J. Biol. Chem. 274, 16665-16668.
  9. Rivetti, C., Guthold, M. & Bustamante, C. (1999). Wrapping of DNA around the E. coli RNA polymerase open promoter complex. EMBO J. 18, 4464-4475.
  10. Rippe, K., Guthold, M., von Hippel, P. H. & Bustamante, C. (1997). Transcriptional activation via DNA-looping:  Visualization of intermediates in the activation pathway of E.coli RNA polymerase-s54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270, 125-138.
  11. Kasas, S., Thomson, N. H., Smith, B. L., Hansma, H. G., Zhu, X., Guthold, M., Bustamante, C., Kool, E. T., Kashlev, M. & Hansma, P. K. (1997). Escherichia coli RNA polymerase activity observed using Atomic Force Microscopy. Biochemistry 36(3), 461-468.
  12. Rivetti, C., Guthold, M. & Bustamante, C. (1996). Scanning Force Microscopy of DNA deposited on mica:  Equilibration versus kinetic trapping studied by polymer chain analysis. J. Mol. Biol. 264, 919-932.
  13. Guthold, M., Bezanilla, M., Erie, D. A., Jenkins, B., Hansma, H. G. & Bustamante, C. (1994). Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope. Proc. Natl. Acad. Sci. USA 91, 12927-12931.
  14. 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, 1243-49.