Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis.


Journal Article

Atomic force microscopy, which is normally used for DNA imaging to gain qualitative results, can also be used for quantitative DNA research, at a single-molecular level. Here, we evaluate the performance of AFM imaging specifically for quantifying supercoiled and relaxed plasmid DNA fractions within a mixture, and compare the results with the bulk material analysis method, gel electrophoresis. The advantages and shortcomings of both methods are discussed in detail. Gel electrophoresis is a quick and well-established quantification method. However, it requires a large amount of DNA, and needs to be carefully calibrated for even slightly different experimental conditions for accurate quantification. AFM imaging is accurate, in that single DNA molecules in different conformations can be seen and counted. When used carefully with necessary correction, both methods provide consistent results. Thus, AFM imaging can be used for DNA quantification, as an alternative to gel electrophoresis.

Full Text

Duke Authors

Cited Authors

  • Jiang, Y; Rabbi, M; Mieczkowski, PA; Marszalek, PE

Published Date

  • September 2010

Published In

Volume / Issue

  • 114 / 37

Start / End Page

  • 12162 - 12165

PubMed ID

  • 20799746

Pubmed Central ID

  • 20799746

Electronic International Standard Serial Number (EISSN)

  • 1520-5207

International Standard Serial Number (ISSN)

  • 1520-6106

Digital Object Identifier (DOI)

  • 10.1021/jp105603k


  • eng