Time-lapse imaging of conformational changes in supercoiled DNA by scanning force microscopy

Fuji Nagami, Giampaolo Zuccheri, Bruno Samorì, Reiko Kuroda

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


Most of the scanning force microscopy (SFM) images of supercoiled DNA on untreated mica thus far reported have not shown tight plectonemic structure seen by electron microscopy, but instead less coiled molecules and sometimes a partly "condensed" state with intimate chain-chain interactions. By observing time-lapse images of conformational changes of DNA induced by decreasing ionic strength of imaging buffer in solution SFM, we could show that the process of water rinsing, an indispensable step for preparation of dried samples, may be responsible for some of the conformational anomalies in the images previously reported. We have studied several protocols to observe supercoiled DNA molecules by SFM and discuss the merits and the demerits. Images obtained following uranyl acetate treatment may be ideal for the detection of DNA damage, as the supercoiled and nicked forms are easily distinguishable.

Original languageEnglish
Pages (from-to)170-176
Number of pages7
JournalAnalytical Biochemistry
Issue number2
Publication statusPublished - 2002 Jan 15
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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