High-resolution imaging of plasmid DNA in liquids in dynamic mode atomic force microscopy using a carbon nanofiber tip

Masashi Kitazawa, Shuichi Ito, Akira Yagi, Nobuaki Sakai, Yoshitugu Uekusa, Ryo Ohta, Kazuhisa Inaba, Akari Hayashi, Yasuhiko Hayashi, Masaki Tanemura

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Abstract

To understand the motion of DNA and DNA complexes, the real-time visualization of living DNA in liquids is quite important. Here, we report the high-resolution imaging of plasmid DNA in water using a rapid-scan atomic force microscopy (AFM) system equipped with a carbon nanofiber (CNF) probe. To achieve a rapid high-resolution scan, small SiN cantilevers with dimensions of 2 (width) × 0.1 (thickness) × 9μm (length) and a bent end (tip view structure) were employed as base cantilevers onto which single CNFs were grown. The resonant frequencies of the cantilever were 1.5 MHz in air and 500 kHz in water, and the spring constant was calculated to be 0.1 N/m. Single CNFs, typically 88 nm in length, were formed on an array of the cantilevers in a batch process by the ion-irradiation method. An AFM image of a plasmid DNA taken in water at 0.2fps (5s/image) using a batch-fabricated CNF-tipped cantilever clearly showed the helix turns of the double strand DNA. The average helical pitch measured 3.4 nm (σ: 0.5 nm), which was in good agreement with that determined by the X-ray diffraction method, 3.4 nm. Thus, it is presumed that the combined use of the rapid-scan AFM system with the ion-induced CNF probe is promising for the dynamic analysis of biomolecules.

Original languageEnglish
Article number08LB14
JournalJapanese journal of applied physics
Volume50
Issue number8 PART 4
DOIs
Publication statusPublished - Aug 1 2011
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Engineering(all)
  • Physics and Astronomy(all)

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  • Cite this

    Kitazawa, M., Ito, S., Yagi, A., Sakai, N., Uekusa, Y., Ohta, R., Inaba, K., Hayashi, A., Hayashi, Y., & Tanemura, M. (2011). High-resolution imaging of plasmid DNA in liquids in dynamic mode atomic force microscopy using a carbon nanofiber tip. Japanese journal of applied physics, 50(8 PART 4), [08LB14]. https://doi.org/10.1143/JJAP.50.08LB14