Studying the structural dynamics of bipedal dna motors with single-molecule fluorescence spectroscopy

Rula Masoud, Roman Tsukanov, Toma E. Tomov, Noa Plavner, Miran Liber, Eyal Nir

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


We present a test case example of a detailed single-molecule fluorescence study of one of the most sophisticated and complex DNA devices introduced to date, a recently published autonomous bipedal DNA motor. We used the diffusion-based single-molecule Förster resonance energy transfer technique, coupled to alternating laser excitation (sm-FRET-ALEX), to monitor the motor assembly and operation. The study included verification of the formation of the correct structures, and of the correct motor operation, determination of the formation and stepping reaction yields, and identification of side products. Finally, the mechanisms of the motor assembly and operation were elucidated by measuring the reaction kinetics profile of track-walker binding and of lifting of the walker's leg upon fuel addition. The profiles revealed a fast phase, in which about half of the reaction was completed, followed by a slow phase which adds somewhat to the yield, reflecting the incomplete motor assembly and operation identified in the equilibrium experiments. Although further study is needed to fully understand the reasons for the incomplete assembly and operation, this work demonstrates that single-molecule fluorescence, based on its ability to provide detailed in situ structural dynamics information, inaccessible for traditional methods, constitutes an excellent tool for chaperoning the development of DNA-based technology.

Original languageEnglish
Pages (from-to)6272-6283
Number of pages12
JournalACS Nano
Issue number7
StatePublished - 24 Jul 2012


  • ALEX
  • DNA dynamics
  • DNA motor
  • DNA nanotechnology
  • FRET
  • single-molecule fluorescence

ASJC Scopus subject areas

  • General Materials Science
  • General Engineering
  • General Physics and Astronomy


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